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1S8D

Structural basis for degenerate recognition of HIV peptide variants by cytotoxic lymphocyte, variant SL9-3A
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
1SYV 211 3 Å 50 %
1SYV 211 2 Å 50 %
2AV1 187 1 Å 50 %
2CLR 172 3 Å 75 %
2CLR 172 2 Å 75 %
2CLR 169 1 Å 75 %
1S8D 1 3 Å 95 %
1S8D 1 2 Å 95 %
1S8D 1 1 Å 95 %

Properties

C
A
9
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

69
0
C=28 E=21 H=48 S=3
C=89 S=11
28.0524
44.2012
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

-18.99 kCal *
-4.75 kCal *
-8.38 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

1s8dA01
d1s8da2
HLA class I histocompatibility antigen. A-2 alpha chain
P01892
1A02_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.