MolNFT v1 · #165337 · protein
Crystal structure of the T-cell receptor GVY01 bound to HLA A2*01- gvydgrehtv
6TRO · MHC class I antigen: “Crystal structure of the T-cell receptor GVY01 bound to HLA A2*01- gvydgrehtv”. X-ray diffraction, 10 pockets (best druggability 0.70). MolNFT v1 #165337 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6TRO
- Type
- protein
- Length
- 814 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class I antigen; Beta-2-microglobulin; Mage-A4 peptide (amino acids 230-239); T-cell…
- UniProt
- A0A5B8RNS7, P61769
- Pockets
- 10 · best druggability 0.70
Structure
x-ray diffraction · 5 distinct chains · 12% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MHC class I antigen | protein | 273 | 27% helix, 40% strand | A0A5B8RNS7 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 48% strand | P61769 |
| C | Mage-A4 peptide (amino acids 230-239) | protein | 10 | 0% helix, 0% strand | — |
| D | T-cell receptor alpha chain | protein | 189 | 2% helix, 49% strand | — |
| E | T-cell receptor beta chain | protein | 242 | 7% helix, 48% strand | — |
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1030 | 0.70 | 0.75 | 77 | empty |
| 2 | 546 | 0.69 | 0.78 | 49 | empty |
| 3 | 149 | 0.60 | 0.84 | 23 | empty |
| 4 | 149 | 0.49 | 0.78 | 30 | empty |
| 5 | 175 | 0.47 | 0.76 | 25 | empty |
Interfaces
7 interfaces between chains.
- D–E · 2233 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1440 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 840 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 649 Ų buried · 10 hydrogen bonds · protein-protein
- C–E · 225 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6TRO · Crystal structure of the T-cell receptor GVY01 bound to HLA A2*01-GVYDGREHTV · 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 A0A5B8RNS7
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 6TRO · PDBe 6TRO · UniProt A0A5B8RNS7 · UniProt P61769
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