MMCIF USER GUIDE

MMCIF USER GUIDE
PDBx/mmCIF
Dictionaries
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PDBx/mmCIF User Guide
Dictionary Version 5
INTRODUCTION
Protein Data Bank Exchange macromolecular Crystallographic Information Framework, PDBx/mmCIF, provides the foundation for the deposition, annotation, and archiving of structural data across various experimental techniques.
PDBx/mmCIF uses data blocks to organize related information and data.
A data block is a logical partition of a data file designated by a
data_
record.
A data block may be named by appending a text string after the
data_
record and a
data block is terminated by either another
data_
record or by the end of the file.
An example of identifying data block at the beginning of the model file for the PDB entry 4HHB:
data_4HHB
_entry.id
4HHB
_audit_conform.dict_name
mmcif_pdbx.dic
_audit_conform.dict_version
5.367
_audit_conform.dict_location
PDBx/mmCIF format utilizes the ASCII character set. All data items are identified by name, begin with the underscore character, and are composed of a category name followed by an attribute name. The category name is separated from the attribute name by a period.
An example of PDBx/mmCIF data item (
_category.attribute
):
_entity.id
Data items are presented in two styles: key-value and tabular.
An example of a key-value style where the PDBx/mmCIF item is followed directly by a corresponding value:
_cell.entry_id
4HHB
_cell.length_a
63.150
_cell.length_b
83.590
_cell.length_c
53.800
_cell.angle_alpha
90.00
_cell.angle_beta
99.34
_cell.angle_gamma
90.00
_cell.Z_PDB
An example of a tabular style used when there are multiple values for each item. In this style, a
loop_
record is followed by rows of data item names and then white-space delimited data values:
loop_
_audit_author.
name
_audit_author.
pdbx_ordinal
_audit_author.
identifier_ORCID
'Fermi, G.'
0000-000x-xxxx-xxxx
'Perutz, M.F'
0000-000x-xxxx-xxxx
The hash symbol (#) is used to separate categories to improve readability, but is not strictly necessary. It is also used to indicate comments.
Numbers and single-word data values (i.e., those not containing white space) are listed by themselves:
_cell.length_a
63.150
A single value composed of multiple words separated by white-space need to be quoted:
_audit_author.name
'Fermi, G.'
A single value encompassing multiple line data values can be listed on a new line within a pair of semicolons:
loop_
_entity_poly.entity_id
_entity_poly.type
_entity_poly.nstd_linkage
_entity_poly.nstd_monomer
_entity_poly.pdbx_seq_one_letter_code
_entity_poly.pdbx_seq_one_letter_code_can
_entity_poly.pdbx_strand_id
_entity_poly.pdbx_target_identifier
1 'polypeptide (L)' no no
;VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSD
LHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR
;VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSD
LHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR
A,C ?
There are two special characters used as placeholders for mmCIF item values which for some reason cannot be explicitly assigned. The question mark (?) is used to mark an item value as missing. A period (.) may be used to identify that there is no appropriate value for the item or that a value has been intentionally omitted.
The PDBx/mmCIF Dictionary supports primary data types (integers, real numbers, and text), defines boundary conditions and controlled vocabularies, and provides the ability to link data items together to express relationships (
e.g.
, parent-child related data items).
For example, the entity identifier assigned to a molecule in the "parent"
_entity
data category (shown here) is referred to in the "child" categories (as shown in the subsequent example):
loop_
_entity.id
_entity.type
_entity.src_method
_entity.pdbx_description
_entity.formula_weight
_entity.pdbx_number_of_molecules
_entity.pdbx_ec
_entity.pdbx_mutation
_entity.pdbx_fragment
_entity.details
polymer
nat
'Hemoglobin subunit alpha'
14981.087
polymer
nat
'Hemoglobin subunit beta'
16032.274
non-polymer
syn
'PROTOPORPHYRIN IX CONTAINING FE'
616.487
water
nat
water
18.015
93
Example of a "child" category describing the source information for each polymer entity listed in the above "parent" category:
loop_
_entity_src_nat.entity_id
_entity_src_nat.pdbx_src_id
_entity_src_nat.pdbx_alt_source_flag
_entity_src_nat.pdbx_beg_seq_num
_entity_src_nat.pdbx_end_seq_num
_entity_src_nat.common_name
_entity_src_nat.pdbx_organism_scientific
_entity_src_nat.pdbx_ncbi_taxonomy_id
sample
140
horse
'Equus caballus'
9796
sample
146
horse
'Equus caballus'
9796
The primary PDBx/mmCIF resource
mmcif.wwpdb.org
contains all relevant data dictionaries and documentation, as well as a detailed description of the format's development and history.
The below sections present some key PDBx/mmCIF categories with descriptions and examples, and aim to help users to understand and adopt the PDBx/mmCIF format.
HEADER AND KEYWORDS
PDBx/mmCIF category
Legacy PDB format records
Description
_struct_keywords
HEADER KEYWDS
Keywords that describe the structure.
Example:
_struct_keywords.entry_id
8HRI
_struct_keywords.text
'SARS-CoV-2, Delta, Spike protein, VIRAL PROTEIN'
_struct_keywords.pdbx_keywords
'VIRAL PROTEIN'
TITLE AND AUTHORSHIP
PDBx/mmCIF category
Legacy PDB format records
Description
_struct
TITLE
Structure title.
Example:
_struct.entry_id
8HYP
_struct.title
'Crystal structure of AtHPPD-Y18400 complex'
PDBx/mmCIF category
Legacy PDB format records
Description
_audit_author
AUTHOR
Structure author(s).
Example:
loop_
_audit_author.name
_audit_author.pdbx_ordinal
_audit_author.identifier_ORCID
'Fermi, G.'
'Perutz, M.F.'
CITATION
PDBx/mmCIF category
Legacy PDB format record
Description
_citation
JRNL
Literature citations relevant to the contents of the entry.
Notes:
The
_citation.id
'primary' is used for the citation describing structure determination and refinement.
The corresponding authors for each citation are listed in the 'child'
_citation_author
category (see below).
Example:
loop_
_citation.id
_citation.title
_citation.journal_abbrev
_citation.journal_volume
_citation.page_first
_citation.page_last
_citation.year
_citation.journal_id_ASTM
_citation.country
_citation.journal_id_ISSN
_citation.journal_id_CSD
_citation.book_publisher
_citation.pdbx_database_id_PubMed
_citation.pdbx_database_id_DOI
primary
'Interaction of coxsackievirus B3 with the full length coxsackievirus-adenovirus receptor.'
Nat.Struct.Biol.
874
878
2001
NSBIEW
US
1072-8368
2024
11573093
10.1038/nsb1001-874
'ISOLATION OF A COMMON RECEPTOR FOR COXSACKIE B VIRUSES AND ADENOVIRUSES 2 AND 5'
Science
275
1320
1323
1997
SCIEAS
US
0036-8075
0038
10.1126/science.275.5304.1320
PDBx/mmCIF category
Legacy PDB format records
Description
_citation_author
JRNL
Citation author(s).
Notes:
The value in
_citation_author.citation_id
item points to the relevant citation information in the 'parent'
_citation
category (see above) linking citations with the corresponding authors.
Example:
loop_
_citation_author.citation_id
_citation_author.name
_citation_author.ordinal
_citation_author.identifier_ORCID
primary
'He, Y.'
primary
'Chipman, P.R.'
primary
'Howitt, J.'
primary
'Bator, C.M.'
primary
'Whitt, M.A.'
primary
'Baker, T.S.'
primary
'Kuhn, R.J.'
primary
'Anderson, C.W.'
primary
'Freimuth, P.'
primary
'Rossman, M.G.'
10
'Bergelson, J.M.'
11
'Cunningham, J.A.'
12
'Droguett, G.'
13
'Kurt-Jones, E.A.'
14
'Krithivas, A.'
15
'Hong, J.S.'
16
'Horwitz, M.S.'
17
'Crowell, R.L.'
18
'Finberg, R.W.'
19
EXPERIMENTAL METHOD
PDBx/mmCIF category
Legacy PDB format records
Description
_exptl
EXPDTA
Experimental method used to collect data.
Example:
_exptl.entry_id
4HHB
_exptl.method
'X-RAY DIFFRACTION'
_exptl.crystals_number
Example:
loop_
_exptl.entry_id
_exptl.crystals_number
_exptl.details
_exptl.method
_exptl.method_details
8W48
'X-RAY DIFFRACTION'
8W48
'NEUTRON DIFFRACTION'
MACROMOLECULES
Entry Composition and Details
PDBx/mmCIF category
Legacy PDB format records
Description
_entity
COMPND
Details about each unique molecular entity (protein, nucleic acid, carbohydrate, small molecule) present in the structure.
Notes:
_entity.id
is a unique identifier of all unique polymer
and non-polymer molecules in the structure. This value is referred to
in many 'child' categories within the model file connecting all the information
pertaining to a particular molecular entity together.
_entity.type
can be:
polymer
, branched, non-polymer, or water.
Each polymer entity is expected to have a corresponding record in the
_entity_poly
_entity_poly_seq
and
_pdbx_poly_seq_scheme
categories.
_entity.src_method
defines the type of method by which the entity was produced:
naturally obtained (
nat
), recombinantly expressed (
man
), or chemically synthesized (
syn
).
Source information for each polymer entity must be provided in either
_entity_src_nat
(naturally obtained),
_entity_src_gen
(recombinantly expressed), or
_pdbx_entity_src_syn
(chemically synthesized).
Example:
loop_
_entity.id
_entity.type
_entity.src_method
_entity.pdbx_description
_entity.formula_weight
_entity.pdbx_number_of_molecules
_entity.pdbx_ec
_entity.pdbx_mutation
polymer
man
'Secreted effector kinase SteC'
19731.074
2.7.-.-
C276S
non-polymer
nat
'ADENOSINE MONOPHOSPHATE'
347.221
non-polymer
syn
'MAGNESIUM ION'
24.305
water
nat
water
18.015
167
Source and Expression System
PDBx/mmCIF category
Legacy PDB format records
Description
_entity_src_gen
SOURCE
Details of the source from which the entity was obtained in cases where the source
was genetically manipulated, including the organism from which the gene was obtained
and the host organism for gene expression and details about the host organism
(e.g., the plasmid used).
Notes:
_entity_src_gen.pdbx_gene_src_scientific_name
corresponds to the scientific name of the organism from which the molecule originates.
_entity_src_gen.pdbx_host_org_scientific_name
corresponds to the scientific name of the organism that served as host for the production of the entity.
Example:
_entity_src_gen.entity_id
_entity_src_gen.pdbx_src_id
_entity_src_gen.pdbx_alt_source_flag
sample
_entity_src_gen.pdbx_seq_type
'Biological sequence'
_entity_src_gen.pdbx_beg_seq_num
_entity_src_gen.pdbx_end_seq_num
299
_entity_src_gen.pdbx_gene_src_scientific_name
'Severe acute respiratory syndrome coronavirus 2'
_entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id
2697049
_entity_src_gen.pdbx_host_org_scientific_name
'Escherichia coli BL21 (DE3)'
_entity_src_gen.pdbx_host_org_ncbi_taxonomy_id
469008
PDBx/mmCIF category
Legacy PDB format records
Description
_entity_src_nat
SOURCE
Details of the source from which the entity was obtained in cases
where the entity was isolated directly from a natural source.
Example:
_entity_src_nat
_entity_src_nat.pdbx_src_id
_entity_src_nat.pdbx_alt_source_flag
sample
_entity_src_nat.pdbx_beg_seq_num
_entity_src_nat.pdbx_end_seqe_num
129
_entity_src_nat.common_name
chicken
_entity_src_nat.pdbx_organism_scientific
'Gallus gallus'
_entity_src_nat.pdbx_ncbi_taxonomy_id
9031
PDBx/mmCIF category
Legacy PDB format records
Description
_pdbx_entity_src_syn
SOURCE
Details of the source from which the entity was obtained in cases where the entity was chemically synthesized.
Example:
_pdbx_entity_src_syn.entity_id
_pdbx_entity_src_syn.pdbx_src_id
_pdbx_entity_src_syn.pdbx_alt_source_flag
sample
_pdbx_entity_src_syn.pdbx_beg_seq_num
_pdbx_entity_src_syn.pdbx_end_seq_num
64
_pdbx_entity_src_syn.organism_scientific
'Mandarin fish ranavirus'
_pdbx_entity_src_syn.ncbi_taxonomy_id
2487147
Sample Sequence
PDBx/mmCIF category
Legacy PDB format records
Description
_entity_poly
SEQRES
Details about the polymer, such as polymer type, corresponding chain IDs and studied polymer sequence.
