PDB/UniProt Mapping

Query the database

Query by PDB code

PDB code: Chain ID: (optional) Residue ID: (optional)

Example PDB codes: 1yqv, 1crn

Complete alignment

Query by UniProt accession

Accession code: Residue number: (optional)

Example accession codes: P00698, P01542

Complete alignment

Query by SwissProt ID

Identifier: Residue number: (optional)

Example identifiers: LYSC_CHICK, CRAM_CRAAB

Complete alignment

Download the mapping

Download the complete mapping from the PDB to UniProt entries:

• Chain level (gzipped text file)
• Residue level (gzipped text file)
• Mutations in PDB files (gzipped XML file) with respect to the UniProt entries.

16.02.11: Note the files are now supplied gzipped as the uncompressed residue level mapping had now reached 1.7G (gzipped it is <15% of that size).

Columns in the chain mapping are:

• PDB code
• PDB Chain label (@ = blank chain)
• UniProt Accession

Columns in the residue mapping are:

• PDB code
• PDB Chain label (@ = blank chain)
• PDB Sequential residue number (avoid using this!)
• PDB Residue type (3-letter code)
• PDB Residue number (as it appears in the PDB file)
• UniProt Accession
• UniProt Residue type (1-letter code)
• UniProt Sequential residue number

Interrogate the mapping from your scripts

You may also access the mapping directly from your scripts. [Instructions]

How it works...

You may download a draft manuscript now published in Bioinformatics. If you use PDBSWS, please cite the paper:
Martin, Andrew C. R. (2005) Mapping PDB chains to UniProtKB entries, Bioinformatics, 21:4297-4301

Links

• Seq2Struct Another server providing similar facilities