MolNFT v1 · #143298 · protein
Crystal structure of the KFJ37 TCR-ny-eso-1-HLA-B*07:02 complex
6AVG · Beta-2-microglobulin: “Crystal structure of the KFJ37 TCR-ny-eso-1-HLA-B*07:02 complex”. X-ray diffraction, 20 pockets (best druggability 0.77). MolNFT v1 #143298 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6AVG
- Type
- protein
- Length
- 1,653 residues
- Chains
- 10
- 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, A0A0B4J1U6, P01889
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 6 distinct chains · 15% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H, A | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P61769 |
| C, B | T-cell receptor alpha variable 4,TCR alpha chain | protein | 196 | 5% helix, 40% strand | A0A0B4J268 |
| D, E | T-cell receptor beta variable 9,TCR beta chain | protein | 245 | 6% helix, 49% strand | A0A0B4J1U6 |
| G | HLA class I histocompatibility antigen, B-7 alpha chain | protein | 272 | 27% helix, 39% strand | P01889 |
| F | HLA class I histocompatibility antigen, B-7 alpha chain | protein | 275 | 26% helix, 40% strand | P01889 |
| Q, P | Ala-pro-arg-gly-pro-his-gly-gly-ala-ala-ser-gly-leu | protein | 13 | 0% helix, 0% strand | — |
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 519 | 0.77 | 0.84 | 77 | empty |
| 2 | 758 | 0.72 | 0.78 | 76 | empty |
| 3 | 1067 | 0.72 | 0.76 | 85 | empty |
| 4 | 540 | 0.68 | 0.78 | 49 | empty |
| 5 | 191 | 0.65 | 0.85 | 49 | empty |
Interfaces
20 interfaces between chains.
- B–E · 1938 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1901 Ų buried · 19 hydrogen bonds · protein-protein
- A–F · 1371 Ų buried · 23 hydrogen bonds · protein-protein
- H–G · 1359 Ų buried · 20 hydrogen bonds · protein-protein
- G–P · 828 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 6AVG · Crystal structure of the KFJ37 TCR-NY-ESO-1-HLA-B*07:02 complex · the same entry in another collection · chain P against P, 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 G against A, TM-score 0.98
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain H 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 P61769
- Every structure of UniProt A0A0B4J268
- Every structure of UniProt A0A0B4J1U6
- Every structure of UniProt P01889
- Elsewhere: RCSB PDB 6AVG · PDBe 6AVG · UniProt P61769 · UniProt A0A0B4J268 · UniProt A0A0B4J1U6 · UniProt P01889
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