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
- 5INC
- 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
- 12 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | HLA class I histocompatibility antigen, B-58 alpha chain | protein | 277 | 27% helix, 40% strand | P10319 |
| B, D | Beta-2-microglobulin | protein | 99 | 0% helix, 52% strand | P61769 |
| E, F | Gln-ala-thr-gln-glu-val-lys-asn-TRP | protein | 9 | 0% helix, 0% strand | — |
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 995 | 0.81 | 0.83 | 93 | empty |
| 2 | 505 | 0.72 | 0.81 | 55 | empty |
| 3 | 559 | 0.70 | 0.80 | 53 | empty |
| 4 | 141 | 0.43 | 0.76 | 26 | empty |
| 5 | 95 | 0.41 | 0.78 | 18 | empty |
Interfaces
7 interfaces between chains.
- C–D · 1401 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1356 Ų buried · 18 hydrogen bonds · protein-protein
- C–F · 894 Ų buried · 24 hydrogen bonds · protein-protein
- A–E · 853 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 569 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 5INC · 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 5INC · PDBe 5INC · UniProt P10319 · UniProt P61769
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