text: user1847: 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!
  
  user298: 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:
  
  
  user266: 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.
  
original_text: 1847: <p>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.</p>
  
  <p>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.</p>
  
  <p>Any ideas?</p>
  
  <p>Thank you!</p>
   298: <p>The UniProt website offers an <a href="http://www.uniprot.org/uploadlists/" rel="nofollow noreferrer">ID mapping tool</a> that tends to work pretty well:</p>
  
  <p><a href="https://i.stack.imgur.com/VXN4K.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/VXN4K.png" alt="UniProt ID mapping tool screenshot"></a></p>
  
  <p>Then, hit "submit" and you will get the list of corresponding PDB IDs:</p>
  
  <p><a href="https://i.stack.imgur.com/n7SIH.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/n7SIH.png" alt="UniProt ID mapping tool results screenshot"></a></p>
   266: <p>You can use the SIFTS mapping: <a href="http://www.ebi.ac.uk/pdbe/docs/sifts/" rel="nofollow noreferrer">http://www.ebi.ac.uk/pdbe/docs/sifts/</a></p>
  
  <p>From <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531078/" rel="nofollow noreferrer">an article</a>:</p>
  
  <blockquote>
    <p>The Structure Integration with Function, Taxonomy and Sequences
    resource (SIFTS; <a href="http://pdbe.org/sifts" rel="nofollow noreferrer">http://pdbe.org/sifts</a>) 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.</p>
  </blockquote>
  
  <p>It has no web interface for querying. You just download CSV (or TSV) file with all the mapping data.</p>
  