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1U8J

Crystal structure of the HIV-1 Cross Neutralizing Monoclonal Antibody 2F5 in complex with gp41 Peptide ELDKWAG
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
3D0L 19 3 Å 50 %
1U91 16 2 Å 50 %
3D0V 14 3 Å 75 %
3D0V 14 2 Å 75 %
3D0V 14 1 Å 50 %
3D0V 14 1 Å 75 %
1U8I 8 3 Å 95 %
1U8I 8 2 Å 95 %
1U8I 8 1 Å 95 %

Properties

C
AB
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

15
0
B=10 C=45 E=15 S=10 T=20
B=14 C=57 T=29
24.9607
40.1673
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

-9.08 kCal *
-3.57 kCal *
-3.35 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

1u8jA01
d1u8ja2
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.