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3D0L

Crystal structure of the HIV-1 broadly neutralizing antibody 2F5 in complex with the gp41 FP-MPER Hyb3K construct 514GIGALFLGFLGAAGS528KK-Ahx-655KNEQELLELDKWASLWN671
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 %
3D0L 1 3 Å 95 %
3D0L 1 2 Å 95 %
3D0L 1 1 Å 95 %

Properties

C
AB
10
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
20
C=44 E=24 G=8 S=8 T=16
C=30 E=20 G=30 T=20
55.8152
71.2629
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

-16.02 kCal *
-3.13 kCal *
-4.3 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

Ig kappa chain C region
P01834
IGKC_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.