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
1	polymer	man	'Secreted effector kinase SteC'	19731.074	4	2.7.-.-	C276S
2	non-polymer	nat	'ADENOSINE MONOPHOSPHATE'	347.221	4	?	?
3	non-polymer	syn	'MAGNESIUM ION'	24.305	5	?	?
4	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	1
_entity_src_gen.pdbx_src_id	1
_entity_src_gen.pdbx_alt_source_flag	sample
_entity_src_gen.pdbx_seq_type	'Biological sequence'
_entity_src_gen.pdbx_beg_seq_num	1
_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	1
_entity_src_nat.pdbx_src_id	1
_entity_src_nat.pdbx_alt_source_flag	sample
_entity_src_nat.pdbx_beg_seq_num	1
_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	2
_pdbx_entity_src_syn.pdbx_src_id	1
_pdbx_entity_src_syn.pdbx_alt_source_flag	sample
_pdbx_entity_src_syn.pdbx_beg_seq_num	1
_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
1	'polypeptide (L)'	no	no
;VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR
;
;VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR
;
A,C	?
2	'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
1	1	VAL	n
1	2	LEU	n
1	3	SER	n
1	4	PRO	n
1	5	ALA	n
1	6	ASP	n
... (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
A	1	1	VAL	1	1	1	VAL	VAL	A	.	n
A	1	2	LEU	2	2	2	LEU	LEU	A	.	n
A	1	3	SER	3	3	3	SER	SER	A	.	n
A	1	4	PRO	4	4	4	PRO	PRO	A	.	n
A	1	5	ALA	5	5	5	ALA	ALA	A	.	n
A	1	6	ASP	6	6	6	ASP	ASP	A	.	n
A	1	7	LYS	7	7	7	LYS	LYS	A	.	n
A	1	8	THR	8	8	8	THR	THR	A	.	n
A	1	9	ASN	9	9	9	ASN	ASN	A	.	n
A	1	10	VAL	10	10	10	VAL	VAL	A	.	n
A	1	11	LYS	11	11	11	LYS	LYS	A	.	n
A	1	12	ALA	12	12	12	ALA	ALA	A	.	n
A	1	13	ALA	13	13	13	ALA	ALA	A	.	n
A	1	14	TRP	14	14	14	TRP	TRP	A	.	n
A	1	15	GLY	15	15	15	GLY	GLY	A	.	n
A	1	16	LYS	16	16	16	LYS	LYS	A	.	n
A	1	17	VAL	17	17	17	VAL	VAL	A	.	n
A	1	18	GLY	18	18	18	GLY	GLY	A	.	n
A	1	19	ALA	19	19	19	ALA	ALA	A	.	n
... (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
A	N	N	1	?
B	N	N	1	?
C	N	N	1	?
D	N	N	1	?
E	N	N	2	?
F	N	N	2	?
G	N	N	2	?
H	N	N	2	?

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	1
_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	1
_struct_ref.pdbx_seq_one_letter_code
;TAIVTNVKHFGGMGSALRLSEAGHTVACHDESFKQKDELEAFAETYPQLKPMSEQEPAELIEAVTSAYGQVDVLVSNDIF APEFQPIDKYAVEDYRGAVEALQIRPFALVNAVASQMKKRKSGHIIFITSATPFGPWKELSTYTSARAGACTLANALSKE LGEYNIPVFAIGPNYLHSEDSPYFYPTEPWKTNPEHVAHVKKVTALQRLGTQKELGELVAFLASGSCDYLTGQVFWLAGG FPMIERWPGMPE
;
_struct_ref.pdbx_align_begin	3

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
1	1	5KWE	A	20	?	271	?	Q93D82	3	?	254	?	3	254
2	1	5KWE	B	20	?	271	?	Q93D82	3	?	254	?	3	254
3	1	5KWE	C	20	?	271	?	Q93D82	3	?	254	?	3	254
4	1	5KWE	D	20	?	271	?	Q93D82	3	?	254	?	3	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

UNP

Q93D82

'expression tag'

-7

5KWE

GLY

UNP

Q93D82

'expression tag'

-6

5KWE

LEU

UNP

Q93D82

'expression tag'

-5

5KWE

VAL

UNP

Q93D82

'expression tag'

-4

5KWE

PRO

UNP

Q93D82

'expression tag'

-3

5KWE

ARG

UNP

Q93D82

'expression tag'

-2

5KWE

GLY

UNP

Q93D82

'expression tag'

-1

5KWE

SER

UNP

Q93D82

'expression tag'

5KWE

HIS

UNP

Q93D82

'expression tag'

5KWE

ALA

UNP

Q93D82

'expression tag'

5KWE

ASN

170

UNP

Q93D82

CYS

153

'engineered mutation'

153