Run PepSite on a PDB structure

PDB code:   PDB chain:  Use non-prot/hoh ats in surf calc?

Peptide sequence: ?

Run PepSite on your own PDB file

 Use non-prot/hoh ats in surf calc?

Peptide sequence: ?

You have predicted binding of the peptide GTPPPNYDSL on the protein surface from PDB 2joc, chain "A" (Itchy E3 ubiquitin protein ligase).

The interactive visualization below shows the protein structure and a predicted peptide binding spot. (Don't see anything?) To learn the basic controls, click here.

To display a different prediction, click on the correponding row from the table below, which shows the top matches ranked according to statistical significance (p-value).

rank p-value N
1 0.01375 6 ----- thr-2 pro-3 pro-4 pro-5 asn-6 tyr-7 ----- ----- -----
2 0.01484 6 ----- thr-2 pro-3 pro-4 pro-5 asn-6 tyr-7 ----- ----- -----
3 0.01667 6 ----- thr-2 pro-3 pro-4 pro-5 asn-6 tyr-7 ----- ----- -----
4 0.02894 6 ----- ----- pro-3 pro-4 pro-5 asn-6 tyr-7 asp-8 ----- -----
5 0.03336 6 ----- ----- pro-3 pro-4 pro-5 asn-6 tyr-7 asp-8 ----- -----
6 0.03407 5 ----- thr-2 pro-3 pro-4 pro-5 asn-6 ----- ----- ----- -----
7 0.03648 5 ----- ----- pro-3 pro-4 pro-5 asn-6 tyr-7 ----- ----- -----
8 0.03671 5 ----- thr-2 pro-3 pro-4 pro-5 asn-6 ----- ----- ----- -----
9 0.0378 5 ----- ----- pro-3 pro-4 pro-5 asn-6 tyr-7 ----- ----- -----
10 0.04111 5 ----- thr-2 pro-3 pro-4 pro-5 asn-6 ----- ----- ----- -----

Each row from the table above is colored according to statistical significance (p-value) following the color scale below (red = highly significant; yellow = moderately significant; white = not significant).

You can download a PDB file with the top matches or with the interacting receptor residues. For a description of the format used, click here.