MolNFT v1 · #122343 · protein
Crystal structure of HLA-B5801, a protective HLA allele for HIV-1 infection
5IM7 · HLA-B*58:01 heavy chain: “Crystal structure of HLA-B5801, a protective HLA allele for HIV-1 infection”. X-ray diffraction, 10 pockets (best druggability 0.83). MolNFT v1 #122343 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5IM7
- Type
- protein
- Length
- 770 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA-B*58:01 heavy chain; Beta-2-microglobulin; Gln-ala-ser-gln-glu-val-lys-asn-TRP
- UniProt
- P61769
- Pockets
- 10 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | HLA-B*58:01 heavy chain | protein | 277 | 28% helix, 41% strand | — |
| B, D | Beta-2-microglobulin | protein | 99 | 0% helix, 52% strand | P61769 |
| E, F | Gln-ala-ser-gln-glu-val-lys-asn-TRP | protein | 9 | 0% helix, 0% strand | — |
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 978 | 0.83 | 0.84 | 109 | empty |
| 2 | 517 | 0.69 | 0.79 | 47 | empty |
| 3 | 538 | 0.69 | 0.79 | 52 | empty |
| 4 | 62 | 0.44 | 0.83 | 16 | empty |
| 5 | 61 | 0.42 | 0.82 | 19 | empty |
Interfaces
7 interfaces between chains.
- C–D · 1431 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1363 Ų buried · 22 hydrogen bonds · protein-protein
- A–E · 911 Ų buried · 19 hydrogen bonds · protein-protein
- C–F · 899 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 589 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 5IM7 · 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 B 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 P61769
- Elsewhere: RCSB PDB 5IM7 · PDBe 5IM7 · UniProt P61769
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