Research workbench
Crystal structure of HLA-B*5801 complex with HIV-1 gag derived peptide TW10
Analyse Crystal structure of HLA-B*5801 complex with HIV-1 gag derived peptide TW10 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5V5L
- Type
- protein
- Length
- 774 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class I histocompatibility antigen, B-58 alpha chain; Beta-2-microglobulin; TW10
- UniProt
- P10319, P61769
- Pockets
- 13 · best druggability 0.82
Structure
x-ray diffraction · 5 distinct chains · 20% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility antigen, B-58 alpha chain | protein | 278 | 28% helix, 39% strand | P10319 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C | HLA class I histocompatibility antigen, B-58 alpha chain | protein | 277 | 28% helix, 41% strand | P10319 |
| D | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P61769 |
| E, F | TW10 | protein | 10 | 0% helix, 0% strand | — |
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1081 | 0.82 | 0.83 | 102 | empty |
| 2 | 600 | 0.68 | 0.78 | 58 | empty |
| 3 | 507 | 0.68 | 0.79 | 50 | empty |
| 4 | 53 | 0.65 | 0.95 | 20 | empty |
| 5 | 88 | 0.44 | 0.80 | 23 | empty |
Interfaces
7 interfaces between chains.
- C–D · 1410 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1365 Ų buried · 27 hydrogen bonds · protein-protein
- A–E · 906 Ų buried · 21 hydrogen bonds · protein-protein
- C–F · 875 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 494 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 5V5L · Crystal structure of HLA-B*5801 complex with HIV-1 gag derived peptide TW10 · the same entry in another collection · chain F against F, TM-score 1.00
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain D against A, TM-score 0.99
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 P10319
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 5V5L · PDBe 5V5L · UniProt P10319 · UniProt P61769
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