I have a list of Protein ID such as Q9S9U6, A2XLL2, Q06402. What name is this ID? UniProtKB ID? And how can I get PDB ID from this list? Is its PDB ID only one?

I'm using Python.

Get a list of PDB ids from a list of sequence protein number?

That method of this link gives me some IDs but not only one and usually empty.

  • $\begingroup$ I just wanna get an adjacency matrix from those IDs(Q9S9U6, A2XLL2, Q06402). $\endgroup$
    – MH Lee
    Dec 17, 2020 at 9:56
  • 1
    $\begingroup$ ebi.ac.uk/pdbe/docs/sifts/quick.html has the file you need for Uniprot <-> PDB $\endgroup$ Dec 17, 2020 at 14:06
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    $\begingroup$ Not all proteins have knows structures, so it is expected that PDB IDs will not exist for all input UniProt IDs. Plus, some protein structures exist in multiple conformations, so there is no 1:1 mapping either. $\endgroup$
    – Ram RS
    Dec 17, 2020 at 17:54

2 Answers 2


Get their sequences and then search the pdb (by his API) for the obtained sequences



sequence This service employs the MMseqs2 software and performs fast sequence matching searches (BLAST-like) based on a user-provided FASTA sequence (with E-value or % Identity cutoffs). Following search targets are available: pdb_protein_sequence: all current protein sequences in PDB...


I think this should help you : https://biit.cs.ut.ee/gprofiler/convert


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