PPI3D database information

PDB release date2026-10-28
Number of PDB entries226043
Number of biological assemblies330988
Number of proteins954276
Number of peptides26068
Number of nucleic acids24994
Number of SCOPe domains188370


Number of protein-protein interaction interfaces1060040
Clusters at sequence similarity > 95%103822
Clusters at sequence similarity > 95% and interface residue contacts similarity > 50%174668
Clusters at sequence similarity > 40%62800
Clusters at sequence similarity > 40% and interface residue contacts similarity > 50%139889
Clusters at sequence similarity > 40% and interface area similarity > 50%102084


Number of domain-domain interaction interfaces198314
Clusters at sequence similarity > 95%22464
Clusters at sequence similarity > 95% and interface residue contacts similarity > 50%36454
Clusters at sequence similarity > 40%13622
Clusters at sequence similarity > 40% and interface residue contacts similarity > 50%27355
Clusters at sequence similarity > 40% and interface area similarity > 50%23023


Number of all binding sites2563497
Clusters at sequence similarity > 95%79641
Clusters at sequence similarity > 95% and residue interface areas similarity > 50%302233
Clusters at sequence similarity > 40%42396
Clusters at sequence similarity > 40% and residue interface areas similarity > 50%218775
Clusters at sequence similarity > 40% and binding site area similarity > 50%173166


Number of protein-protein binding sites2120080
Clusters at sequence similarity > 95%68681
Clusters at sequence similarity > 95% and residue interface areas similarity > 50%252244
Clusters at sequence similarity > 40%36782
Clusters at sequence similarity > 40% and residue interface areas similarity > 50%185130
Clusters at sequence similarity > 40% and binding site area similarity > 50%146340


Number of protein-peptide binding sites33837
Clusters at sequence similarity > 95%4919
Clusters at sequence similarity > 95% and residue interface areas similarity > 50%6977
Clusters at sequence similarity > 40%2882
Clusters at sequence similarity > 40% and residue interface areas similarity > 50%5455
Clusters at sequence similarity > 40% and binding site area similarity > 50%4437


Number of protein-nucleic acid binding sites195124
Clusters at sequence similarity > 95%10710
Clusters at sequence similarity > 95% and residue interface areas similarity > 50%17628
Clusters at sequence similarity > 40%5786
Clusters at sequence similarity > 40% and residue interface areas similarity > 50%12191
Clusters at sequence similarity > 40% and binding site area similarity > 50%9351


Number of domain-domain binding sites396506
Clusters at sequence similarity > 95%18898
Clusters at sequence similarity > 95% and residue interface areas similarity > 50%51826
Clusters at sequence similarity > 40%10726
Clusters at sequence similarity > 40% and residue interface areas similarity > 50%36233
Clusters at sequence similarity > 40% and binding site area similarity > 50%31432