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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:

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


  • Seq2Struct Another server providing similar facilities

Last data update...

The data were last updated on
22 Mar 2017 (Corrected download dataset from 27 Nov 2016 - queryable data unchanged)


The residue mapping download file was missing some entries. This resulted from some software not running properly on a new server.