Research workbench
Crystal structure of HLA-B5801, a protective HLA allele for HIV-1 infection
Analyse Crystal structure of HLA-B5801, a protective HLA allele for HIV-1 infection in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IND
- Type
- protein
- Length
- 770 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…
- UniProt
- P10319, P61769
- Pockets
- 7 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | HLA class I histocompatibility antigen, B-58 alpha chain | protein | 277 | 27% helix, 41% strand | P10319 |
| B, D | Beta-2-microglobulin | protein | 99 | 0% helix, 52% strand | P61769 |
| E, F | Gln-ala-ser-gln-asp-val-lys-asn-TRP | protein | 9 | 0% helix, 0% strand | — |
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1047 | 0.82 | 0.83 | 114 | empty |
| 2 | 489 | 0.71 | 0.81 | 52 | empty |
| 3 | 518 | 0.70 | 0.80 | 57 | empty |
| 4 | 72 | 0.43 | 0.81 | 18 | empty |
| 5 | 68 | 0.42 | 0.80 | 16 | empty |
Interfaces
7 interfaces between chains.
- C–D · 1369 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1334 Ų buried · 22 hydrogen bonds · protein-protein
- A–E · 908 Ų buried · 16 hydrogen bonds · protein-protein
- C–F · 902 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 558 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 5IND · Crystal structure of HLA-B5801, a protective HLA allele for HIV-1 infection · 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 5IND · PDBe 5IND · UniProt P10319 · UniProt P61769
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