Research workbench
Structural basis for degenerate recognition of HIV peptide variants by cytotoxic lymphocyte, variant SL9-3A
Analyse Structural basis for degenerate recognition of HIV peptide variants by… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1S8D
- Type
- protein
- Length
- 383 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class I histocompatibility antigen, a-2 alpha chain; Beta-2-microglobulin; Gag peptide
- UniProt
- Q9TQH5, P01884
- Pockets
- 6 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility antigen, a-2 alpha chain | protein | 275 | 27% helix, 40% strand | Q9TQH5 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P01884 |
| C | Gag peptide | protein | 9 | 0% helix, 0% strand | — |
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 696 | 0.68 | 0.76 | 59 | empty |
| 2 | 92 | 0.48 | 0.81 | 21 | empty |
| 3 | 64 | 0.47 | 0.83 | 19 | empty |
| 4 | 53 | 0.38 | 0.81 | 16 | empty |
| 5 | 62 | 0.31 | 0.75 | 15 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1314 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 787 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 1S8D · Structural basis for degenerate recognition of HIV peptide variants by cytotoxic… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q9TQH5
- Every structure of UniProt P01884
- Elsewhere: RCSB PDB 1S8D · PDBe 1S8D · UniProt Q9TQH5 · UniProt P01884
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