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: 3d structure 3d structure databases bioinformatics covid-19 dna epidemiology function analysis image/movie protein proteomics repository rna structural biology structure virology
License: CC0-1.0
Links: Homepage
Publications: 2025 ProteinsPlus: a publicly available resource for protein structure mining; 2025 RNAproDB: A Webserver and Interactive Database for Analyzing Protein-RNA Interactions; 2024 DIONYSUS: a database of protein-carbohydrate interfaces; 2024 FURNA: A database for functional annotations of RNA structures; 2021 Protein Data Bank Japan: Celebrating our 20th anniversary during a global pandemic as the Asian hub of three dimensional macromolecular structural data; 2017 New tools and functions in data-out activities at Protein Data Bank Japan (PDBj); 2016 Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures; 2013 SAbDab: the structural antibody database; https://bioregistry.io/pubmed:22110033; 2011 Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format; 2011 Protein Data Bank Japan (PDBj): an interview with Haruki Nakamura of Osaka University by Wendy A. Warr; 2010 PDBj Mine: design and implementation of relational database interface for Protein Data Bank Japan; 2002 [Development of PDBj: Advanced database for protein structures]

Identifier Standards

Pattern for Local Unique Identifiers: Local unique 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
Format String for RDF URIs: https://rdf.wwpdb.org/pdb/$1
Example RDF URI: https://rdf.wwpdb.org/pdb/2gc4

Contacts

Contact: Haruki Nakamura 0000-0001-6690-5863

Ontology

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

Provided By: pdbsum validatordb viperdb
In Collection (4): Resources mentioned in "Sharing biological data: why, when, and how" ChEBI Data Sources Global Biodata Coalition - Global Core Biodata Resources Synapse.org external links

Mappings to External Registries

Mappings from records in Bioregistry to external registries comprises the metaregistry. This resource has 14 mappings to external registries 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`

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.

Provider Name	Provider Code	URI
PDB Structure	`pdb`	https://www.wwpdb.org/pdb?id=pdb_00002gc4
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 Bioregistry are listed here. These are typically inherited from Identifiers.org or Prefix Commons, and need extra curation.

Provider Name	Provider Code	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
Protein Databank through PDBsum	`ebi`	https://www.ebi.ac.uk/pdbsum/2gc4
furna	`furna`	https://seq2fun.dcmb.med.umich.edu/furna/pdb.cgi?pdbid=157d
Protein Databank in Europe (PDBe)	`pdbe`	https://www.ebi.ac.uk/pdbe/entry/pdb/2gc4
Protein Data Bank Japan (PDBj)	`pdbj`	https://pdbj.org/mine/summary/2gc4
ProteinsPlus	`proteinsplus`	https://proteins.plus/2gc4
RCSB PDB	`rcsb`	https://www.rcsb.org/structure/2gc4
RNA Protein Database	`rnaprodb`	https://rnaprodb.usc.edu/2gc4
The Structural Antibody Database	`sabdab`	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 license:

>>> import bioregistry as br
>>> br.get_license("pdb")
'CC0-1.0'

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'