MolNFT v1 · #82788 · protein
The complex between H27-14 TCR and HLA-A24 bound to HIV-1 NEF134- 10(WT) peptide
3VXR · HLA class I histocompatibility antigen, a-24 alpha chain: “The complex between H27-14 TCR and HLA-A24 bound to HIV-1 NEF134- 10(WT) peptide”. X-ray diffraction, 13 pockets (best druggability 0.74). MolNFT v1 #82788 on GenesisL1: 3D…
- PDB
- 3VXR
- Type
- protein
- Length
- 820 residues
- Chains
- 5
- 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; H27-14…
- UniProt
- P05534, P61769, Q9YYU8
- Pockets
- 13 · best druggability 0.74
Structure
x-ray diffraction · 5 distinct chains · 12% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility antigen, a-24 alpha chain | protein | 274 | 27% helix, 39% strand | P05534 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| D | H27-14 TCR alpha chain | protein | 194 | 5% helix, 50% strand | — |
| E | H27-14 TCR beta chain | protein | 242 | 6% helix, 49% strand | — |
| C | 10-mer peptide from protein nef | protein | 10 | 0% helix, 0% strand | Q9YYU8 |
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 997 | 0.74 | 0.77 | 79 | empty |
| 2 | 617 | 0.68 | 0.77 | 53 | empty |
| 3 | 469 | 0.63 | 0.76 | 72 | empty |
| 4 | 184 | 0.53 | 0.79 | 34 | empty |
| 5 | 92 | 0.51 | 0.83 | 18 | empty |
Interfaces
7 interfaces between chains.
- D–E · 2219 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 1372 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 943 Ų buried · 21 hydrogen bonds · protein-protein
- A–E · 470 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 358 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 3VXR · The complex between H27-14 TCR and HLA-A24 bound to HIV-1 Nef134-10(wt) peptide · the same entry in another collection · chain A against A, 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 0.97
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 Q9YYU8
- Elsewhere: RCSB PDB 3VXR · PDBe 3VXR · UniProt P05534 · UniProt P61769 · UniProt Q9YYU8
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