PPI3D database information

PDB release date2024-09-04
Number of PDB entries199781
Number of biological assemblies298303
Number of proteins786114
Number of peptides22405
Number of nucleic acids19727
Number of SCOPe domains188370


Number of protein-protein interaction interfaces796448
Clusters at sequence similarity > 95%83363
Clusters at sequence similarity > 95% and interface residue contacts similarity > 50%136391
Clusters at sequence similarity > 40%51566
Clusters at sequence similarity > 40% and interface residue contacts similarity > 50%109006
Clusters at sequence similarity > 40% and interface area similarity > 50%82298


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%23052


Number of all binding sites1981070
Clusters at sequence similarity > 95%68117
Clusters at sequence similarity > 95% and residue interface areas similarity > 50%240539
Clusters at sequence similarity > 40%37378
Clusters at sequence similarity > 40% and residue interface areas similarity > 50%174243
Clusters at sequence similarity > 40% and binding site area similarity > 50%140682


Number of protein-protein binding sites1592896
Clusters at sequence similarity > 95%57454
Clusters at sequence similarity > 95% and residue interface areas similarity > 50%195542
Clusters at sequence similarity > 40%31850
Clusters at sequence similarity > 40% and residue interface areas similarity > 50%143799
Clusters at sequence similarity > 40% and binding site area similarity > 50%115957


Number of protein-peptide binding sites28697
Clusters at sequence similarity > 95%4290
Clusters at sequence similarity > 95% and residue interface areas similarity > 50%5973
Clusters at sequence similarity > 40%2512
Clusters at sequence similarity > 40% and residue interface areas similarity > 50%4648
Clusters at sequence similarity > 40% and binding site area similarity > 50%3800


Number of protein-nucleic acid binding sites144897
Clusters at sequence similarity > 95%8356
Clusters at sequence similarity > 95% and residue interface areas similarity > 50%13377
Clusters at sequence similarity > 40%4781
Clusters at sequence similarity > 40% and residue interface areas similarity > 50%9489
Clusters at sequence similarity > 40% and binding site area similarity > 50%7477


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%31485