PPI3D database information

PDB release date2026-10-14
Number of PDB entries225545
Number of biological assemblies330363
Number of proteins951462
Number of peptides26005
Number of nucleic acids24946
Number of SCOPe domains188370


Number of protein-protein interaction interfaces1056087
Clusters at sequence similarity > 95%103466
Clusters at sequence similarity > 95% and interface residue contacts similarity > 50%173912
Clusters at sequence similarity > 40%62597
Clusters at sequence similarity > 40% and interface residue contacts similarity > 50%139252
Clusters at sequence similarity > 40% and interface area similarity > 50%101666


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 sites2554982
Clusters at sequence similarity > 95%79422
Clusters at sequence similarity > 95% and residue interface areas similarity > 50%301151
Clusters at sequence similarity > 40%42288
Clusters at sequence similarity > 40% and residue interface areas similarity > 50%217986
Clusters at sequence similarity > 40% and binding site area similarity > 50%172583


Number of protein-protein binding sites2112174
Clusters at sequence similarity > 95%68470
Clusters at sequence similarity > 95% and residue interface areas similarity > 50%251232
Clusters at sequence similarity > 40%36676
Clusters at sequence similarity > 40% and residue interface areas similarity > 50%184372
Clusters at sequence similarity > 40% and binding site area similarity > 50%145772


Number of protein-peptide binding sites33781
Clusters at sequence similarity > 95%4911
Clusters at sequence similarity > 95% and residue interface areas similarity > 50%6956
Clusters at sequence similarity > 40%2878
Clusters at sequence similarity > 40% and residue interface areas similarity > 50%5438
Clusters at sequence similarity > 40% and binding site area similarity > 50%4429


Number of protein-nucleic acid binding sites194571
Clusters at sequence similarity > 95%10681
Clusters at sequence similarity > 95% and residue interface areas similarity > 50%17578
Clusters at sequence similarity > 40%5780
Clusters at sequence similarity > 40% and residue interface areas similarity > 50%12175
Clusters at sequence similarity > 40% and binding site area similarity > 50%9339


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