Notes:
_entity_poly.pdbx_seq_one_letter_code
describes the sequence of protein or nucleic acid polymers in standard one-letter codes of amino acids or nucleotides.
Non-standard amino acids/nucleotides are represented by their Chemical Component Dictionary (CCD) codes
in parenthesis. Deoxynucleotides are represented by the specially-assigned 2-letter CCD codes
in parenthesis, with 'D' prefix added to their ribonucleotide counterparts. For hybrid polymers,
each residue is represented by the code of its individual type. A cyclic polymer is represented
in linear sequence from the chosen start to end.
_entity_poly.pdbx_seq_one_letter_code_can
describes the canonical sequence of
protein or nucleic acid polymer in standard one-letter codes of amino acids or nucleotides, corresponding to the sequence in
_entity_poly.pdbx_seq_one_letter_code
Non-standard amino acids/nucleotides are represented by the codes of their parents if parent is specified in
_chem_comp.mon_nstd_parent_comp_id, or by letter 'X' if parent is not specified. Deoxynucleotides are
represented by their canonical one-letter codes of A, C, G, or T. For modifications with several
parent amino acids, all corresponding parent amino acid codes will be listed (ex. chromophores).
Example:
loop_
_entity_poly.entity_id
_entity_poly.type
_entity_poly.nstd_linkage
_entity_poly.nstd_monomer
_entity_poly.pdbx_seq_one_letter_code
_entity_poly.pdbx_seq_one_letter_code_can
_entity_poly.pdbx_strand_id
_entity_poly.pdbx_target_identifier
'polypeptide (L)'
no
no
;VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR
;VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR
A,C
'polypeptide (L)'
no
no
;VHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH
;VHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH
B,D
PDBx/mmCIF category
Legacy PDB format records
Description
_entity_poly_seq
SEQRES
Specifies the sequence of monomers in a polymer. Allowance is made for the possibility
of microheterogeneity in a sample by allowing a given sequence number to be correlated
with more than one monomer ID. The corresponding ATOM_SITE entries should reflect this heterogeneity.
Notes:
_entity_poly_seq.hetero
defines a flag to indicate whether this monomer in the polymer is heterogeneous in sequence.
Example:
loop_
_entity_poly_seq.entity_id
_entity_poly_seq.num
_entity_poly_seq.mon_id
_entity_poly_seq.hetero
VAL
LEU
SER
PRO
ALA
ASP
... (truncated for brevity)
PDBx/mmCIF category
Legacy PDB format records
Description
_pdbx_poly_seq_scheme
N/A
Residue level nomenclature mapping for polymer entities.
Notes:
_pdbx_poly_seq_scheme.asym_id
represents a unique and sequential identifier of each molecule in the model. Pointer to _atom_site.label_asym_id in the coordinate section.
_pdbx_poly_seq_scheme.pdb_strand_id
represents PDB chain ID.
Example:
loop_
_pdbx_poly_seq_scheme.asym_id
_pdbx_poly_seq_scheme.entity_id
_pdbx_poly_seq_scheme.seq_id
_pdbx_poly_seq_scheme.mon_id
_pdbx_poly_seq_scheme.ndb_seq_num
_pdbx_poly_seq_scheme.pdb_seq_num
_pdbx_poly_seq_scheme.auth_seq_num
_pdbx_poly_seq_scheme.pdb_mon_id
_pdbx_poly_seq_scheme.auth_mon_id
_pdbx_poly_seq_scheme.pdb_strand_id
_pdbx_poly_seq_scheme.pdb_ins_code
_pdbx_poly_seq_scheme.hetero
VAL
VAL
VAL
LEU
LEU
LEU
SER
SER
SER
PRO
PRO
PRO
ALA
ALA
ALA
ASP
ASP
ASP
LYS
LYS
LYS
THR
THR
THR
ASN
ASN
ASN
10
VAL
10
10
10
VAL
VAL
11
LYS
11
11
11
LYS
LYS
12
ALA
12
12
12
ALA
ALA
13
ALA
13
13
13
ALA
ALA
14
TRP
14
14
14
TRP
TRP
15
GLY
15
15
15
GLY
GLY
16
LYS
16
16
16
LYS
LYS
17
VAL
17
17
17
VAL
VAL
18
GLY
18
18
18
GLY
GLY
19
ALA
19
19
19
ALA
ALA
... (truncated for brevity)
PDBx/mmCIF category
Legacy PDB format records
Description
_struct_asym
N/A
Details about instances of molecular entities.
Notes:
The category provides correspondence between molecule ASYM_ID
_struct_asym.id
a unique identifier of each molecule in the model) and corresponding Entity ID
_entity.id
).
ASYM_ID can be different from the author provided or PDB assigned chain identifier (chain ID), ASYM_ID is
assigned sequentially starting from letter A to all polymer and non-polymer molecule instances in the structure.
A group of water molecules associated with the same polymer chain is assigned one ASYM_ID.
Example:
loop_
_struct_asym.id
_struct_asym.pdbx_blank_PDB_chainid_flag
_struct_asym.pdbx_modified
_struct_asym.entity_id
_struct_asym.details
Sequence Reference
PDBx/mmCIF category
Legacy PDB format records
Description
_struct_ref
DBREF
Relates the sequence of the polymer entities described in the structure to the
information archived in external sequence databases (UniProt, GeneBank, PDB, etc.).
Notes:
_struct_ref.pdbx_seq_one_letter_code
provides an external database sequence expressed as a string of one-letter amino acid codes. If no external database reference is provided,
the PDB entry itself is used as a database reference (self-reference) in which case the studied sample sequence is provided here.
Example:
_struct_ref.id
_struct_ref.db_name
UNP
_struct_ref.db_code
Q93D82_RHIRD
_struct_ref.pdbx_db_accession
Q93D82
_struct_ref.pdbx_db_isoform
_struct_ref.entity_id
_struct_ref.pdbx_seq_one_letter_code
;TAIVTNVKHFGGMGSALRLSEAGHTVACHDESFKQKDELEAFAETYPQLKPMSEQEPAELIEAVTSAYGQVDVLVSNDIF
APEFQPIDKYAVEDYRGAVEALQIRPFALVNAVASQMKKRKSGHIIFITSATPFGPWKELSTYTSARAGACTLANALSKE
LGEYNIPVFAIGPNYLHSEDSPYFYPTEPWKTNPEHVAHVKKVTALQRLGTQKELGELVAFLASGSCDYLTGQVFWLAGG
FPMIERWPGMPE
_struct_ref.pdbx_align_begin
PDBx/mmCIF category
Legacy PDB format records
Description
_struct_ref_seq
DBREF
Provides the residue ranges used for the alignment between the sequence
of an entity described in the structure and the sequence in the referenced
database entry.
Example:
loop_
_struct_ref_seq.align_id
_struct_ref_seq.ref_id
_struct_ref_seq.pdbx_PDB_id_code
_struct_ref_seq.pdbx_strand_id
_struct_ref_seq.seq_align_beg
_struct_ref_seq.pdbx_seq_align_beg_ins_code
_struct_ref_seq.seq_align_end
_struct_ref_seq.pdbx_seq_align_end_ins_code
_struct_ref_seq.pdbx_db_accession
_struct_ref_seq.db_align_beg
_struct_ref_seq.pdbx_db_align_beg_ins_code
_struct_ref_seq.db_align_end
_struct_ref_seq.pdbx_db_align_end_ins_code
_struct_ref_seq.pdbx_auth_seq_align_beg
_struct_ref_seq.pdbx_auth_seq_align_end
5KWE
20
271
Q93D82
254
254
5KWE
20
271
Q93D82
254
254
5KWE
20
271
Q93D82
254
254
5KWE
20
271
Q93D82
254
254
PDBx/mmCIF category
Legacy PDB format records
Description
_struct_ref_seq_dif
SEQADV
Lists differences (if any) between the sequence of the polymer entity
described in the structure and the sequence of the referenced database entry
with corresponding annotation (conflict, engineered mutation, variant,
expression tag, etc.).
Example:
loop_
_struct_ref_seq_dif.align_id
_struct_ref_seq_dif.pdbx_pdb_id_code
_struct_ref_seq_dif.mon_id
_struct_ref_seq_dif.pdbx_pdb_strand_id
_struct_ref_seq_dif.seq_num
_struct_ref_seq_dif.pdbx_pdb_ins_code
_struct_ref_seq_dif.pdbx_seq_db_name
_struct_ref_seq_dif.pdbx_seq_db_accession_code
_struct_ref_seq_dif.db_mon_id
_struct_ref_seq_dif.pdbx_seq_db_seq_num
_struct_ref_seq_dif.details
_struct_ref_seq_dif.pdbx_auth_seq_num
_struct_ref_seq_dif.pdbx_ordinal
5KWE
MET
UNP
Q93D82
'initiating methionine'
-16
5KWE
GLY
UNP
Q93D82
'expression tag'
-15
5KWE
HIS
UNP
Q93D82
'expression tag'
-14
5KWE
HIS
UNP
Q93D82
'expression tag'
-13
5KWE
HIS
UNP
Q93D82
'expression tag'
-12
5KWE
HIS
UNP
Q93D82
'expression tag'
-11
5KWE
HIS
UNP
Q93D82
'expression tag'
-10
5KWE
HIS
UNP
Q93D82
'expression tag'
-9
5KWE
SER
UNP
Q93D82
'expression tag'
-8
5KWE
SER
10
UNP
Q93D82
'expression tag'
-7
10
5KWE
GLY
11
UNP
Q93D82
'expression tag'
-6
11
5KWE
LEU
12
UNP
Q93D82
'expression tag'
-5
12
5KWE
VAL
13
UNP
Q93D82
'expression tag'
-4
13
5KWE
PRO
14
UNP
Q93D82
'expression tag'
-3
14
5KWE
ARG
15
UNP
Q93D82
'expression tag'
-2
15
5KWE
GLY
16
UNP
Q93D82
'expression tag'
-1
16
5KWE
SER
17
UNP
Q93D82
'expression tag'
17
5KWE
HIS
18
UNP
Q93D82
'expression tag'
18
5KWE
ALA
19
UNP
Q93D82
'expression tag'
19
5KWE
ASN
170
UNP
Q93D82
CYS
153
'engineered mutation'
153
20
OLIGOSACCHARIDES
Entry Composition and Details
PDBx/mmCIF category
Legacy PDB format records
Description
_entity
COMPND
Details about each unique molecular entity (protein, nucleic acid, carbohydrate, small molecule) present in the structure.
Example:
loop_
_entity.id
_entity.type
_entity.src_method
_entity.pdbx_description
_entity.formula_weight
_entity.pdbx_number_of_molecules
_entity.pdbx_ec
_entity.pdbx_mutation
_entity.pdbx_fragment
_entity.details
polymer
man
'FUCOLECTIN-RELATED PROTEIN'
66769.758
YES
'CATALYTIC MODULE, RESIDUES 31-589'
branched
man
"alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose"
681.7
water
nat
water
18.015
334
PDBx/mmCIF category
Legacy PDB format records
Description
_pdbx_entity_branch
N/A
Specifies the list of branched entities and the type.
Example:
_pdbx_entity_branch.entity_id
_pdbx_entity_branch.type
oligosaccharide
PDBx/mmCIF category
Legacy PDB format records
Description
_pdbx_entity_branch_descriptor
N/A
Provides string descriptors of entity chemical structure.
Example:
loop_
_pdbx_entity_branch_descriptor.ordinal
_pdbx_entity_branch_descriptor.entity_id
_pdbx_entity_branch_descriptor.descriptor
_pdbx_entity_branch_descriptor.type
_pdbx_entity_branch_descriptor.program
_pdbx_entity_branch_descriptor.program_version
"LFucpa1-2DGalpb1-4[LFucpa1-3]DGlcpNAcb1-ROH"
"Glycam Condensed Sequence"
GMML
1.0
"WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2-3-2/a3-b1_a4-c1_c2-d1"
WURCS
PDB2Glycan
1.1
"[][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-Galp]{[(2+1)][a-L-Fucp]{}}}"
LINUCS
PDB-CARE
Sequence
PDBx/mmCIF category
Legacy PDB format records
Description
_pdbx_entity_branch_list
N/A
Specifies the list of monomers in a branched entity. Allowance is made for the possibility of
microheterogeneity in a sample by allowing a given sequence number to be correlated with more than one monomer ID.
