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PepX contains 505 unique protein-peptide interface clusters from 1431 PDBs, representing the diversity of structural information on protein-peptide complexes available in the Protein Data Bank. 47% of all protein-peptide complexes available from the PDB are clustered within only 10 classes, containing complexes with peptides bound to MHC, thrombins, α-ligand binding domains, SH3 domains, PDZ domains and other (see Figure on the right).

References

  • Vanhee, P., J. Reumers, et al. (2009). "PepX: A structural database of non-redundant protein-peptide complexes" NAR Database Issue 2010.pubmed.gif
  • Vanhee, P., F. Stricher, et al. (2009). "Protein-peptide interactions adopt the same structural motifs as monomeric protein folds." Structure, August 2009. pubmed.gif

Example protein-peptide complexes from PepX

14
Crystal structure of the HIV-1 Cross Neutralizing Monoclonal Antibody 2F5 in complex with gp41 Peptide LLELDKWASLW
2f5, antibody, gp41, hiv, immune system, neutralizing
21
STREPTAVIDIN-CYCLO-AC-[CHPQFC]-NH2, PH 3.6
Complex (biotin-binding protein/peptide), cyclic peptide discovered by phage display
15
COMPLEX OF THROMBIN WITH DESIGNED INHIBITOR 7165
blood coagulation, calcium-binding, glycoprotein, Hydrolase, plasma, serine protease
33
THREE-DIMENSIONAL STRUCTURE OF CHYMOTRYPSIN INACTIVATED WITH (2S) N-ACETYL-L-ALANYL-L-PHENYLALANYL-CHLOROETHYL KETONE: IMPLICATIONS FOR THE MECHANISM OF INACTIVATION OF SERINE PROTEASES BY CHLOROKETONES
Hydrolase(serine proteinase)
more
The binding interface of the protein-peptide complex is shown in grey, the peptide is shown in red. Note that only the interface of the protein-peptide complex is shown. Gaps between residues may occur.