PPI3D database information

PDB release date2026-07-08
Number of PDB entries222132
Number of biological assemblies326091
Number of proteins929059
Number of peptides25666
Number of nucleic acids24255
Number of SCOPe domains188370


Number of protein-protein interaction interfaces1022754
Clusters at sequence similarity > 95%100455
Clusters at sequence similarity > 95% and interface residue contacts similarity > 50%168815
Clusters at sequence similarity > 40%61092
Clusters at sequence similarity > 40% and interface residue contacts similarity > 50%135268
Clusters at sequence similarity > 40% and interface area similarity > 50%98987


Number of domain-domain interaction interfaces198376
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%27387
Clusters at sequence similarity > 40% and interface area similarity > 50%23055


Number of all binding sites2480916
Clusters at sequence similarity > 95%77772
Clusters at sequence similarity > 95% and residue interface areas similarity > 50%292628
Clusters at sequence similarity > 40%41646
Clusters at sequence similarity > 40% and residue interface areas similarity > 50%212151
Clusters at sequence similarity > 40% and binding site area similarity > 50%168264


Number of protein-protein binding sites2045508
Clusters at sequence similarity > 95%66858
Clusters at sequence similarity > 95% and residue interface areas similarity > 50%243413
Clusters at sequence similarity > 40%36033
Clusters at sequence similarity > 40% and residue interface areas similarity > 50%178872
Clusters at sequence similarity > 40% and binding site area similarity > 50%141639


Number of protein-peptide binding sites33275
Clusters at sequence similarity > 95%4823
Clusters at sequence similarity > 95% and residue interface areas similarity > 50%6822
Clusters at sequence similarity > 40%2834
Clusters at sequence similarity > 40% and residue interface areas similarity > 50%5334
Clusters at sequence similarity > 40% and binding site area similarity > 50%4349


Number of protein-nucleic acid binding sites187561
Clusters at sequence similarity > 95%10264
Clusters at sequence similarity > 95% and residue interface areas similarity > 50%16927
Clusters at sequence similarity > 40%5652
Clusters at sequence similarity > 40% and residue interface areas similarity > 50%11860
Clusters at sequence similarity > 40% and binding site area similarity > 50%9132


Number of domain-domain binding sites396622
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%31489