Example:
loop_
_pdbx_entity_branch_list.entity_id
_pdbx_entity_branch_list.comp_id
_pdbx_entity_branch_list.num
_pdbx_entity_branch_list.hetero
NAG
GAL
FUC
FUC
PDBx/mmCIF category
Legacy PDB format records
Description
_pdbx_branch_scheme
N/A
Residue level nomenclature mapping for branch chain entities.
Example:
loop_
_pdbx_branch_scheme.asym_id
_pdbx_branch_scheme.entity_id
_pdbx_branch_scheme.mon_id
_pdbx_branch_scheme.num
_pdbx_branch_scheme.pdb_asym_id
_pdbx_branch_scheme.pdb_mon_id
_pdbx_branch_scheme.pdb_seq_num
_pdbx_branch_scheme.auth_asym_id
_pdbx_branch_scheme.auth_mon_id
_pdbx_branch_scheme.auth_seq_num
_pdbx_branch_scheme.hetero
NAG
NAG
NAG
1592
GAL
GAL
GAL
1591
FUC
FUC
FUC
1590
FUC
FUC
FUC
1593
Connectivity
PDBx/mmCIF category
Legacy PDB format records
Description
_pdbx_entity_branch_link
N/A
Details about the linkages between components within a branched entity.
Example:
loop_
_pdbx_entity_branch_link.link_id
_pdbx_entity_branch_link.entity_id
_pdbx_entity_branch_link.entity_branch_list_num_1
_pdbx_entity_branch_link.comp_id_1
_pdbx_entity_branch_link.atom_id_1
_pdbx_entity_branch_link.leaving_atom_id_1
_pdbx_entity_branch_link.atom_stereo_config_1
_pdbx_entity_branch_link.entity_branch_list_num_2
_pdbx_entity_branch_link.comp_id_2
_pdbx_entity_branch_link.atom_id_2
_pdbx_entity_branch_link.leaving_atom_id_2
_pdbx_entity_branch_link.atom_stereo_config_2
_pdbx_entity_branch_link.value_order
_pdbx_entity_branch_link.details
GAL
C1
O1
NAG
O4
HO4
sing
FUC
C1
O1
GAL
O2
HO2
sing
FUC
C1
O1
NAG
O3
HO3
sing
PDBx/mmCIF category
Legacy PDB format records
Description
_struct_conn
LINK
SSBOND
Details about the connections between portions of the structure.
These can be covalent bonds, disulfide bridges, hydrogen bonds, and so on.
Example:
loop_
_struct_conn.id
_struct_conn.conn_type_id
_struct_conn.pdbx_leaving_atom_flag
_struct_conn.pdbx_PDB_id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.pdbx_ptnr1_label_alt_id
_struct_conn.pdbx_ptnr1_PDB_ins_code
_struct_conn.pdbx_ptnr1_standard_comp_id
_struct_conn.ptnr1_symmetry
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.pdbx_ptnr2_label_alt_id
_struct_conn.pdbx_ptnr2_PDB_ins_code
_struct_conn.ptnr1_auth_asym_id
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr2_auth_asym_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_symmetry
_struct_conn.pdbx_ptnr3_label_atom_id
_struct_conn.pdbx_ptnr3_label_seq_id
_struct_conn.pdbx_ptnr3_label_comp_id
_struct_conn.pdbx_ptnr3_label_asym_id
_struct_conn.pdbx_ptnr3_label_alt_id
_struct_conn.pdbx_ptnr3_PDB_ins_code
_struct_conn.details
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_value_order
_struct_conn.pdbx_role
covale1
covale
one
ASN
91
ND2
1_555
NAG
C1
ASN
91
NAG
409
1_555
1.440
N-Glycosylation
covale2
covale
one
ASN
207
ND2
1_555
NAG
C1
ASN
207
NAG
1_555
1.418
N-Glycosylation
covale3
covale
one
ASN
305
ND2
1_555
NAG
C1
ASN
305
NAG
1_555
1.451
N-Glycosylation
covale4
covale
both
NAG
O4
1_555
NAG
C1
NAG
NAG
1_555
1.357
covale5
covale
both
NAG
O4
1_555
NAG
C1
NAG
NAG
1_555
1.369
covale6
covale
both
NAG
O4
1_555
BMA
C1
NAG
BMA
1_555
1.374
covale7
covale
both
BMA
O6
1_555
MAN
C1
BMA
MAN
1_555
1.363
covale8
covale
both
BMA
O3
1_555
MAN
C1
BMA
MAN
1_555
1.353
covale9
covale
both
MAN
O3
1_555
MAN
C1
MAN
MAN
1_555
1.346
LIGANDS
Entry composition & details
PDBx/mmCIF category
Legacy PDB format records
Description
_entity
COMPOUND
Details about each unique molecular entity (protein, nucleic acid, carbohydrate, small molecule)
present in the structure.
Example:
loop_
_entity.id
_entity.type
_entity.src_method
_entity.pdbx_description
_entity.formula_weight
_entity.pdbx_number_of_molecules
_entity.pdbx_ec
_entity.pdbx_mutation
_entity.pdbx_fragment
_entity.details
polymer
man
'3C-like proteinase'
33825.547
3.4.22.69
non-polymer
syn
;(1R,2S,5S)-N-{(1E,2S)-1-imino-3[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-
3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide
501.542
water
nat
water
18.015
83
PDBx/mmCIF category
Legacy PDB format records
Description
_pdbx_entity_nonpoly
N/A
Provides mapping between entity and the non polymer component.
Example:
loop_
_pdbx_entity_nonpoly.entity_id
_pdbx_entity_nonpoly.name
_pdbx_entity_nonpoly.comp_id
;(1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl}-6,6-dimethyl-
3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide
4WI
water
HOH
PDBx/mmCIF category
Legacy PDB format records
Description
_chem_comp
HET
HETNAM
HETSYN
FORMUL
Details about each of the chemical components from which the relevant chemical structures can be constructed,
such as name, synonym, mass, or formula.
Example:
loop_
_chem_comp.id
_chem_comp.type
_chem_comp.mon_nstd_flag
_chem_comp.name
_chem_comp.pdbx_synonyms
_chem_comp.formula
_chem_comp.formula_weight
4WI
non-polymer
;(1R,2S,5S)-N{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-
3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide
'PF-07321332, bound form; nirmatrelvir, bound form; Paxlovid, bound form' 'C23 H34 F3
N5 O4' 501.542
ALA
'L-peptide linking'
ALANINE
'C3 H7 N O2'
89.093
ARG
'L-peptide linking'
ARGININE
'C6 H15 N4 O2 1'
175.209
ASN
'L-peptide linking'
ASPARAGINE
'C4 H8 N2 O3'
132.118
ASP
'L-peptide linking'
'ASPARTIC ACID'
'C4 H7 N O4'
133.103
... (truncated for brevity)
PDBx/mmCIF category
Legacy PDB format records
Description
_pdbx_nonpoly_scheme
N/A
Residue level nomenclature mapping for non-polymer entities.
Example:
loop_
_pdbx_nonpoly_scheme.asym_id
_pdbx_nonpoly_scheme.entity_id
_pdbx_nonpoly_scheme.mon_id
_pdbx_nonpoly_scheme.ndb_seq_num
_pdbx_nonpoly_scheme.pdb_seq_num
_pdbx_nonpoly_scheme.auth_seq_num
_pdbx_nonpoly_scheme.pdb_mon_id
_pdbx_nonpoly_scheme.auth_mon_id
_pdbx_nonpoly_scheme.pdb_strand_id
_pdbx_nonpoly_scheme.pdb_ins_code
4WI
401
4WI
UNL
HOH
501
12
HOH
HOH
HOH
502
85
HOH
HOH
HOH
503
52
HOH
HOH
HOH
504
27
HOH
HOH
HOH
505
29
HOH
HOH
HOH
506
HOH
HOH
HOH
507
23
HOH
HOH
HOH
508
55
HOH
HOH
HOH
509
42
HOH
HOH
HOH
10
510
53
HOH
HOH
... (truncated for brevity)
Connectivity
PDBx/mmCIF category
Legacy PDB format records
Description
_struct_conn
LINK
Details about the connections between portions of the structure.
These can be covalent bonds, disulfide bridges, hydrogen bonds, and so on.
Example:
_struct_conn.id
covale1
_struct_conn.conn_type_id
covale
_struct_conn.pdbx_leaving_atom_flag
none
_struct_conn.pdbx_PDB_id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_comp_id
CYS
_struct_conn.ptnr1_label_seq_id
145
_struct_conn.ptnr1_label_atom_id
SG
_struct_conn.pdbx_ptnr1_label_alt_id
_struct_conn.pdbx_ptnr1_PDB_ins_code
_struct_conn.pdbx_ptnr1_standard_comp_id
_struct_conn.ptnr1_symmetry
1_555
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_comp_id
4WI
_struct_conn.ptnr2_label_seq_id
_struct_conn.ptnr2_label_atom_id
C3
_struct_conn.pdbx_ptnr2_label_alt_id
_struct_conn.pdbx_ptnr2_PDB_ins_code
_struct_conn.ptnr1_auth_asym_id
_struct_conn.ptnr1_auth_comp_id
CYS
_struct_conn.ptnr1_auth_seq_id
145
_struct_conn.ptnr2_auth_asym_id
_struct_conn.ptnr2_auth_comp_id
4WI
_struct_conn.ptnr2_auth_seq_id
401
_struct_conn.ptnr2_symmetry
1_555
_struct_conn.pdbx_ptnr3_label_atom_id
_struct_conn.pdbx_ptnr3_label_seq_id
_struct_conn.pdbx_ptnr3_label_comp_id
_struct_conn.pdbx_ptnr3_label_asym_id
_struct_conn.pdbx_ptnr3_label_alt_id
_struct_conn.pdbx_ptnr3_PDB_ins_code
_struct_conn.details
_struct_conn.pdbx_dist_value
1.804
_struct_conn.pdbx_value_order
_struct_conn.pdbx_role
PDBx/mmCIF category
Legacy PDB format records
Description
_chem_comp_bond
N/A
Details about the bonds and bond orders between atoms in a chemical component.
Example:
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_aromatic_flag
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_ordinal
4WI
O1
C8
doub
4WI
C8
N2
sing
4WI
C8
C5
sing
4WI
N2
C7
sing
4WI
C4
C5
sing
4WI
C4
C2
sing
4WI
C5
C6
sing
4WI
N5
C3
doub
4WI
C3
C2
sing
4WI
C7
C6
sing
10
4WI
C2
N1
sing
11
4WI
N2
H9
sing
69
... (truncated for brevity)
PDBx/mmCIF category
Legacy PDB format records
Description
_chem_comp_atom
N/A
Details about the atoms in a chemical component.
Example:
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.pdbx_aromatic_flag
_chem_comp_atom.pdbx_stereo_config
_chem_comp_atom.pdbx_ordinal
4WI
C8
4WI
C3
4WI
C1
4WI
C13
4WI
C21
4WI
C6
4WI
C7
4WI
C10
4WI
C5
4WI
C9
10
4WI
C11
11
... (truncated for brevity)
Information Specific To Macromolecular Crystallography (MX)
Sample preparation
PDBx/mmCIF category
Legacy PDB format records
Description
_exptl_crystal_grow
REMARK 280
Details about the conditions and methods used to grow the crystal.
Example:
_exptl_crystal_grow.apparatus
_exptl_crystal_grow.crystal_id
_exptl_crystal_grow.method
'VAPOR DIFFUSION, SITTING DROP'
_exptl_crystal_grow.pH
5.5
_exptl_crystal_grow.pdbx_details
'0.4uL protein, 0.4 uL 100mM Bis-Tri pH 5.5, 25% PEG 3350,
0.2M NaCl equilibrated against a well of 0.5M LiCl'
_exptl_crystal_grow.temp
298
PDBx/mmCIF category
Legacy PDB format records
Description
_exptl_crystal
REMARK 280
Results of experimental measurements on the crystal or crystals used,
such as shape, size or density.
Example:
_exptl_crystal.density_Matthews
2.16
_exptl_crystal.density_percent_sol
43.08
_exptl_crystal.id
Data collection
PDBx/mmCIF category
Legacy PDB format records
Description
_diffrn
REMARK 200
Details about the diffraction experiment ambient conditions.
Example:
_diffrn.id
_diffrn.ambient_temp
100
_diffrn.crystal_id
_diffrn.details
_diffrn.pdbx_serial_crystal_experiment
PDBx/mmCIF category
Legacy PDB format records
Description
_diffrn_detector
REMARK 200
Details about the detector used to measure the scattered radiation,
including any analyser and post-sample collimation.
