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2D0N

Crystal structure of the C-terminal SH3 domain of the adaptor protein GADS in complex with SLP-76 motif peptide reveals a unique SH3-SH3 interaction
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 %
2VWF 4 1 Å 75 %
2D0N 1 3 Å 95 %
2D0N 1 2 Å 95 %
2D0N 1 1 Å 95 %

Properties

B
AC
9
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

24
0
B=12 C=29 E=24 G=18 S=12 T=6
C=67 G=33
25.5428
38.8651
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

-9.73 kCal *
-1.11 kCal *
-2.96 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

2d0nA00
d2d0na1
GRB2-related adaptor protein 2
O89100
GRAP2_MOUSE
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.