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1A8K

CRYSTALLOGRAPHIC ANALYSIS OF HUMAN IMMUNODEFICIENCY VIRUS 1 PROTEASE WITH AN ANALOG OF THE CONSERVED CA-P2 SUBSTRATE: INTERACTIONS WITH FREQUENTLY OCCURRING GLUTAMIC ACID RESIDUE AT P2\' POSITION OF SUBSTRATES
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 %
1A8K 2 3 Å 75 %
1A8K 2 2 Å 75 %
1A8K 2 1 Å 75 %
1A8K 1 3 Å 95 %
1A8K 1 2 Å 95 %
1A8K 1 1 Å 95 %

Properties

C
AB
6
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

41
33
B=10 C=17 E=41 S=21 T=10
B=17 C=50 E=33
23.8788
29.8405
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

-13.24 kCal *
-8.27 kCal *
-2.44 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

1a8kA00
d1a8ka_
Gag-Pol polyprotein
P03367
POL_HV1BR
RVP
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.