Example:
_diffrn_detector.diffrn_id
_diffrn_detector.details
mirrors
_diffrn_detector.detector
PIXEL
_diffrn_detector.type
'DECTRIS EIGER X 16M'
_diffrn_detector.pdbx_collection_date
2022-10-07
PDBx/mmCIF category
Legacy PDB format records
Description
_diffrn_radiation
REMARK 200
Details about the radiation used in measuring the diffraction intensities,
its collimation and monochromatization before the sample.
Example:
_diffrn_radiation.diffrn_id
_diffrn_radiation.monochromomator
'Si (111)'
_diffrn_radiation.wavelength_id
_diffrn_radiation.pdbx_monochromatic_or_laue_m_l
_diffrn_radiation.pdbx_diffrn_protocol
'SINGLE WAVELENGTH'
_diffrn_radiation.pdbx_scattering_type
x-ray
PDBx/mmCIF category
Legacy PDB format records
Description
_diffrn_radiation_wavelength
REMARK 200
Details about the wavelength of the radiation used to measure the diffraction intensities.
Several wavelengths can be provided here to describe for example multi-wavelength experiments,
such as MAD.
Example:
loop_
_diffrn_radiation_wavelength.id
_diffrn_radiation_wavelength.wavelength
_diffrn_radiation_wavelength.wt
1.0
1.0
0.9793
1.0
PDBx/mmCIF category
Legacy PDB format records
Description
_diffrn_source
REMARK 200
Details of the source of radiation used in the diffraction experiment.
Example:
_diffrn_source.current
_diffrn_source.details
_diffrn_source.diffrn_id
_diffrn_source.power
_diffrn_source.size
_diffrn_source.source
SYNCHROTRON
_diffrn_source.target
_diffrn_source.type
'NSLS-II BEAMLINE 17-ID-2'
_diffrn_source.voltage
_diffrn_source.pdbx_wavelength_list
0.9793
_diffrn_source.pdbx_synchrotron_beamline
17-ID-2
_diffrn_source.pdbx_synchrotron_site
NSLS-II
PDBx/mmCIF category
Legacy PDB format records
Description
_software
REMARK 3
REMARK 200
Details about the software used in the structure analysis,
which implies any software used in the generation of any data items
associated with the structure determination and structure representation.
Example:
loop_
_software.citation_id
_software.classification
_software.compiler_name
_software.compiler_version
_software.contact_author
_software.contact_author_email
_software.date
_software.description
_software.dependencies
_software.hardware
_software.language
_software.location
_software.mods
_software.name
_software.os
_software.os_version
_software.type
_software.version
_software.pdbx_ordinal
refinement
PHENIX
1.20.1_4487
'data scaling'
SCALA
'data reduction'
XDS
phasing
PHASER
Data collection and processing statistics
PDBx/mmCIF category
Legacy PDB format records
Description
_reflns
REMARK 200
Overall data collection statistics for the X-ray diffraction experiment.
Example:
_reflns.d_resolution_high
1.660
_reflns.d_resolution_low
62.942
_reflns.pdbx_number_measured_all
560202
_reflns.number_obs
112977
_reflns.pdbx_Rmerge_I_obs
0.040
_reflns.pdbx_netI_over_sigmaI
17.990
_reflns.pdbx_chi_squared
1.115
_reflns.percent_possible_obs
99.400
_reflns.observed_criterion_sigma_I
-3.000
_reflns.pdbx_Rrim_I_all
0.045
_reflns.pdbx_CC_half
0.999
_reflns.B_iso_Wilson_estimate
38.223
_reflns.pdbx_diffrn_id
_reflns.pdbx_ordinal
_reflns.entry_id
7GT6
_reflns.observed_criterion_sigma_F
_reflns.number_all
_reflns.pdbx_Rsym_value
_reflns.pdbx_redundancy
PDBx/mmCIF category
Legacy PDB format records
Description
_reflns_shell
REMARK 200
Data collection statistics for the X-ray diffraction experiment broken into resolution shells.
Example:
loop_
_reflns_shell.pdbx_diffrn_id
_reflns_shell.pdbx_ordinal
_reflns_shell.d_res_high
_reflns_shell.d_res_low
_reflns_shell.number_measured_obs
_reflns_shell.number_measured_all
_reflns_shell.number_unique_obs
_reflns_shell.pdbx_rejects
_reflns_shell.Rmerge_I_obs
_reflns_shell.meanI_over_sigI_obs
_reflns_shell.pdbx_Rsym_value
_reflns_shell.pdbx_chi_squared
_reflns_shell.pdbx_redundancy
_reflns_shell.percent_possible_obs
_reflns_shell.pdbx_netI_over_sigmaI_obs
_reflns_shell.number_possible
_reflns_shell.number_unique_all
_reflns_shell.Rmerge_F_all
_reflns_shell.Rmerge_F_obs
_reflns_shell.Rmerge_I_all
_reflns_shell.meanI_over_sigI_all
_reflns_shell.percent_possible_all
_reflns_shell.pdbx_Rrim_I_all
_reflns_shell.pdbx_Rpim_I_all
_reflns_shell.pdbx_CC_half
1.660
1.760
73562
18124
0.896
1.320
18441
98.300
1.035
0.529
1.760
1.890
73368
17113
0.473
2.780
17267
99.100
0.538
0.845
1.890
2.040
83887
15933
0.253
5.910
16040
99.300
0.282
0.968
2.040
2.230
77815
14753
0.130
11.180
14824
99.500
0.144
0.990
2.230
2.490
69475
13360
0.079
17.740
13398
99.700
0.088
0.996
2.490
2.880
62385
11722
0.050
27.680
11738
99.900
0.056
0.998
2.880
3.520
52823
9992
0.032
42.650
9997
99.900
0.036
0.999
3.520
4.970
40142
7731
0.024
57.810
7734
100.000
0.027
0.999
4.920
62.942
22745
4249
0.023
62.870
4252
99.900
0.025
0.999
Refinement
PDBx/mmCIF category
Legacy PDB format records
Description
_refine
REMARK 3
Details about the structure-refinement statistics.
Example:
_refine.entry_id
7GT6
_refine.pdbx_refine_id
'X-RAY DIFFRACTION'
_refine.ls_d_res_high
1.6600
_refine.ls_d_res_low
62.9400
_refine.pdbx_ls_sigma_F
0.000
_refine.ls_percent_reflns_obs
99.3700
_refine.ls_number_reflns_obs
56491
_refine.pdbx_ls_cross_valid_method
THROUGHOUT
_refine.pdbx_R_Free_selection_details
RANDOM
_refine.details
'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY'
_refine.ls_R_factor_all
_refine.ls_R_factor_obs
0.2007
_refine.ls_R_factor_R_word
0.1996
_refine.ls_R_factor_R_free
0.2276
_refine.ls_percent_reflns_R_free
3.9000
_refine.ls_number_reflns_R_free
2321
_refine.B_iso_mean
37.3880
_refine.aniso_B[1][1]
0.5500
_refine.aniso_B[2][2]
0.5500
_refine.aniso_B[3][3]
-1.7900
_refine.aniso_B[1][2]
0.2800
_refine.aniso_B[1][3]
0.0000
_refine.aniso_B[2][3]
0.0000
_refine.correlation_coeff_Fo_to_Fc
0.9620
_refine.correlation_coeff_Fo_to_Fc_free
0.9530
_refine.pdbx_overall_ESU_R
0.0890
_refine.pdbx_overall_ESU_R_Free
0.0900
_refine.overall_SU_ML
0.0740
_refine.overall_SU_B
2.3210
_refine.solvent_model_details
MASK
_refine.pdbx_solvent_vdw_probe_radii
1.2000
_refine.pdbx_solvent_ion_probe_radii
0.8000
_refine.pdbx_solvent_shrinkage_radii
0.8000
_refine.pdbx_method_to_determine_struct
'MOLECULAR REPLACEMENT'
_refine.pdbx_stereochemistry_target_values
'MAXIMUM LIKELIHOOD'
_refine.B_iso_max
135.070
_refine.B_iso_min
19.500
_refine.pdbx_diffrn_id
PDBx/mmCIF category
Legacy PDB format records
Description
_refine_ls_shell
REMARK 3
Details about the results of the least-squares refinement broken down into shells of resolution.
Example:
loop_
_refine_ls_shell.d_res_high
_refine_ls_shell.d_res_low
_refine_ls_shell.pdbx_total_number_of_bins_used
_refine_ls_shell.percent_reflns_obs
_refine_ls_shell.number_reflns_R_work
_refine_ls_shell.R_factor_all
_refine_ls_shell.R_factor_R_work
_refine_ls_shell.R_factor_R_free
_refine_ls_shell.percent_reflns_R_free
_refine_ls_shell.number_reflns_R_free
_refine_ls_shell.R_factor_R_free_error
_refine_ls_shell.number_reflns_all
_refine_ls_shell.number_reflns_obs
_refine_ls_shell.redundancy_reflns_obs
_refine_ls_shell.pdbx_refine_id
2.500
2.6316
97.0
4166
0.4102
0.4078
135
4301
4301
'X-RAY DIFFRACTION'
2.6316
2.7964
100.0
4242
0.3417
0.3548
156
4398
4398
'X-RAY DIFFRACTION'
2.7964
3.0123
100.0
4332
0.2683
0.3923
113
4445
4445
'X-RAY DIFFRACTION'
3.0123
3.3153
100.0
4285
0.2135
0.2780
158
4443
4443
'X-RAY DIFFRACTION'
3.3153
3.7947
98.0
4266
0.2193
0.2524
137
4403
4403
'X-RAY DIFFRACTION'
3.7947
4.7796
99.0
4312
0.1696
0.2265
156
4468
4468
'X-RAY DIFFRACTION'
4.7796
39.7236
100.0
4512
0.1794
0.1675
160
4672
4672
'X-RAY DIFFRACTION'
PDBx/mmCIF category
Legacy PDB format records
Description
_refine_ls_restr
REMARK 3
Details about the restraints applied to various classes of parameters during the least-squares refinement.
Notes:
The following PDB to PDB/mmCIF Data Item Correspondences provide description of the restraint types:
Example:
loop_
_refine_ls_restr.pdbx_refine_id
_refine_ls_restr.type
_refine_ls_restr.number
_refine_ls_restr.dev_ideal
_refine_ls_restr.dev_ideal_target
_refine_ls_restr.weight
_refine_ls_restr.pdbx_restraint_function
'X-RAY DIFFRACTION'
r_bond_refined_d
3714
0.048
0.025
'X-RAY DIFFRACTION'
r_bond_other_d
2730
0.001
0.015
'X-RAY DIFFRACTION'
r_angle_refined_deg
3919
1.717
1.662
'X-RAY DIFFRACTION'
r_angle_other_deg
6334
1.410
1.601
'X-RAY DIFFRACTION'
r_dihedral_angle_1_deg
355
6.689
5.000
'X-RAY DIFFRACTION'
r_dihedral_angle_2_deg
169
29.721
21.361
'X-RAY DIFFRACTION'
r_dihedral_angle_3_deg
545
14.366
15.000
'X-RAY DIFFRACTION'
r_dihedral_angle_4_deg
26
24.117
15.000
'X-RAY DIFFRACTION'
r_chiral_restr
357
0.088
0.200
'X-RAY DIFFRACTION'
r_gen_planes_refined
3323
0.009
0.020
'X-RAY DIFFRACTION'
r_gen_planes_other
705
0.001
0.020
'X-RAY DIFFRACTION'
r_mcbond_it
1792
3.161
3.442
'X-RAY DIFFRACTION'
r_mcbond_other
1753
3.149
3.416
'X-RAY DIFFRACTION'
r_mcangle_it
1735
4.416
5.214
PDBx/mmCIF category
Legacy PDB format records
Description
_pdbx_initial_refinement_model
N/A
The starting model(s) used in structure determination.
Example:
_pdbx_initial_refinement_model.id
_pdbx_initial_refinement_model.entity_id_list
_pdbx_initial_refinement_model.type
'experimental model'
_pdbx_initial_refinement_model.source_name
PDB
_pdbx_initial_refinement_model.accession_code
6HA3
_pdbx_initial_refinement_model.details
Crystallographic and Coordinate Transformation Section
PDBx/mmCIF category
Legacy PDB format records
Description
_symmetry
CRYST1
Details about the space group symmetry.
Example:
_symmetry.entry_id
8VCW
_symmeetry.cell_setting
_symmetry.Int_Tables_number
19
_symmetry.space_group_name_Hall
_symmetry.space_group_name_H-M
'P 21 21 21'
_symmeetry.pdbx_full_space_group_name_H-M
PDBx/mmCIF category
Legacy PDB format records
Description
_cell
CRYST1
Details about the crystallographic cell parameters.
