MolNFT v1 · #143297 · protein
Crystal structure of the KFJ5 TCR-ny-eso-1-HLA-B*07:02 complex
6AVF · Beta-2-microglobulin: “Crystal structure of the KFJ5 TCR-ny-eso-1-HLA-B*07:02 complex”. X-ray diffraction, 9 pockets (best druggability 0.72). MolNFT v1 #143297 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6AVF
- Type
- protein
- Length
- 819 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-2-microglobulin; T-cell receptor alpha variable 4,TCR alpha chain; T-cell receptor…
- UniProt
- P61769, A0A0B4J268, A0A5B6, P01889
- Pockets
- 9 · best druggability 0.72
Structure
x-ray diffraction · 5 distinct chains · 13% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| M | Beta-2-microglobulin | protein | 93 | 0% helix, 47% strand | P61769 |
| A | T-cell receptor alpha variable 4,TCR alpha chain | protein | 202 | 5% helix, 43% strand | A0A0B4J268 |
| B | T-cell receptor beta variable 28,TCR beta chain | protein | 242 | 7% helix, 53% strand | A0A5B6 |
| P | Ala-pro-arg-gly-pro-his-gly-gly-ala-ala-ser-gly-leu | protein | 13 | 23% helix, 0% strand | — |
| H | HLA class I histocompatibility antigen, B-7 alpha chain | protein | 269 | 27% helix, 38% strand | P01889 |
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 651 | 0.72 | 0.79 | 51 | empty |
| 2 | 997 | 0.70 | 0.75 | 82 | empty |
| 3 | 361 | 0.56 | 0.75 | 52 | empty |
| 4 | 182 | 0.47 | 0.75 | 29 | empty |
| 5 | 146 | 0.42 | 0.75 | 30 | empty |
Interfaces
7 interfaces between chains.
- A–B · 2269 Ų buried · 24 hydrogen bonds · protein-protein
- M–H · 1318 Ų buried · 19 hydrogen bonds · protein-protein
- P–H · 870 Ų buried · 22 hydrogen bonds · protein-protein
- A–H · 546 Ų buried · 6 hydrogen bonds · protein-protein
- A–P · 270 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6AVF · Crystal structure of the KFJ5 TCR-NY-ESO-1-HLA-B*07:02 complex · the same entry in another collection · chain H against H, TM-score 1.00
- P01889 · AlphaFold monomer V2.0 prediction for HLA class I histocompatibility antigen, B alpha… · a predicted model of the same protein · chain H against A, TM-score 0.97
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain M against A, TM-score 0.97
- A0A5B6 · AlphaFold monomer V2.0 prediction for T cell receptor beta variable 28 (A0A5B6) · a predicted model of the same protein · chain B against A, TM-score 0.39
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 P61769
- Every structure of UniProt A0A0B4J268
- Every structure of UniProt A0A5B6
- Every structure of UniProt P01889
- Elsewhere: RCSB PDB 6AVF · PDBe 6AVF · UniProt P61769 · UniProt A0A0B4J268 · UniProt A0A5B6 · UniProt P01889
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