PepX: a structural database of protein-peptide complexes

In the download section, you can find

• the contents of the PepX database: both SQL files and Tab Separeted Values (TSV) are provided.
• the PDB files of the protein-peptide complexes from pdb.org, and the files with the binding site residues

Note that you can also use REST webservices to query the PepX database. Learn how to do this.