Example:
_cell.angle_alpha
90.00
_cell.angle_beta
90.00
_cell.angle_gamma
90.00
_cell.entry_id
8VCW
_cell.length_a
38.209
_cell.length_b
50.7776
_cell.length_c
161.878
_cell.Z_PDB
PDBx/mmCIF category
Legacy PDB format records
Description
_atom_sites
SCALE
Details about the matrix used to transform fractional coordinates to Cartesian coordinates.
Example:
_atom_sites.entry_id
8VCW
_atom_sites.Cartn_transf_matrix[1][1]
_atom_sites.Cartn_transf_matrix[1][2]
_atom_sites.Cartn_transf_matrix[1][3]
_atom_sites.Cartn_transf_matrix[2][1]
_atom_sites.Cartn_transf_matrix[2][2]
_atom_sites.Cartn_transf_matrix[2][3]
_atom_sites.Cartn_transf_matrix[3][1]
_atom_sites.Cartn_transf_matrix[3][2]
_atom_sites.Cartn_transf_matrix[3][3]
_atom_sites.Cartn_transf_vector[1]
_atom_sites.Cartn_transf_vector[2]
_atom_sites.Cartn_transf_vector[3]
_atom_sites.Cart_transform_axes
_atom_sites.fract_transf_matrix[1][1]
0.026172
_atom_sites.fract_transf_matrix[1][2]
0.000000
_atom_sites.fract_transf_matrix[1][3]
0.000000
_atom_sites.fract_transf_matrix[2][1]
0.000000
_atom_sites.fract_transf_matrix[2][2]
0.019694
_atom_sites.fract_transf_matrix[2][3]
0.000000
_atom_sites.fract_transf_matrix[3][1]
0.000000
_atom_sites.fract_transf_matrix[3][2]
0.000000
_atom_sites.fract_transf_matrix[3][3]
0.006177
_atom_sites.fract_transf_vector[1]
0.00000
_atom_sites.fract_transf_vector[2]
0.00000
_atom_sites.fract_transf_vector[3]
0.00000
Information Specific To Electron Microscopy (3DEM)
Sample Description
PDBx/mmCIF category
Legacy PDB format records
Description
_em_entity_assembly
REMARK 245
Details about each component of the complex.
Notes:
An isolated protein would be classified in _em_entity_assembly.type as "COMPLEX".
The other categories refer to large-scale samples, such as "CELL", "VIRUS", etc.
Example:
_em_entity_assembly.id
_em_entity_assembly.parent_id
_em_entity_assembly.source
RECOMBINANT
_em_entity_assembly.type
COMPLEX
_em_entity_assembly.name
'Core tetramer assembly (p2) of the phiPA3 bacteriophage PhuN protein'
_em_entity_assembly.details
_em_entity_assembly.synonym
_em_entity_assembly.oligomeric_details
_em_entity_assembly.entity_id_list
PDBx/mmCIF category
Legacy PDB format records
Description
_em_entity_assembly_molwt
N/A
Details about the molecular weight of an assembly component of the sample.
Example:
loop_
_em_entity_assembly_molwt.entity_assembly_id
_em_entity_assembly_molwt.id
_em_entity_assembly_molwt.units
_em_entity_assembly_molwt.value
MEGADALTONS
30.5
PDBx/mmCIF category
Legacy PDB format records
Description
_em_entity_assembly_naturalsource
N/A
Details about the natural source for EM assemblies and assembly components.
Example:
_em_entity_assembly_naturalsource.cell
_em_entity_assembly_naturalsource.cellular_location
_em_entity_assembly_naturalsource.entity_assembly_id
_em_entity_assembly_naturalsource.id
_em_entity_assembly_naturalsource.ncbi_tax_id
998086
_em_entity_assembly_naturalsource.organism
'Pseudomonas phage PhiPA3'
_em_entity_assembly_naturalsource.organelle
_em_entity_assembly_naturalsource.organ
_em_entity_assembly_naturalsource.strain
_em_entity_assembly_naturalsource.tissue
PDBx/mmCIF category
Legacy PDB format records
Description
_em_entity_assembly_recombinant
N/A
Details about the recombinant expression of the assembly or assembly component.
Example:
_em_entity_assembly_recombinant.cell
_em_entity_assembly_recombinant.entity_assembly_id
_em_entity_assembly_recombinant.id
_em_entity_assembly_recombinant.ncbi_tax_id
562
_em_entity_assembly_recombinant.organism
'Escherichia coli'
_em_entity_assembly_recombinant.plasmid
_em_entity_assembly_recombinant.strain
'BL21 Star (DE3)pLysS'
EM Experiment
PDBx/mmCIF category
Legacy PDB format records
Description
_em_experiment
REMARK 245
High-level classification of the EM experiment.
Example:
_em_experiment.entry_id
8FNE
_em_experiment.id
_em_experiment.reconstruction_method
'SINGLE PARTICLE'
_em_experiment.aggregation_state
'2D ARRAY'
_em_experiment.entity_assembly_id
Sample preparation
PDBx/mmCIF category
Legacy PDB format records
Description
_em_specimen
REMARK 245
Details about specimens prepared for imaging by electron microscopy.
Example:
_em_specimen.concentration
_em_specimen.details
_em_specimen.embedding_applied
NO
_em_specimen.experiment_id
_em_specimen.id
_em_specimen.shadowing_applied
NO
_em_specimen.staining_applied
NO
_em_specimen.vitrification_applied
YES
PDBx/mmCIF category
Legacy PDB format records
Description
_em_buffer
REMARK 245
Details of the sample buffer.
Example:
_em_buffer.id
_em_buffer.specimen_id
_em_buffer.name
_em_buffer.details
'0.25 complete Protease Inhibitor Tablet also included'
_em_buffer.pH
6.5
PDBx/mmCIF category
Legacy PDB format records
Description
_em_buffer_component
N/A
Details of the sample buffer components.
Example:
loop_
_em_buffer_component.buffer_id
_em_buffer_component.concentration
_em_buffer_component.concentration_units
_em_buffer_component.formula
_em_buffer_component.id
_em_buffer_component.name
20
mM
BisTrisPropane
150
mM
'Sodium Chloride'
mM
DTT
mM
EDTA
mM
'Magnesium Chloride'
mM
ATP
PDBx/mmCIF category
Legacy PDB format records
Description
_em_staining
N/A
Details about the staining procedure used in the specimen preparation.
Example:
_em_staining.id
_em_staining.specimen_id
_em_staining.material
'Uranyl Acetate'
_em_staining.type
NEGATIVE
_em_staining.details
'Negatively stained EM specimens were prepared using a carbon-sandwich
technique and uranyl-acetate stain.'
PDBx/mmCIF category
Legacy PDB format records
Description
_em_embedding
N/A
Details about the embedding procedure used in the specimen preparation.
Example:
_em_embedding.details
'3% trehalose'
_em_embedding.id
_em_embedding.material
trehalose
_em_embedding.specimen_id
PDBx/mmCIF category
Legacy PDB format records
Description
_em_shadowing
N/A
Details about the shadowing of an EM specimen.
Example:
_em_shadowing.id
_em_shadowing.specimen_id
_em_shadowing.angle
45
_em_shadowing.thickness
_em_shadowing.material
Platinum
_em_shadowing.details
'shadowing was used to create a platinum replica'
PDBx/mmCIF category
Legacy PDB format records
Description
_em_sample_support
REMARK 245
Details of the electron microscope grid type,
grid support film and pretreatment of the whole before sample is applied.
Example:
_em_sample_support.id
_em_sample_support.film_material
'HOLEY CARBON'
_em_sample_support.grid_material
COPPER
_em_sample_support.grid_mesh_size
400
_em_sample_support.details
'GLOW DISCHARGED 120 seconds'
PDBx/mmCIF category
Legacy PDB format records
Description
_em_support_film
N/A
Describes films supporting the specimen.
Example:
_em_support_film.id
_em_support_film.material
CARBON
PDBx/mmCIF category
Legacy PDB format records
Description
_em_grid_pretreatment
N/A
Describes glow discharge pretreatment for an EM grid.
Example:
_em_grid_pretreatment.id
_em_grid_pretreatment.sample_support_id
_em_grid_pretreatment.type
'GLOW DISCHARGE'
_em_grid_pretreatment.time
12
PDBx/mmCIF category
Legacy PDB format records
Description
_em_vitrification
REMARK 245
Details about the method and cryogen used in rapid freezing
of the sample on the grid prior to its insertion in the electron microscope.
Example:
_em_vitrification.entry_id
8FNE
_em_vitrification.id
_em_vitrification.specimen_id
_em_vitrification.cryogen_name
ETHANE
_em_vitrification.humidity
100
_em_vitrification.temp
_em_vitrification.chamber_temperature
283.15
_em_vitrification.instrument
'FEI VITROBOT MARK IV'
_em_vitrification.method
_em_vitrification.time_resolved_state
_em_vitrification.citation_id
_em_vitrification.details
Imaging
PDBx/mmCIF category
Legacy PDB format records
Description
_em_imaging
REMARK 245
Details about the parameters used in imaging the sample in the electron microscope.
Example:
_em_imaging.entry_id
8FNE
_em_imaging.id
_em_imaging.microscope_model
'FEI TITAN KRIOS'
_em_imaging.specimen_holder_type
_em_imaging.specimen_holder_model
'FEI TITAN KRIOS AUTOGRID HOLDER'
_em_imaging.accelerating_voltage
300
_em_imaging.illumination_mode
'FLOOD BEAM'
_em_imaging.mode
'BRIGHT FIELD'
_em_imaging.nominal_cs
2.7
_em_imaging.nominal_defocus_min
800
_em_imaging.nominal_defocus_max
2500
_em_imaging.nominal_magnification
105000
_em_imaging.electron_source
'FIELD EMISSION GUN'
_em_imaging.specimen_id
_em_imaging.cryogen
NITROGEN
PDBx/mmCIF category
Legacy PDB format records
Description
_em_image_scans
REMARK 245
Details of the image scanning device (microdensitometer) and parameters for digitization of the image.
Example:
_em_image_scans.entry_id
1DYL
_em_image_scans.id
_em_image_scans.number_digital_images
48
PDBx/mmCIF category
Legacy PDB format records
Description
_em_tomography
N/A
Microscopy parameters only relevant for tomography.
Example:
_em_tomography.id
_em_tomography.imaging_id
_em_tomography.dual_tilt_axis_rotation
90.0
_em_tomography.axis1_angle_increment
_em_tomography.axis1_min_angle
-70.00
_em_tomography.axis1_max_angle
70.0
_em_tomography.axis2_angle_increment
_em_tomography.axis2_min_angle
-70.0
_em_tomography.axis2_max_angle
70.0
PDBx/mmCIF category
Legacy PDB format records
Description
_em_imaging_optics
N/A
Description of a few specialist optics apparatus.
Example:
_em_imaging_optics.id
_em_imaging_optics.imaging_id
_em_imaging_optics.chr_aberration_corrector
'CEOS manufactured Cc corrector'
_em_imaging_optics.energyfilter_lower
_em_imaging_optics.energyfilter_upper
15
_em_imaging_optics.energyfilter_name
FEI
_em_imaging_optics.phase_plate
_em_imaging_optics.sph_aberration_corrector
PDBx/mmCIF category
Legacy PDB format records
Description
_em_focused_ion_beam
N/A
Description of sectioning by focused_ion_beam.
Example:
No example available
PDBx/mmCIF category
Legacy PDB format records
Description
_em_image_recording
REMARK 245
Details of the image recording (either film/microdensitometer or electronic densitometer)
and parameters for image digitization.
Example:
_em_image_recording.average_exposure_time
_em_image_recording.avg_electron_dose_per_subtomogram
_em_image_recording.avg_electron_dose_per_image
67
_em_image_recording.details
_em_image_recording.detector_mode
_em_image_recording.film_or_detector_model
'GATAN K3 BIOQUANTUM (6k x 4k)'
_em_image_recording.id
_em_image_recording.imaging_id
_em_image_recording.num_diffraction_images
_em_image_recording.num_grids_imaged
_em_image_recording.num_real_images
Reconstruction
PDBx/mmCIF category
Legacy PDB format records
Description
_em_3d_reconstruction
REMARK 3
REMARK 245
Details of the 3D reconstruction procedure from 2D projections.
