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

Links

  • Seq2Struct Another server providing similar facilities

Last data update...

The data were last updated on
10 Jul 2018

22.03.17 Downloads

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