Hi Chun,

There are a few options:

You can do an advanced search on the RCSB PDB page. Go to advanced search and choose "Number of Chains (Biological Assembly)" = 2 or more, and then add a second search criteria "Chain Length" and set a small chain size so that at least one of your chains might be a shorter peptides.

If you google "peptide pdb database" here is the top result, I haven't used this database myself though. It looks like it's a curation of the PDB I describe above so you could compare your own search results to PepBDB.

PepBDB: a comprehensive structural database of biological peptide–protein interactions: https://academic.oup.com/bioinformatics/article/35/1/175/5050021

It might be helpful if we know more about what you're looking for. If you want to sort all existing solved structures by features, the RCSB PDB or PepBDB seem like good options.

If you don't need structural information, there are other databases with experimental and inferred annotations of protein-peptide interactions but not solved structures, for example THPdb: Database of FDA-approved peptide and protein therapeutics

Article THPdb: Database of FDA-approved peptide and protein therapeutics

-Amanda

Amanda Lovecraft ,Thanks for the suggestion. I think my goal is more clear now. The peptide sequence I am looking for was epitope peptides. Like flag tag. A database that provide all reported epitope peptides would be great for me.

Chun

Are you looking for sequences only?

Amanda Lovecraft ,I am looking for the sequence of peptide epitope. While on the meantime, the antibody that binds to the epitope is needed as well. If you know this kind of database, that would be great.

Chun