Example:
_em_3d_reconstruction.entry_id
8FNE
_em_3d_reconstruction.id
_em_3d_reconstruction.method
_em_3d_reconstruction.algorithm
_em_3d_reconstruction.citation_id
_em_3d_reconstruction.details
_em_3d_reconstruction.resolution
3.9
_em_3d_reconstruction.resolution_method
'FSC 0.143 CUT-OFF'
_em_3d_reconstruction.magnification_calibration
_em_3d_reconstruction.nominal_pixel_size
_em_3d_reconstruction.actual_pixel_size
_em_3d_reconstruction.num_particles
29303
_em_3d_reconstruction.euler_angles_details
_em_3d_reconstruction.num_class_averages
_em_3d_reconstruction.refinement_type
_em_3d_reconstruction.image_processing_id
_em_3d_reconstruction.symmetry_type
POINT
PDBx/mmCIF category
Legacy PDB format records
Description
_em_particle_selection
N/A
Details of images from scanned micrographs and the number of particles
selected from a scanned set of micrographs.
Example:
_em_particle_selection.id
_em_particle_selection.image_processing_id
_em_particle_selection.num_particles_selected
5267
_em_particle_selection.method
'INTERACTIVE'
_em_particle_selection.details
PDBx/mmCIF category
Legacy PDB format records
Description
_em_image_processing
N/A
Details of the EM image processing procedure.
Example:
_em_image_processing.id
_em_image_processing.image_recording_id
_em_image_processing.details
'The selected images were high-pass filtered and normalized'
PDBx/mmCIF category
Legacy PDB format records
Description
_em_ctf_correction
N/A
Description of the Contrast Transfer Function (CTF) correction.
Example:
_em_ctf_correction.details
_em_ctf_correction.id
_em_ctf_correction.em_image_processing_id
_em_ctf_correction.type
'PHASE FLIPPING ONLY'
Symmetry
PDBx/mmCIF category
Legacy PDB format records
Description
_em_helical_entity
N/A
Details for a helical or filament type of assembly component.
Example:
_em_helical_entity.id
_em_helical_entity.image_processing_id
_em_helical_entity.details
_em_helical_entity.axial_symmetry
C2
_em_helical_entity.angular_rotation_per_subunit
-0.782
_em_helical_entity.axial_rise_per_subunit
4.763
PDBx/mmCIF category
Legacy PDB format records
Description
_pdbx_helical_symmetry
N/A
Details about the helical symmetry group associated with this entry.
Example:
_pdbx_helical_symmetry.entry_id
'1ABC'
_pdbx_helical_symmetry.number_of_operations
35
_pdbx_helical_symmetry.rotation_per_n_subunits
131.84
_pdbx_helical_symmetry.rise_per_n_subunits
6.10
_pdbx_helical_symmetry.n_subunits_divisor
_pdbx_helical_symmetry.dyad_axis
no
_pdbx_helical_symmetry.circular_symmetry
PDBx/mmCIF category
Legacy PDB format records
Description
_em_single_particle_entity
N/A
Details of the enforced symmetry for a single particle entity type.
Example:
_em_single_particle_entity.entry_id
8GA0
_em_single_particle_entity.id
_em_single_particle_entity.image_processing_id
_em_single_particle_entity.point_symmetry
C1
Fitting
PDBx/mmCIF category
Legacy PDB format records
Description
_em_3d_fitting
REMARK 3
Details of the method of fitting atomic coordinates from a coordinate file
into a 3d-em volume map file.
Example:
_em_3d_fitting.id
_em_3d_fitting.entry_id
8FNE
_em_3d_fitting.method
_em_3d_fitting.target_criteria
_em_3d_fitting.details
'The initial model was generated using AlphaFold based on sequence alone.'
_em_3d_fitting.overall_b_value
_em_3d_fitting.ref_space
_em_3d_fitting.ref_protocol
'FLEXIBLE FIT'
PDBx/mmCIF category
Legacy PDB format records
Description
_em_3d_fitting_list
N/A
Details of the initial model used in fitting.
Example:
_em_3d_fitting_list.id
_em_3d_fitting_list.3d_fitting_id
_em_3d_fitting_list.pdb_entry_id
_em_3d_fitting_list.pdb_chain_id
_em_3d_fitting_list.pdb_chain_residue_range
_em_3d_fitting_list.details
_em_3d_fitting_list.chain_id
_em_3d_fitting_list.chain_residue_range
_em_3d_fitting_list.source_name
AlphaFold
_em_3d_fitting_list.type
'in silico model'
_em_3d_fitting_list.accession_code
Software
PDBx/mmCIF category
Legacy PDB format records
Description
_em_software
REMARK 3
Details of the software that was used for data collection,
data processing, data analysis, structure calculations and refinement.
Example:
loop_
_em_software.category
_em_software.details
_em_software.id
_em_software.image_processing_id
_em_software.fitting_id
_em_software.imaging_id
_em_software.name
_em_software.version
'PARTICLE SELECTION'
cryoSPARC
v2.15.0
'PARTICLE SELECTION'
cryoSPARC
v3.3.1
'PARTICLE SELECTION'
'IMAGE ACQUISITION'
SerialEM
v.3.6-v.3.8
MASKING
'CTF CORRECTION'
'LAYERLINE INDEXING'
'DIFFRACTION INDEXING'
'MODEL FITTING'
RosettaRelax
Rosetta
'MODEL FITTING'
10
'UCSF ChimeraX'
'MODEL FITTING'
11
'UCSF Chimera'
OTHER
12
'IMAGE ACQUISITION'
13
'MODEL REFINEMENT'
RosettaRefine
14
Rosetta
'MODEL REFINEMENT'
15
ISOLDE
1.2.1
'INITIAL EULER ASSIGNMENT'
'Ab-Initio Reconstruction'
16
cryoSPARC
v2.15.0
'INITIAL EULER ASSIGNMENT'
17
'FINAL EULER ASSIGNMENT'
18
cisTEM
1.0.0-beta
'FINAL EULER ASSIGNMENT'
19
CLASSIFICATION
20
cisTEM
1.0.0-beta
CLASSIFICATION
21
RECONSTRUCTION
22
Information Specific To Nuclear Magnetic Resonance (NMR)
Ensemble Description
PDBx/mmCIF category
Legacy PDB format records
Description
_pdbx_nmr_ensemble
REMARK 210
Describes the ensemble of deposited structures.
Example:
_pdbx_nmr_ensemble.entry_id
8COO
_pdbx_nmr_ensemble.conformers_calculated_total_number
40
_pdbx_nmr_ensemble.conformers_submitted_total_number
20
_pdbx_nmr_ensemble.conformer_selection_criteria
'structures with the lowest energy'
_pdbx_nmr_ensemble.representative_conformer
_pdbx_nmr_ensemble.average_constraints_per_residue
_pdbx_nmr_ensemble.average_constraint_violations_per_residue
_pdbx_nmr_ensemble.maximum_distance_constraint_violation
_pdbx_nmr_ensemble.average_distance_constraint_violation
_pdbx_nmr_ensemble.maximum_upper_distance_constraint_violation
_pdbx_nmr_ensemble.maximum_lower_distance_constraint_violation
_pdbx_nmr_ensemble.distance_constraint_violation_method
_pdbx_nmr_ensemble.maximum_torsion_angle_constraint_violation
_pdbx_nmr_ensemble.average_torsion_angle_constraint_violation
_pdbx_nmr_ensemble.torsion_angle_constraint_violation_method
PDBx/mmCIF category
Legacy PDB format records
Description
_pdbx_nmr_representative
REMARK 210
Describes selection of the representative structure.
Example:
_pdbx_nmr_representative.entry_id
8COO
_pdbx_nmr_representative.conformer_id
_pdbx_nmr_representative.selection_criteria
'lowest energy'
Sample Preparation
PDBx/mmCIF category
Legacy PDB format records
Description
_pdbx_nmr_sample_details
REMARK 210
Complete description of each NMR sample, including the solvent system used.
Example:
_pdbx_nmr_sample_details.solution_id
_pdbx_nme_sample_details.contents
'300 uM [U-100% 13C; U-100% 15N] sample 1, 95% H2O/5% D2O'
_pdbx_nmr_sample_details.solvent_system
'95% H2O/5% D2O'
_pdbx_nmr_sample_details.label
13C15N_sample
_pdbx_nmr_sample_details.type
solution
_pdbx_nmr_sample_details.details
PDBx/mmCIF category
Legacy PDB format records
Description
_pdbx_nmr_exptl_sample
N/A
The chemical constituents of each NMR sample. Each sample is identified by a
number and each component in the sample is identified by name.
Example:
_pdbx_nmr_exptl_sample.solution_id
_pdbx_nmr_exptl_sample.component
'sample 1'
_pdbx_nmr_exptl_sample.concentration
300
_pdbx_nmr_exptl_sample.concentration_range
_pdbx_nmr_exptl_sample.concentration_units
uM
_pdbx_nmr_exptl_sample.isotopic_labeling
'[U-100% 13C; U-100% 15N]'
PDBx/mmCIF category
Legacy PDB format records
Description
_pdbx_nmr_exptl_sample_conditions
REMARK 210
The experimental conditions used for each sample.
Each set of conditions is identified by a numerical code.
Example:
_pdbx_nmr_exptl_sample_conditions.conditions_id
_pdbx_nmr_exptl_sample_conditions.temperature
310
_pdbx_nmr_exptl_sample_conditions.pressure_units
atm
_pdbx_nmr_exptl_sample_conditions.pressure
ambient
_pdbx_nmr_exptl_sample_conditions.pH
6.5
_pdbx_nmr_exptl_sample_conditions.ionic_strength
0.02
_pdbx_nmr_exptl_sample_conditions.details
'0.3 mM [U-100% 13C; U-100% 15N]'
_pdbx_nmr_exptl_sample_conditions.ionic_strength_err
_pdbx_nmr_exptl_sample_conditions.ionic_strength_units
'Not defined'
_pdbx_nmr_exptl_sample_conditions.label
13C15N_sample
_pdbx_nmr_exptl_sample_conditions.pH_err
_pdbx_nmr_exptl_sample_conditions.pH_units
pH
_pdbx_nmr_exptl_sample_conditions.pressure_err
_pdbx_nmr_exptl_sample_conditions.temperature_err
_pdbx_nmr_exptl_sample_conditions.temperature_units
Data Collection
PDBx/mmCIF category
Legacy PDB format records
Description
_pdbx_nmr_spectrometer
REMARK 210
Details about each spectrometer used to collect data for this deposition.
Example:
loop_
_pdbx_nmr_spectrometer.spectrometer_id
_pdbx_nmr_spectrometer.model
_pdbx_nmr_spectrometer.type
_pdbx_nmr_spectrometer.manufacturer
_pdbx_nmr_spectrometer.field_strength
_pdbx_nmr_spectrometer.details
'AVANCE III'
Bruker
600
'AVANCE III'
Bruker
850
PDBx/mmCIF category
Legacy PDB format records
Description
_pdbx_nmr_exptl
REMARK 210
Information on the experiments that were used to generate constraint data.
Example:
loop_
_pdbx_nmr_exptl.experiment_id
_pdbx_nmr_exptl.conditions_id
_pdbx_nmr_exptl.solution_id
_pdbx_nmr_exptl.type
_pdbx_nmr_exptl.spectrometer_id
_pdbx_nmr_exptl.sample_state
'2D 1H-15N HSQC'
isotropic
'2D 1H-13C HSQC'
isotropic
'3D 1H-13C NOESY aliphatic'
isotropic
'3D 1H-15N NOESY'
isotropic
'2D 1H-1H NOESY'
isotropic
'2D 1H-1H NOESY'
isotropic
Refinement
PDBx/mmCIF category
Legacy PDB format records
Description
_pdbx_nmr_refine
REMARK 210
Method and details of the refinement of the deposited structure.
Example:
_pdbx_nmr_refine.entry_id
8COO
_pdbx_nmr_refine.method
'torsion angle dynamics'
_pdbx_nmr_refine.details
_pdbx_nmr_refine.software_ordinal
Software
PDBx/mmCIF category
Legacy PDB format records
Description
_pdbx_nmr_software
REMARK 3
REMARK 210
Description of the software that was used for data collection,
data processing, data analysis, structure calculations and refinement.
Example:
loop_
_pdbx_nmr_software.ordinal
_pdbx_nmr_software.classification
_pdbx_nmr_software.name
_pdbx_nmr_software.version
_pdbx_nmr_software.authors
refinement
ARIA
;Linge, O'Donoghue and Nilges
'structure calculation'
ARIA
;Linge, O'Donoghue and Nilges
'chemical shift assignment'
XEASY
'Bartels et al.'
