MolNFT v1 · #82791 · protein
The complex between T36-5 TCR and HLA-A24 bound to HIV-1 NEF134-10(2F) peptide
3VXU · HLA class I histocompatibility antigen, a-24 alpha chain: “The complex between T36-5 TCR and HLA-A24 bound to HIV-1 NEF134-10(2F) peptide”. X-ray diffraction, 20 pockets (best druggability 0.75). MolNFT v1 #82791 on GenesisL1: 3D…
- PDB
- 3VXU
- Type
- protein
- Length
- 1,646 residues
- Chains
- 10
- 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; 10-mer…
- UniProt
- P05534, P61769, Q9YYU3
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 5 distinct chains · 12% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | HLA class I histocompatibility antigen, a-24 alpha chain | protein | 274 | 27% helix, 39% strand | P05534 |
| B, G | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P61769 |
| C, H | 10-mer peptide from protein nef | protein | 10 | 0% helix, 0% strand | Q9YYU3 |
| D, I | T36-5 TCR alpha chain | protein | 199 | 3% helix, 41% strand | — |
| E, J | T36-5 TCR beta chain | protein | 241 | 7% helix, 49% strand | — |
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 95 | 0.75 | 0.97 | 23 | empty |
| 2 | 1031 | 0.72 | 0.76 | 102 | empty |
| 3 | 992 | 0.71 | 0.75 | 90 | empty |
| 4 | 686 | 0.71 | 0.78 | 61 | empty |
| 5 | 632 | 0.69 | 0.78 | 59 | empty |
Interfaces
17 interfaces between chains.
- I–J · 2278 Ų buried · 32 hydrogen bonds · protein-protein
- D–E · 2187 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 1304 Ų buried · 16 hydrogen bonds · protein-protein
- F–G · 1300 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 931 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide (disulfide).
Compared structures
- 3VXU · The complex between T36-5 TCR and HLA-A24 bound to HIV-1 Nef134-10(2F) peptide · the same entry in another collection · chain J against J, TM-score 1.00
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain G against A, TM-score 0.97
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 Q9YYU3
- Elsewhere: RCSB PDB 3VXU · PDBe 3VXU · UniProt P05534 · UniProt P61769 · UniProt Q9YYU3
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