How to get PDB ID from sequence accession number ?
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.
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Ram
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Mahmoud Ahmed •
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Mahmoud Ahmed •
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If you are doing this programmatically, you could try going via UniProtKB, and use URLs of the form
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
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Elisabeth Gasteiger
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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.