'peak picking'
XEASY
'Bartels et al.'
ASSEMBLY
PDBx/mmCIF category
Legacy PDB format records
Description
_pdbx_struct_assembly
REMARK 350
Details about the structural elements that form macromolecular assemblies.
Example:
_pdbx_struct_assembly.id
_pdbx_struct_assembly.details
author_and_software_defined_assembly
_pdbx_struct_assembly.method_details
PISA
_pdbx_struct_assembly.oligomeric_details
dimeric
_pdbx_struct_assembly.oligomeric_count
PDBx/mmCIF category
Legacy PDB format records
Description
_pdbx_struct_assembly_gen
REMARK 350
Details about the generation of each macromolecular assembly.
Notes:
_pdbx_struct_assembly_gen.asym_id_list
lists the ASYM_IDs (a unique identifier of each molecule in the model)
of all components forming the assembly including ligands excluding water molecules.
Ligands are included in the
_pdbx_struct_assembly_gen.asym_id_list
Example:
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
1,2
_pdbx_struct_assembly_gen.asym_id_list
A,B,C,D
PDBx/mmCIF category
Legacy PDB format records
Description
_pdbx_struct_assembly_prop
REMARK 350
Details about the calculated total surface area,
buried surface area and free energy gain for an assembly.
Example:
loop_
_pdbx_struct_assembly_prop.biol_id
_pdbx_struct_assembly_prop.type
_pdbx_struct_assembly_prop.value
_pdbx_struct_assembly_prop.details
'ABSA (A^2)'
3090
MORE
-33
'SSA (A^2)'
25780
PDBx/mmCIF category
Legacy PDB format records
Description
_pdbx_struct_oper_list
REMARK 350
Details about the symmetry operations and Cartesian rotation
and translation matrices required to transform the coordinates deposited
with the entry to generate the biological assembly.
Example:
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[3]
'identity operation'
1_555
x,y,z
1.0000000000
0.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
'crystal symmetry operation'
2_555
-x,-y,-z
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
0.0000000000
SECONDARY STRUCTURE
PDBx/mmCIF category
Legacy PDB format records
Description
_struct_conf_type
HELIX
Type of the conformation of the backbone of the polymer.
Example:
_struct_conf_type.id
HELX_P
PDBx/mmCIF category
Legacy PDB format records
Description
_struct_conf
HELIX
Details about the backbone conformation of a segment of polymer.
Example:
loop_
_struct_conf.conf_type_id
_struct_conf.id
_struct_conf.pdbx_PDB_helix_id
_struct_conf.beg_label_comp_id
_struct_conf.beg_label_asym_id
_struct_conf.beg_label_seq_id
_struct_conf.pdbx_beg_PDB_ins_code
_struct_conf.end_label_comp_id
_struct_conf.end_label_asym_id
_struct_conf.end_label_seq_id
_struct_conf.pdbx_end_PDB_ins_code
_struct_conf.beg_auth_comp_id
_struct_conf.beg_auth_asym_id
_struct_conf.beg_auth_seq_id
_struct_conf.end_auth_comp_id
_struct_conf.end_auth_asym_id
_struct_conf.end_auth_seq_id
_struct_conf.pdbx_PDB_helix_class
_struct_conf.details
_struct_conf.pdbx_PDB_helix_length
HELX_P
HELX_P1
AA1
SER
10
GLY
15
SER
10
GLY
15
HELX_P
HELX_P2
AA2
HIS
41
CYS
44
HIS
41
CYS
44
HELX_P
HELX_P3
AA3
GLU
47
ASN
51
GLU
47
ASN
51
HELX_P
HELX_P4
AA4
ASN
53
ARG
60
ASN
53
ARG
60
HELX_P
HELX_P5
AA5
LYS
61
HIS
64
LYS
61
HIS
64
HELX_P
HELX_P6
AA6
ILE
200
ASN
214
ILE
200
ASN
214
15
HELX_P
HELX_P7
AA7
THR
226
TYR
237
THR
226
TYR
237
12
HELX_P
HELX_P8
AA8
THR
243
LEU
250
THR
243
LEU
250
HELX_P
HELX_P9
AA9
LEU
250
GLY
258
LEU
250
GLY
258
HELX_P
HELX_P10
AB1
ALA
260
GLY
275
ALA
260
GLY
275
16
HELX_P
HELX_P11
AB2
THR
292
SER
301
THR
292
SER
301
10
PDBx/mmCIF category
Legacy PDB format records
Description
_struct_sheet
SHEET
Details about the beta sheets.
Example:
loop_
_struct_sheet.id
_struct_sheet.type
_struct_sheet.number_strands
_struct_sheet.details
AA1
AA2
AA3
PDBx/mmCIF category
Legacy PDB format records
Description
_struct_sheet_order
SHEET
Details about the order of the residue ranges that form a beta-sheet. All order links
are pairwise and the specified pairs are assumed to be adjacent to one another
in the sheet.
Example:
loop_
_struct_sheet_order.sheet_id
_struct_sheet_order.range_id_1
_struct_sheet_order.range_id_2
_struct_sheet_order.offset
_struct_sheet_order.sense
AA1
anti-parallel
AA1
anti-parallel
AA1
anti-parallel
AA1
anti-parallel
AA1
anti-parallel
AA1
anti-parallel
AA2
parallel
AA2
anti-parallel
AA2
anti-parallel
AA2
anti-parallel
AA3
parallel
AA3
anti-parallel
PDBx/mmCIF category
Legacy PDB format records
Description
_struct_sheet_range
SHEET
Details about the residue ranges that form a beta-sheet.
Residues are included in a range if they make beta-sheet-type
hydrogen-bonding interactions with at least one adjacent strand and
if there are at least two residues in the range.
Example:
loop_
_struct_sheet_range.sheet_id
_struct_sheet_range.id
_struct_sheet_range.beg_label_comp_id
_struct_sheet_range.beg_label_asym_id
_struct_sheet_range.beg_label_seq_id
_struct_sheet_range.pdbx_beg_PDB_ins_code
_struct_sheet_range.end_label_comp_id
_struct_sheet_range.end_label_asym_id
_struct_sheet_range.end_label_seq_id
_struct_sheet_range.pdbx_end_PDB_ins_code
_struct_sheet_range.beg_auth_comp_id
_struct_sheet_range.beg_auth_asym_id
_struct_sheet_range.beg_auth_seq_id
_struct_sheet_range.end_auth_comp_id
_struct_sheet_range.end_auth_asym_id
_struct_sheet_range.end_auth_seq_id
AA1
VAL
73
LEU
75
VAL
73
LEU
75
AA1
PHE
66
ALA
70
PHE
66
ALA
70
AA1
MET
17
CYS
22
MET
17
CYS
22
AA1
THR
25
LEU
32
THR
25
LEU
32
AA1
VAL
35
PRO
39
VAL
35
PRO
39
AA1
VAL
86
VAL
91
VAL
86
VAL
91
AA1
VAL
77
GLN
83
VAL
77
GLN
83
AA2
LYS
100
PHE
103
LYS
100
PHE
103
AA2
CYS
156
GLU
166
CYS
156
GLU
166
AA2
VAL
148
ASP
153
VAL
148
ASP
153
AA2
THR
111
TYR
118
THR
111
TYR
118
AA2
SER
121
ALA
129
SER
121
ALA
129
AA3
LYS
100
PHE
103
LYS
100
PHE
103
AA3
CYS
156
GLU
166
CYS
156
GLU
166
AA3
HIS
172
THR
175
HIS
172
THR
175
PDBx/mmCIF category
Legacy PDB format records
Description
_pdbx_struct_sheet_hbond
SHEET
Details about the hydrogen bonding between residue ranges in a beta sheet.
Example:
loop_
_pdbx_struct_sheet_hbond.sheet_id
_pdbx_struct_sheet_hbond.range_id_1
_pdbx_struct_sheet_hbond.range_id_2
_pdbx_struct_sheet_hbond.range_1_label_atom_id
_pdbx_struct_sheet_hbond.range_1_label_comp_id
_pdbx_struct_sheet_hbond.range_1_label_asym_id
_pdbx_struct_sheet_hbond.range_1_label_seq_id
_pdbx_struct_sheet_hbond.range_1_PDB_ins_code
_pdbx_struct_sheet_hbond.range_1_auth_atom_id
_pdbx_struct_sheet_hbond.range_1_auth_comp_id
_pdbx_struct_sheet_hbond.range_1_auth_asym_id
_pdbx_struct_sheet_hbond.range_1_auth_seq_id
_pdbx_struct_sheet_hbond.range_2_label_atom_id
_pdbx_struct_sheet_hbond.range_2_label_comp_id
_pdbx_struct_sheet_hbond.range_2_label_asym_id
_pdbx_struct_sheet_hbond.range_2_label_seq_id
_pdbx_struct_sheet_hbond.range_2_PDB_ins_code
_pdbx_struct_sheet_hbond.range_2_auth_atom_id
_pdbx_struct_sheet_hbond.range_2_auth_comp_id
_pdbx_struct_sheet_hbond.range_2_auth_asym_id
_pdbx_struct_sheet_hbond.range_2_auth_seq_id
AA1
LEU
75
LEU
75
VAL
68
VAL
68
AA1
LEU
67
LEU
67
THR
21
THR
21
AA1
VAL
20
VAL
20
LEU
27
LEU
27
AA1
LEU
30
LEU
30
TYR
37
TYR
37
AA1
CYS
38
CYS
38
LEU
87
LEU
87
AA1
LYS
90
LYS
90
ILE
78
ILE
78
AA2
LYS
100
LYS
100
VAL
157
VAL
157
AA2
SER
158
SER
158
ASN
151
ASN
151
AA2
PHE
150
PHE
150
SER
113
SER
113
AA2
ALA
116
ALA
116
SER
123
SER
123
AA3
LYS
100
LYS
100
VAL
157
VAL
157
AA3
MET
165
MET
165
ALA
173
ALA
173
COORDINATE SECTION
PDBx/mmCIF category
Legacy PDB format records
Description
_atom_site
ATOM
HETATM
Details about the atoms in a macromolecular crystal structure,
such as the positional coordinates, temperature factors, and occupancies.
Notes:
_atom_site.label_asym_id
ASYM ID, a unique and sequential identifier of each molecule (starting from letter A)
in the model. This data item is a pointer to
_struct_asym.id
in the
_struct_asym
category.
ASYM_ID can be different from the author provided (or PDB assigned)
chain identifier (Chain ID), ASYM_ID is assigned sequentially starting
from letter A to all polymer and non-polymer molecule instances in the structure.
All water molecules are assigned one ASYM_ID.
_atom_site.auth_asym_id
author provided (or PDB assigned) Chain ID.
_atom_site.label_entity_id
a unique identifier of all unique polymer and non-polymer molecules
in the structure as it is referred to in the
_entity
category.
_atom_site.label_comp_id
PDB assigned residue name.
_atom_site.auth_comp_id
author provided or PDB assigned residue name.
_atom_site.label_seq_id
unique and sequential residue number (starting from 1 including unmodeled residues)
in the polymer sequence.
_atom_site.auth_seq_id
author provided residue number.
