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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 2009.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

89
HUMAN THROMBIN-INHIBITOR COMPLEX
Complex (serine protease/inhibitor), Hydrolase
117
THE 2.1 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF THE HETERODIMER OF THE HUMAN RXRALPHA AND PPARGAMMA LIGAND BINDING DOMAINS RESPECTIVELY BOUND WITH 9-CIS RETINOIC ACID AND GI262570 AND CO-ACTIVATOR PEPTIDES.
The heterodimer of the nuclear receptor ligand binding domains of rxralpha and ppargamma bound respectively with 9-cis retinoic acid and gi262570 and co-activator peptides, Transcription
15
Structure of HIV-1 protease D25N complexed with the rt-rh analogue peptide GLY-ALA-GLU-VAL-PHE*TYR-VAL-ASP-GLY-ALA
hydrolase/hydrolase substrate complex, Peptide design; molecular dynamics; hiv protease; substrate recognition; calorimetry
172
THREE DIMENSIONAL STRUCTURE OF A PEPTIDE EXTENDING OUT ONE END OF A CLASS I MHC BINDING SITE
Histocompatibility antigen
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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.