Registry PDB Structure
The Protein Data Bank is the single worldwide archive of structural data of biological macromolecules.
- Prefix
pdb- Alternative Prefixes
- RCSB_PDB wwpdb pdbj pdbe
- Keywords
- bioinformatics epidemiology protein proteomics structural biology structure virology
- Links
- Homepage @PDBj_en
- 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
- 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
- Publications
-
- 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
- 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]
Metaregistry PDB Structure
The metaregistry provides mappings between the Bioregistry and other registries. There are 11 mappings to external registries for this resource with 7 unique external prefixes.
| Registry Name | Registry Metaprefix | External Prefix | Curate |
|---|---|---|---|
| BioContext | biocontext |
PDB
|
|
EDAM
|
edam |
1127
|
|
FAIRSharing
|
fairsharing |
FAIRsharing.rs2815
|
|
GO
|
go |
PDB
|
|
Identifiers.org
|
miriam |
pdb
|
|
N2T
|
n2t |
pdb
|
|
NCBI
|
ncbi |
PDB
|
|
Prefix Commons
|
prefixcommons |
pdbj
|
|
re3data
|
re3data |
r3d100010910
|
|
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
Providers are various services that resolve CURIEs to URLs. The example CURIE
None:2gc4
is used to demonstrate the provides available for
this resource. Generation of OLS and BioPortal URLs requires additional programmatic
logic beyond string formatting.
| 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 Bioregistry are listed here.
| Code | Name | URL |
|---|---|---|
CURATOR_REVIEW |
Proteopedia | http://proteopedia.org/wiki/index.php/2gc4 |
bio2rdf |
Bio2RDF | http://bio2rdf.org/pdbj:2gc4 |
ebi |
Protein Databank through PDBsum | https://www.ebi.ac.uk/pdbsum/2gc4 |
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 |
rcsb |
RCSB PDB | https://www.rcsb.org/structure/2gc4 |