Research workbench
The complex between T36-5 TCR and HLA-A24 bound to HIV-1 NEF134-10(2F) peptide in space group P212121
Analyse The complex between T36-5 TCR and HLA-A24 bound to HIV-1 NEF134-10(2F) peptide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3W0W
- Type
- protein
- Length
- 834 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; 10-mer…
- UniProt
- P05534, P61769, Q9YYU3
- Pockets
- 14 · best druggability 0.75
Structure
x-ray diffraction · 5 distinct chains · 12% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility antigen, a-24 alpha chain | protein | 279 | 27% helix, 38% strand | P05534 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C | 10-mer peptide from protein nef | protein | 10 | 0% helix, 0% strand | Q9YYU3 |
| D | T36-5 TCR alpha chain | protein | 204 | 5% helix, 45% strand | — |
| E | T36-5 TCR beta chain | protein | 241 | 7% helix, 49% strand | — |
Pockets
14 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 87 | 0.75 | 0.97 | 19 | empty |
| 2 | 895 | 0.75 | 0.78 | 78 | empty |
| 3 | 650 | 0.68 | 0.77 | 54 | empty |
| 4 | 96 | 0.44 | 0.79 | 21 | empty |
| 5 | 124 | 0.43 | 0.77 | 20 | empty |
Interfaces
7 interfaces between chains.
- D–E · 2274 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 1491 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 936 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 493 Ų buried · 4 hydrogen bonds · protein-protein
- A–E · 452 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide (disulfide).
Compared structures
- 3W0W · The complex between T36-5 TCR and HLA-A24 bound to HIV-1 Nef134-10(2F) peptide in space… · 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 0.98
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 3W0W · PDBe 3W0W · UniProt P05534 · UniProt P61769 · UniProt Q9YYU3
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