PPI3D database information

PDB release date2025-02-05
Number of PDB entries204741
Number of biological assemblies304608
Number of proteins816324
Number of peptides23009
Number of nucleic acids20691
Number of SCOPe domains188370


Number of protein-protein interaction interfaces841283
Clusters at sequence similarity > 95%87098
Clusters at sequence similarity > 95% and interface residue contacts similarity > 50%143529
Clusters at sequence similarity > 40%53928
Clusters at sequence similarity > 40% and interface residue contacts similarity > 50%115061
Clusters at sequence similarity > 40% and interface area similarity > 50%86145


Number of domain-domain interaction interfaces198386
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 sites2081107
Clusters at sequence similarity > 95%70146
Clusters at sequence similarity > 95% and residue interface areas similarity > 50%252232
Clusters at sequence similarity > 40%38389
Clusters at sequence similarity > 40% and residue interface areas similarity > 50%183287
Clusters at sequence similarity > 40% and binding site area similarity > 50%147358


Number of protein-protein binding sites1682566
Clusters at sequence similarity > 95%59456
Clusters at sequence similarity > 95% and residue interface areas similarity > 50%206146
Clusters at sequence similarity > 40%32850
Clusters at sequence similarity > 40% and residue interface areas similarity > 50%152018
Clusters at sequence similarity > 40% and binding site area similarity > 50%122038


Number of protein-peptide binding sites29503
Clusters at sequence similarity > 95%4405
Clusters at sequence similarity > 95% and residue interface areas similarity > 50%6152
Clusters at sequence similarity > 40%2581
Clusters at sequence similarity > 40% and residue interface areas similarity > 50%4789
Clusters at sequence similarity > 40% and binding site area similarity > 50%3922


Number of protein-nucleic acid binding sites154458
Clusters at sequence similarity > 95%8808
Clusters at sequence similarity > 95% and residue interface areas similarity > 50%14314
Clusters at sequence similarity > 40%5061
Clusters at sequence similarity > 40% and residue interface areas similarity > 50%10206
Clusters at sequence similarity > 40% and binding site area similarity > 50%8011


Number of domain-domain binding sites396642
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