Research workbench
HLA*A2402 complexed with HIV NEF138 8MER epitope
Analyse HLA*A2402 complexed with HIV NEF138 8MER epitope in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HGB
- Type
- protein
- Length
- 1,528 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class I histocompatibility antigen, a-24 alpha chain; Beta-2-microglobulin; Protein…
- UniProt
- P05534, P61769, P18801
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, G, J | HLA class I histocompatibility antigen, a-24 alpha chain | protein | 274 | 27% helix, 40% strand | P05534 |
| B, E, H, K | Beta-2-microglobulin | protein | 100 | 0% helix, 48% strand | P61769 |
| C, F, I, L | Protein nef | protein | 8 | 0% helix, 0% strand | P18801 |
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1197 | 0.82 | 0.84 | 115 | empty |
| 2 | 524 | 0.74 | 0.82 | 62 | empty |
| 3 | 478 | 0.71 | 0.81 | 47 | empty |
| 4 | 525 | 0.67 | 0.78 | 53 | empty |
| 5 | 556 | 0.67 | 0.77 | 54 | empty |
Interfaces
19 interfaces between chains.
- G–H · 1352 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1334 Ų buried · 18 hydrogen bonds · protein-protein
- D–E · 1329 Ų buried · 20 hydrogen bonds · protein-protein
- J–K · 1284 Ų buried · 18 hydrogen bonds · protein-protein
- G–I · 967 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 5HGB · HLA*A2402 complexed with HIV nef138 8mer epitope · the same entry in another collection · chain L against L, 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 P05534
- Every structure of UniProt P61769
- Every structure of UniProt P18801
- Elsewhere: RCSB PDB 5HGB · PDBe 5HGB · UniProt P05534 · UniProt P61769 · UniProt P18801
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.