PPI3D database information

PDB release date2025-05-14
Number of PDB entries208030
Number of biological assemblies308598
Number of proteins836794
Number of peptides23455
Number of nucleic acids21252
Number of SCOPe domains188370


Number of protein-protein interaction interfaces872850
Clusters at sequence similarity > 95%89486
Clusters at sequence similarity > 95% and interface residue contacts similarity > 50%148146
Clusters at sequence similarity > 40%55331
Clusters at sequence similarity > 40% and interface residue contacts similarity > 50%118931
Clusters at sequence similarity > 40% and interface area similarity > 50%88697


Number of domain-domain interaction interfaces198380
Clusters at sequence similarity > 95%22495
Clusters at sequence similarity > 95% and interface residue contacts similarity > 50%36486
Clusters at sequence similarity > 40%13653
Clusters at sequence similarity > 40% and interface residue contacts similarity > 50%27386
Clusters at sequence similarity > 40% and interface area similarity > 50%23053


Number of all binding sites2150922
Clusters at sequence similarity > 95%71508
Clusters at sequence similarity > 95% and residue interface areas similarity > 50%259598
Clusters at sequence similarity > 40%39031
Clusters at sequence similarity > 40% and residue interface areas similarity > 50%188854
Clusters at sequence similarity > 40% and binding site area similarity > 50%151477


Number of protein-protein binding sites1745700
Clusters at sequence similarity > 95%60791
Clusters at sequence similarity > 95% and residue interface areas similarity > 50%213073
Clusters at sequence similarity > 40%33479
Clusters at sequence similarity > 40% and residue interface areas similarity > 50%157245
Clusters at sequence similarity > 40% and binding site area similarity > 50%125941


Number of protein-peptide binding sites30004
Clusters at sequence similarity > 95%4471
Clusters at sequence similarity > 95% and residue interface areas similarity > 50%6261
Clusters at sequence similarity > 40%2628
Clusters at sequence similarity > 40% and residue interface areas similarity > 50%4887
Clusters at sequence similarity > 40% and binding site area similarity > 50%4002


Number of protein-nucleic acid binding sites160646
Clusters at sequence similarity > 95%8953
Clusters at sequence similarity > 95% and residue interface areas similarity > 50%14664
Clusters at sequence similarity > 40%5141
Clusters at sequence similarity > 40% and residue interface areas similarity > 50%10479
Clusters at sequence similarity > 40% and binding site area similarity > 50%8188


Number of domain-domain binding sites396630
Clusters at sequence similarity > 95%18911
Clusters at sequence similarity > 95% and residue interface areas similarity > 50%51888
Clusters at sequence similarity > 40%10738
Clusters at sequence similarity > 40% and residue interface areas similarity > 50%36292
Clusters at sequence similarity > 40% and binding site area similarity > 50%31486