Research workbench
The complex between C1-28 TCR and HLA-A24 bound to HIV-1 NEF134-10(2F) peptide
Analyse The complex between C1-28 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
- 3VXM
- Type
- protein
- Length
- 824 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
- Ligands
- CO
- Pockets
- 9 · best druggability 0.71
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, 40% strand | P05534 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P61769 |
| C | 10-mer peptide from protein nef | protein | 10 | 0% helix, 0% strand | Q9YYU3 |
| D | C1-28 TCR alpha chain | protein | 198 | 3% helix, 45% strand | — |
| E | C1-28 TCR beta chain | protein | 243 | 7% helix, 51% strand | — |
Ligands and binding sites
- CO · Cobalt (II) ion · metal · 3 copies · chains D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 922 | 0.71 | 0.75 | 84 | empty |
| 2 | 703 | 0.70 | 0.77 | 62 | empty |
| 3 | 168 | 0.58 | 0.82 | 34 | empty |
| 4 | 81 | 0.51 | 0.85 | 23 | empty |
| 5 | 70 | 0.47 | 0.83 | 18 | empty |
Interfaces
7 interfaces between chains.
- D–E · 2146 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1281 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 958 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 620 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 266 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 3VXM · The complex between C1-28 TCR and HLA-A24 bound to HIV-1 Nef134-10(2F) 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 0.98
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 3VXM · PDBe 3VXM · UniProt P05534 · UniProt P61769 · UniProt Q9YYU3
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