How to get PDB ID from sequence accession number ?

Question

[Mahmoud Ahmed]

I have a list of protein accession ids and if it is a known protein. I would like to have the corresponding links to PDB.(i.e corresponding PDB codes). How can I get the PDB codes if I have the GenBank protein accession ids to make software can do this operation automatically?

Example: Having the accession number CAD66663, I would like to have PDB code for this.

[Ram]

You should be able to use upload a bunch of IDs to NCBI BLAST or use standalone blast+ to query against pdb. Some filtration should get you the PDB ids.

Answer 1

[Elisabeth Gasteiger]

If you are doing this programmatically, you could try going via UniProtKB, and use URLs of the form

http://www.uniprot.org/uniprot/?query=database%3A%28type%3Aembl%20CAD66663%29&format=tab&columns=id%2Cdatabase%28PDB%29

In this particular case, there is no PDB cross-reference in UniProtKB, but here is a case where there is:

http://www.uniprot.org/uniprot/?query=CAA26306&sort=score&format=tab&columns=id%2Cdatabase%28PDB%29