Example:
loop_
_atom_site.group_PDB
_atom_site.id
_atom_site.type_symbol
_atom_site.label_atom_id
_atom_site.label_alt_id
_atom_site.label_comp_id
_atom_site.label_asym_id
_atom_site.label_entity_id
_atom_site.label_seq_id
_atom_site.pdbx_PDB_ins_code
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.occupancy
_atom_site.B_iso_or_equiv
_atom_site.pdbx_formal_charge
_atom_site.auth_seq_id
_atom_site.auth_comp_id
_atom_site.auth_asym_id
_atom_site.auth_atom_id
_atom_site.pdbx_PDB_model_num
ATOM
MET
10.121
49.201
18.054
1.00
88.02
40
MET
ATOM
CA
MET
8.837
48.574
18.359
1.00
85.54
40
MET
CA
ATOM
MET
7.968
48.387
17.110
1.00
78.31
40
MET
ATOM
MET
6.906
47.764
17.17
1.00
77.36
40
MET
ATOM
CB
MET
8.081
49.393
19.407
1.00
91.19
40
MET
CB
ATOM
CG
MET
8.647
49.264
20.815
1.00
97.92
40
MET
CG
ATOM
SD
MET
8.520
47.577
21.459
1.00
99.09
40
MET
SD
ATOM
CE
MET
10.226
47.245
21.909
1.00
96.88
40
MET
CE
ATOM
GLY
8.409
48.936
15.983
1.00
64.64
41
GLY
ATOM
10
CA
GLY
7.802
48.609
14.715
1.00
44.08
41
GLY
CA
ATOM
11
GLY
8.184
47.194
14.310
1.00
37.87
41
GLY
ATOM
12
GLY
8.744
46.415
15.082
1.00
32.33
41
GLY
ATOM
13
LEU
7.868
46.866
13.059
1.00
29.81
42
LEU
ATOM
14
CA
LEU
8.194
45.563
12.503
1.00
26.22
42
LEU
CA
..... (truncated for brevity)
HETATM
7475
O1
GOL
12.399
17.309
2.493
1.00
49.81
302
GOL
O1
HETATM
7476
C2
GOL
11.119
19.504
2.235
1.00
58.42
302
GOL
C2
HETATM
7477
O2
GOL
11.275
19.672
0.870
1.00
52.72
302
GOL
O2
HETATM
7478
C3
GOL
11.147
20.886
2.974
1.00
60.69
302
GOL
C3
HETATM
7479
O3
GOL
11.560
21.902
2.108
1.00
56.04
302
GOL
O3
..... (truncated for brevity)
HETATM
7536
HOH
-0.397
5.714
-2.954
1.00
55.09
401
HOH
HETATM
7537
HOH
1.933
22.895
0.037
1.00
41.11
402
HOH
HETATM
7538
HOH
18.942
20.641
12.691
1.00
35.07
403
HOH
HETATM
7539
HOH
-0.984
8.117
1.053
1.00
44.71
404
HOH
HETATM
7540
HOH
-0.000
-0.000
-4.882
0.50
38.73
405
HOH
HETATM
7541
HOH
6.821
7.758
19.352
1.00
65.84
406
HOH
HETATM
7542
HOH
6.505
18.912
6.900
1.00
43.17
407
HOH
HETATM
7543
HOH
-4.255
12.564
-7.163
1.00
53.88
408
HOH
PDBx/mmCIF category
Legacy PDB format records
Description
_atom_site_anisotrop
ANISOU
Details about the anisotropic displacement parameters.
Notes:
Represent elements of the standard anisotropic atomic displacement matrix U,
which appears in the structure-factor term as:
T = exp{-2 pi
sum
[sum
(U
ij
)]}
h = the Miller indices
= the reciprocal space cell lengths
In the legacy PDB format files the same anisotropic temperature factors
are scaled by a factor of
10
Angstroms
and are presented as integers.
Example:
loop_
_atom_site_anisotrop.id
_atom_site_anisotrop.type_symbol
_atom_site_anisotrop.pdbx_label_atom_id
_atom_site_anisotrop.pdbx_label_alt_id
_atom_site_anisotrop.pdbx_label_comp_id
_atom_site_anisotrop.pdbx_label_asym_id
_atom_site_anisotrop.pdbx_label_seq_id
_atom_site_anisotrop.pdbx_PDB_ins_code
_atom_site_anisotrop.U[1][1]
_atom_site_anisotrop.U[2][2]
_atom_site_anisotrop.U[3][3]
_atom_site_anisotrop.U[1][2]
_atom_site_anisotrop.U[1][3]
_atom_site_anisotrop.U[2][3]
_atom_site_anisotrop.pdbx_auth_seq_id
_atom_site_anisotrop.pdbx_auth_comp_id
_atom_site_anisotrop.pdbx_auth_asym_id
_atom_site_anisotrop.pdbx_auth_atom_id
MET
1.2107
1.0696
1.0693
0.0076
-0.0422
-0.3059
40
MET
CA
MET
1.1724
1.0654
1.0125
0.0219
-0.0147
-0.3086
40
MET
CA
MET
1.0644
0.9574
0.9537
0.0404
-0.0040
-0.2902
40
MET
MET
1.0413
0.9680
0.9301
0.0495
0.0180
-0.2876
40
MET
CB
MET
1.2482
1.1430
1.0736
0.0301
-0.0016
-0.3458
40
MET
CB
CG
MET
1.3496
1.2585
1.1122
0.0134
-0.0061
-0.3622
40
MET
CG
SD
MET
1.3676
1.3267
1.0707
0.0023
0.0074
-0.3342
40
MET
SD
CE
MET
1.3559
1.3081
1.0171
-0.0205
-0.0277
-0.3192
40
MET
CE
GLY
0.8894
0.7460
0.8208
0.0436
-0.0202
-0.2751
41
GLY
10
CA
GLY
0.6158
0.4733
0.5858
0.0581
-0.0157
-0.2497
41
GLY
CA
11
GLY
0.5329
0.4169
0.4891
0.0499
-0.0142
-0.2242
41
GLY
12
GLY
0.4693
0.3760
0.3830
0.0353
-0.0147
-0.2254
41
GLY
..... (truncated for brevity)
MISCELLANEOUS RECORDS
PDBx/mmCIF category
Legacy PDB format records
Description
_database_2
N/A
Records the database identifiers of the structure.
Example:
loop_
_database_2.database_id
_database_2.database_code
_database_2.pdbx_database_accession
_database_2.pdbx_DOI
PDB
8GDR
pdb_00008gdr
10.2210/pdb8gdr/pdb
WWPDB
D_1000272577
EMDB
EMD-29950
PDBx/mmCIF category
Legacy PDB format records
Description
_pdbx_database_status
N/A
Details about the deposition date, deposition and processing wwPDB partner site,
status of the model file and associated experimental data in the PDB archive.
Example:
_pdbx_database_status.status_code
REL
_pdbx_database_status.status_code_sf
REL
_pdbx_database_status.status_code_mr
_pdbx_database_status.entry_id
8CQO
_pdbx_database_status.recvd_initial_deposition_date
2023-03-06
_pdbx_database_status.SG_entry
_pdbx_database_status.deposit_site
PDBE
_pdbx_database_status.process_site
PDBE
_pdbx_database_status.status_code_cs
_pdbx_database_status.status_code_nmr_data
_pdbx_database_status.methods_development_category
_pdbx_database_status.pdb_format_compatible
PDBx/mmCIF category
Legacy PDB format records
Description
_pdbx_database_PDB_obs_spr
SPRSDE
OBSLTE
Details about the obsolete/superseded PDB entries.
Example:
_pdbx_database_PDB_obs_spr.id
SPRSDE
_pdbx_database_PDB_obs_spr.date
1984-07-17
_pdbx_database_PDB_obs_spr.pdb_id
4HHB
_pdbx_database_PDB_obs_spr.replace_pdb_id
1HHB
_pdbx_database_PDB_obs_spr.details
PDBx/mmCIF category
Legacy PDB format records
Description
_pdbx_database_related
REMARK 900
Contains references to entries that are related to the entry.
Example:
loop_
_pdbx_database_related.db_name
_pdbx_database_related.details
_pdbx_database_related.db_id
_pdbx_database_related.content_type
EMDB
;Composite map used in construction of PDB 8GDR -
SARS-Cov2 S protein structure in complex with neutralizing monoclonal antibody 002-S21B10.
EMD-29950
'associated EM volume'
EMDB
;Overall map of SARS-Cov2 S protein structure in complex with neutralizing monoclonal
antibody 002-S21B10. Used in construction of composite map EMD-29950.
EMD-29975
'consensus EM volume'
EMDB
;Locally refined map of SARS-Cov2 S protein structure in complex with neutralizing
monoclonal antibody 002-S21B10. Used in construction of composite map EMD-29950.
EMD-40007
'focused EM volume'
PDB
'Structure of SARS-Cov2 S protein structure in complex with neutralizing
monoclonal antibody 002-S21B10'
8GDR
unspecified
PDBx/mmCIF category
Legacy PDB format records
Description
_database_PDB_caveat
CAVEAT
Details about the outstanding issues with the structure flagged by the Protein Data Bank.
Example:
loop_
_database_PDB_caveat.id
_database_PDB_caveat.text
'THR A 137 HAS WRONG CHIRALITY AT ATOM CB'
'THR B 12 HAS WRONG CHIRALITY AT ATOM CB'
'THR B 50 HAS WRONG CHIRALITY AT ATOM CB'
'ASN C 78 HAS WRONG CHIRALITY AT ATOM CA'
'THR C 118 HAS WRONG CHIRALITY AT ATOM CB'
'HIS D 2 HAS WRONG CHIRALITY AT ATOM CA'
'SER D 72 HAS WRONG CHIRALITY AT ATOM CA'
'ASP D 73 HAS WRONG CHIRALITY AT ATOM CA'
'LEU D 78 HAS WRONG CHIRALITY AT ATOM CA'
10
'LYS D 144 HAS WRONG CHIRALITY AT ATOM CA'
PDBx/mmCIF category
Legacy PDB format records
Description
_pdbx_audit_support
N/A
Details about funding support for the entry.
Example:
_pdbx_audit_support.funding_organization
'National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)'
_pdbx_audit_support.country
'United States'
_pdbx_audit_support.grant_number
'XXX XXXXXXX'
_pdbx_audit_support.ordinal
PDBx/mmCIF category
Legacy PDB format records
Description
_pdbx_contact_author
N/A
Details about the name and email address of the principal investigator.
Example:
_pdbx_contact_author.id
_pdbx_contact_author.email
j.smith@domain.name
_pdbx_contact_author.name_first
John
_pdbx_contact_author.name_last
Smith
_pdbx_contact_author.name_mi
_pdbx_contact_author.role
'principal investigator/group leader'
_pdbx_contact_author.identifier_ORCID
0000-000x-xxxx-xxxx
ENTRY REVISION HISTORY
PDBx/mmCIF category
Legacy PDB format records
Description
_pdbx_audit_revision_history
REVDAT
Entry file type, major and minor revision version numbers and corresponding revision dates.
Example:
loop_
_pdbx_audit_revision_history.ordinal
_pdbx_audit_revision_history.data_content_type
_pdbx_audit_revision_history.major_revision
_pdbx_audit_revision_history.minor_revision
_pdbx_audit_revision_history.revision_date
'Structure model'
2023-09-20
'Sturcture model'
2023-10-04
PDBx/mmCIF category
Legacy PDB format records
Description
_pdbx_audit_revision_details
REVDAT
Entry file type, type classification of the revision (initial release, coordinate replacement,
obsolete, remediation) and additional details describing the revision.
Notes:
Major version revision corresponds to updates to the atomic coordinates, polymer sequence(s),
and/or chemical identity of a ligand. All other changes are defined as minor.
wwPDB retains all major versions with the latest minor versions of an entry within the PDB archive.
Example:
_pdbx_audit_revision_details.revision_ordinal
_pdbx_audit_revision_details.data_content_type
'Structure model'
_pdbx_audit_revision_details.provider
repository
_pdbx_audit_revision_details.type
'Initial release'
_pdbx_audit_revision_details.description
_pdbx_audit_revision_details.details
PDBx/mmCIF category
Legacy PDB format records
Description
_pdbx_audit_revision_group
REVDAT
mmCIF groups affected by revision
Example:
_pdbx_audit_revision_group.ordinal
_pdbx_audit_revision_group.revision_ordinal
_pdbx_audit_revision_group.data_content_type
'Structure model'
_pdbx_audit_revision_group.group
'Database references'
PDBx/mmCIF category
Legacy PDB format records
Description
_pdbx_audit_revision_category
REVDAT
mmCIF categories affected by revision
Example:
loop_
_pdbx_audit_revision_category.ordinal
_pdbx_audit_revision_category.revision_ordinal
_pdbx_audit_revision_category.data_content_type
_pdbx_audit_revision_category.category
'Structure model'
citation
'Structure model'
citation_author
PDBx/mmCIF category
Legacy PDB format records
Description
_pdbx_audit_revision_item
REVDAT
mmCIF category items affected by revision.
Example:
loop_
_pdbx_audit_revision_item.ordinal
_pdbx_audit_revision_item.revision_ordinal
_pdbx_audit_revision_item.data_content_type
_pdbx_audit_revision_item.item
'Structure model'
'_citation.country'
'Structure model'
'_citation.journal_abbrev'
'Structure model'
'_citation.journal_id_ASTM'
'Structure model'
'_citation.journal_id_CSD
'Structure model'
'_citation.journal_id_ISSN'
'Structure model'
'_citation.journal_volume'
'Structure model'
'_citation.page_first'
'Structure model'
'_citation.page_last'
'Structure model'
'_citation.pdbx_database_id_DOI '
10
'Structure model'
'_citation.pdbx_database_id_PubMed'
11
'Structure model'
'_citation.title'
12
'Structure model'
'_citation.year'
Revised: June 7, 2024
© wwPDB