Registry PDB Structure

Suggest

The Protein Data Bank is the single worldwide archive of structural data of biological macromolecules.

Prefix

pdb

Alternative Prefixes

wwpdb pdbe RCSB_PDB pdbj

Keywords

bioinformatics epidemiology protein proteomics structural biology structure virology

Links

Homepage

Contact

Haruki Nakamura 0000-0001-6690-5863

Pattern for Local Unique Identifiers

Local identifiers in PDB Structure should match this regular expression:
^[0-9][A-Za-z0-9]{3}$

Example Local Unique Identifier

2gc4 Resolve
157d Resolve
9ii2 Resolve

Pattern for CURIES

Compact URIs (CURIEs) constructed from PDB Structure should match this regular expression:
^pdb:[0-9][A-Za-z0-9]{3}$

Example CURIE

pdb:2gc4
pdb:157d
pdb:9ii2

Publications

Ontology

A summary of the relations in the Semantic Farm schema can be found here.

Provided By: pdbsum validatordb viperdb
In Collection: Resources mentioned in "Sharing biological data: why, when, and how" ChEBI Data Sources Global Biodata Coalition - Global Core Biodata Resources Synapse.org external links

Metaregistry PDB Structure

The metaregistry provides mappings between the Semantic Farm and other registries. There are 14 mappings to external registries for this resource with 9 unique external prefixes.

Registry Name	Registry Metaprefix	External Prefix
BioContext	`biocontext`	`PDB`
EDAM	`edam`	`1127`
FAIRSharing	`fairsharing`	`FAIRsharing.rs2815`
GO	`go`	`PDB`
Integbio	`integbio`	`nbdc00613`
Identifiers.org	`miriam`	`pdb`
N2T	`n2t`	`pdb`
NCBI	`ncbi`	`PDB`
Pathguide	`pathguide`	`398`
Prefix Commons	`prefixcommons`	`pdbj`
re3data	`re3data`	`r3d100010910`
TogoID	`togoid`	`Pdb`
UniProt	`uniprot`	`DB-0172`
Wikidata	`wikidata`	`P638`

RDF Information

When using this resource in RDF, the following URI format should be used:

https://rdf.wwpdb.org/pdb/$1

Providers

Suggest

A provider turns a local unique identifiers from a resource into a URI. Many providers are also resolvable as URLs (i.e., they can be used in a web browser).

The local unique identifier 2gc4 is used to demonstrate the providers available for PDB Structure. Some providers may use a different example, which is displayed in the table below. A guide for curating additional providers can be found here.

Name	Metaprefix	URI
PDB Structure	`pdb`	https://www.wwpdb.org/pdb?id=2gc4
PDB Structure (RDF)	`rdf`	https://rdf.wwpdb.org/pdb/2gc4
Bioregistry	`bioregistry`	https://bioregistry.io/pdb:2gc4
Identifiers.org	`miriam`	https://identifiers.org/pdb:2gc4
Name-to-Thing	`n2t`	https://n2t.net/pdb:2gc4

Extra Providers

Additional providers curated in the Semantic Farm are listed here. These are typically inherited from Identifiers.org or Prefix Commons, and need extra curation.

Code	Name	URL
	Proteopedia	http://proteopedia.org/wiki/index.php/2gc4
`bio2rdf`	Bio2RDF	http://bio2rdf.org/pdbj:2gc4
`dionysus`	DIONYSUS	https://www.dsimb.inserm.fr/DIONYSUS/structure/2gc4
`ebi`	Protein Databank through PDBsum	https://www.ebi.ac.uk/pdbsum/2gc4
`furna`	furna	https://seq2fun.dcmb.med.umich.edu/furna/pdb.cgi?pdbid=157d
`pdbe`	Protein Databank in Europe (PDBe)	https://www.ebi.ac.uk/pdbe/entry/pdb/2gc4
`pdbj`	Protein Data Bank Japan (PDBj)	https://pdbj.org/mine/summary/2gc4
`proteinsplus`	ProteinsPlus	https://proteins.plus/2gc4
`rcsb`	RCSB PDB	https://www.rcsb.org/structure/2gc4
`rnaprodb`	RNA Protein Database	https://rnaprodb.usc.edu/2gc4
`sabdab`	The Structural Antibody Database	https://opig.stats.ox.ac.uk/webapps/sabdab-sabpred/sabdab/structureviewer/?pdb=9ii2

Normalize prefixes. This can be any capitalization or punctuation variant of the synonyms listed below.

>>> import bioregistry as br
>>> br.normalize_prefix("wwpdb")
'pdb'

Get all synonyms:

>>> import bioregistry as br
>>> br.get_synonyms("pdb")
{'wwpdb', 'pdbe', 'RCSB_PDB', 'pdbj'}

This name annotation was originally annotated in Bioregistry and is redistributed under the CC0 license.

Get the name:

>>> import bioregistry as br
>>> br.get_name("pdb")
'PDB Structure'

Get the homepage:

>>> import bioregistry as br
>>> br.get_homepage("pdb")
'https://www.wwpdb.org/'

Get the contact's name:

>>> import bioregistry as br
>>> br.get_contact_name("pdb")
'Haruki Nakamura'

Get the contact's email:

>>> import bioregistry as br
>>> br.get_contact_email("pdb")
'harukin@protein.osaka-u.ac.jp'

Get the contact's ORCiD identifier:

>>> import bioregistry as br
>>> br.get_contact_orcid("pdb")
'0000-0001-6690-5863'