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1SEM

STRUCTURAL DETERMINANTS OF PEPTIDE-BINDING ORIENTATION AND OF SEQUENCE SPECIFICITY IN SH3 DOMAINS
The binding interface of the protein-peptide complex is shown in grey, the peptide is shown in red. Images produced by YASARA. Note that only the interface of the protein-peptide complex is shown. Gaps between residues may occur. The image on the top is borrowed from the PDB.

Clusters

This protein-peptide complex appears in the following clusters

Cluster Images Centroid Images Centroid PDB ID Number of PDBs Threshold Structural Alignment
1OEB 28 3 Å 50 %
1OEB 28 2 Å 50 %
1UJ0 17 3 Å 75 %
1UJ0 17 2 Å 75 %
1CKB 15 1 Å 50 %
2O9V 7 1 Å 75 %
1SEM 1 3 Å 95 %
1SEM 1 2 Å 95 %
1SEM 1 1 Å 95 %

Properties

C
A
7
General information on the complex, such as the receptor and peptide chains. Click on the PDB icon to see this complex in the PDB

Interface Statistics

13
0
B=13 C=44 E=13 G=13 S=19
C=100
31.1896
43.1588
The DSSP algorithm was used to assign secondary structure to binding site and peptide. The B-Factors are averaged across the PDB and show the flexibility of the binding site and peptide.

Binding Energy

-8.47 kCal *
-0.76 kCal *
-2.9 kCal *
The binding affinity and contribution of backbone and sidechain hydrogen bonds for the protein-peptide complex were calculated using the FoldX force field.
*: the absolute energies are not precise, however FoldX is accurate for relative energies. Learn More.

Categorization

1semA00
d1sema_
Sex muscle abnormal protein 5
P29355
SEM5_CAEEL
SH3_1
Note that only the receptor chain(s) is categorized.

Direct link to External Databases

AffinDB FireDB PLD PROCOGNATE PDBSum 3DID
The links are established based on the PDB Identifier of the protein-peptide complex.