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3G03

Structure of human MDM2 in complex with high affinity peptide
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
3DAB 10 3 Å 50 %
3DAC 10 3 Å 75 %
3DAB 10 2 Å 50 %
3DAC 10 2 Å 75 %
3DAB 10 1 Å 50 %
3DAC 10 1 Å 75 %
3G03 1 3 Å 95 %
3G03 1 2 Å 95 %
3G03 1 1 Å 95 %

Properties

B
ACD
11
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

60
55
B=5 C=10 H=60 T=25
C=27 H=55 T=18
37.3041
50.4746
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

-19.5 kCal *
-1.84 kCal *
-1.29 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

E3 ubiquitin-protein ligase Mdm2
Q00987
MDM2_HUMAN
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.

BriX Covers

BriX is a structural classification of protein fragments. The library comprises fragments ranging from 4 to 14 amino acids that are clustered against 6 different distance thresholds. This has lead to an alphabet of around 2000 frequently observed letters or structural classes per chain length. These classes are accessible through a search and a browse interface on the BriX website. The peptide is associated with its corresponding structural class from the database of protein fragment clusters (BriX). In these fragment clusters, sets of protein fragments with highly similar backbone structure are grouped. Each protein fragment class represents a natural variation on a typical backbone conformation, with a given length and starting from the given residue in the original peptide. To find out more, consult this help page.
Peptide Chain Peptide Residue BriX Fragment Length BriX Threshold Covering BriX Class
B 17 10 0.8 Å 50, 315, 3740, 3962, 6564, 6755, 6756, 8659, 10211, 11396, 15080
B 18 10 0.8 Å 187, 951, 953, 1116, 1534, 3498, 4399, 4532, 4735, 4932, 9352, 9354, 10789, 12362, 12466, 12894, 14052