Cross-reference with PDB database 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!
The UniProt website offers an ID mapping tool that tends to work pretty well:



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