PPI3D database information

PDB release date2024-04-10
Number of PDB entries194469
Number of biological assemblies291430
Number of proteins756700
Number of peptides21783
Number of nucleic acids18798
Number of SCOPe domains188370


Number of protein-protein interaction interfaces750537
Clusters at sequence similarity > 95%80370
Clusters at sequence similarity > 95% and interface residue contacts similarity > 50%130498
Clusters at sequence similarity > 40%50183
Clusters at sequence similarity > 40% and interface residue contacts similarity > 50%104448
Clusters at sequence similarity > 40% and interface area similarity > 50%79619


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 sites1880628
Clusters at sequence similarity > 95%66362
Clusters at sequence similarity > 95% and residue interface areas similarity > 50%231265
Clusters at sequence similarity > 40%36682
Clusters at sequence similarity > 40% and residue interface areas similarity > 50%167801
Clusters at sequence similarity > 40% and binding site area similarity > 50%136185


Number of protein-protein binding sites1501074
Clusters at sequence similarity > 95%55733
Clusters at sequence similarity > 95% and residue interface areas similarity > 50%187067
Clusters at sequence similarity > 40%31162
Clusters at sequence similarity > 40% and residue interface areas similarity > 50%137922
Clusters at sequence similarity > 40% and binding site area similarity > 50%111811


Number of protein-peptide binding sites27739
Clusters at sequence similarity > 95%4154
Clusters at sequence similarity > 95% and residue interface areas similarity > 50%5749
Clusters at sequence similarity > 40%2442
Clusters at sequence similarity > 40% and residue interface areas similarity > 50%4472
Clusters at sequence similarity > 40% and binding site area similarity > 50%3667


Number of protein-nucleic acid binding sites137235
Clusters at sequence similarity > 95%8066
Clusters at sequence similarity > 95% and residue interface areas similarity > 50%12747
Clusters at sequence similarity > 40%4650
Clusters at sequence similarity > 40% and residue interface areas similarity > 50%9040
Clusters at sequence similarity > 40% and binding site area similarity > 50%7179


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