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I have a list of several thousand proteins and their UNIPROT IDs. I'm looking for an efficient method of cross-referencing it against the PDB tertiary structure database, and get a list of those proteins with a tertiary structure in the PDB database.

I've tried to BLASTP the list of UNIPROT IDs against the PDB database, using the NCBI BLAST portal but encountered too many errors of "Error: Failed to read the Blast query: Sequence ID not found", making the process of manual filtering not convenient and not efficient.

Any ideas?

Thank you!

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The UniProt website offers an ID mapping tool that tends to work pretty well:

UniProt ID mapping tool screenshot

Then, hit "submit" and you will get the list of corresponding PDB IDs:

UniProt ID mapping tool results screenshot

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  • $\begingroup$ Thank you, it worked. Please aid a PDB-Noob like myself to understand the results: ibb.co/jTMGmb How come each of the UNIPROT ID received several different PDB IDs? ibb.co/b5fRmb $\endgroup$
    – Adrian Smith
    Dec 29, 2017 at 12:50
  • $\begingroup$ @AdrianSmith that's how PDB works. You'll have one structure for the active site, another for the active site bound by foo, one for the active site bound by bar, another structure for the protein in complex with something else. . . This should be clear enough if you just click on the results you got and see their descriptions. $\endgroup$
    – terdon ♦
    Dec 29, 2017 at 13:14
  • $\begingroup$ Thanks for the explanation. I'm looking for a specific protein-target structure (I have a list of ligand-protein interactions and i'm looking for the 3d structure of the binding site if available). Is there any way to search through all of the different "structures"? Does the PDB site offer such a curated database? $\endgroup$
    – Adrian Smith
    Dec 29, 2017 at 14:31
  • $\begingroup$ @AdrianSmith no idea, I'm afraid. I've almost never used PDB. I suggest you ask a new question explaining what you need in more detail. Ideally, give an example UniProt ID and explain what you would want to see from it. $\endgroup$
    – terdon ♦
    Dec 29, 2017 at 16:20
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You can use the SIFTS mapping: http://www.ebi.ac.uk/pdbe/docs/sifts/

From an article:

The Structure Integration with Function, Taxonomy and Sequences resource (SIFTS; http://pdbe.org/sifts) is a close collaboration between the Protein Data Bank in Europe (PDBe) and UniProt. The two teams have developed a semi-automated process for maintaining up-to-date cross-reference information to UniProt entries, for all protein chains in the PDB entries present in the UniProt database. This process is carried out for every weekly PDB release and the information is stored in the SIFTS database.

It has no web interface for querying. You just download CSV (or TSV) file with all the mapping data.

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  • $\begingroup$ Thank you. I'll try it if the ID mapping tool won't provide. $\endgroup$
    – Adrian Smith
    Dec 29, 2017 at 12:55

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