Question: How to get PDB ID from sequence accession number ?
gravatar for Mahmoud Ahmed
3.1 years ago by
Mahmoud Ahmed0 wrote:

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?

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


blast protein ncbi pdb • 3.4k views
ADD COMMENTlink modified 3.1 years ago by Elisabeth Gasteiger1.6k • written 3.1 years ago by Mahmoud Ahmed0

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.

ADD REPLYlink written 3.1 years ago by RamRS20k
gravatar for Elisabeth Gasteiger
3.1 years ago by
Elisabeth Gasteiger1.6k wrote:

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:

ADD COMMENTlink written 3.1 years ago by Elisabeth Gasteiger1.6k
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