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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

10
Structure of the human Mdmx protein bound to the p53 tumor suppressor transactivation domain
apoptosis, cell cycle, disease mutation, dna-binding, hdm2, hdm4, hdmx, mdm-4, mdm-x, mdm2, mdm4, Mdmx, nucleus, oncogene, p53, Transcription, tumor
21
STREPTAVIDIN-CYCLO-AC-[CHPQFC]-NH2, PH 3.6
Complex (biotin-binding protein/peptide), cyclic peptide discovered by phage display
46
HUMAN THROMBIN HIRUGEN INHIBITOR COMPLEX.
acute phase, blood coagulation, calcium, disease mutation, gamma-carboxyglutamic acid, glycoprotein, Hydrolase, inhibitor, kringle, polymorphism, Protease, protease inhibitor, serine protease, serine protease inhibitor, sulfation, thrombin, zymogen
22
Crystal structure of the autoimmune MHC class II I-Au complexed with myelin basic protein 1-11 at 2.2A
autoimmune disease, crystal structure, experimental autoimmune encephalomyelitis, h-2u, i-au, immune system, mhc class ii, myelin basic protein, unique register
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.