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2NXD

Structure of HIV-1 protease D25N complexed with rt-rh analogue peptide GLY-ALA-ASP-ILE-PHE*TYR-LEU-ASP-GLY-ALA
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
2FNT 22 3 Å 50 %
1KJ7 20 2 Å 50 %
1KJ7 19 1 Å 50 %
2NXL 15 3 Å 75 %
2NXL 15 2 Å 75 %
2NXL 15 1 Å 75 %
2NXD 1 3 Å 95 %
2NXD 1 2 Å 95 %
2NXD 1 1 Å 95 %

Properties

P
A
8
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

31
0
B=17 C=20 E=31 S=23 T=9
B=50 C=50
44.543
93.1982
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

-9.98 kCal *
-4.68 kCal *
-0.72 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

2nxdA00
Gag-Pol polyprotein
P03369
POL_HV1A2
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.