Research workbench
Structure of human mait a-F7 TCR in complex with patient MR1-R9H-ac-6- fp
Analyse Structure of human mait a-F7 TCR in complex with patient MR1-R9H-ac-6- fp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6W9U
- Type
- protein
- Length
- 1,599 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Major histocompatibility complex class I-related gene protein; Beta-2-microglobulin…
- UniProt
- Q95460, P61769
- Ligands
- TKG, CL
- Pockets
- 17 · best druggability 0.80
Structure
x-ray diffraction · 8 distinct chains · 12% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Major histocompatibility complex class I-related gene protein | protein | 265 | 29% helix, 40% strand | Q95460 |
| B | Beta-2-microglobulin | protein | 98 | 0% helix, 52% strand | P61769 |
| C | Major histocompatibility complex class I-related gene protein | protein | 268 | 27% helix, 41% strand | Q95460 |
| D | TCR-alpha chain | protein | 186 | 2% helix, 48% strand | — |
| E | TCR-beta chain | protein | 239 | 6% helix, 51% strand | — |
| F | Beta-2-microglobulin | protein | 100 | 0% helix, 51% strand | P61769 |
| G | TCR-alpha chain | protein | 199 | 5% helix, 45% strand | — |
| H | TCR-beta chain | protein | 244 | 7% helix, 50% strand | — |
Ligands and binding sites
- TKG · 1-[[6-(1-$l^{1}-oxidanylethyl)-4-$l^{3}-oxidanylidene-2,3,6,8~{a}-tetrahydropteridin-2-yl]-$l^{2}-azanyl]ethanone · ligand · 2 copies · chains A, G, C, D
- CL · Chloride ion · ion · chains A
- GOL · Glycerol · additive · 4 copies · chains A, H, C, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1116 | 0.80 | 0.82 | 96 | empty |
| 2 | 369 | 0.77 | 0.87 | 46 | TKG |
| 3 | 347 | 0.76 | 0.87 | 53 | TKG |
| 4 | 1168 | 0.72 | 0.76 | 83 | empty |
| 5 | 936 | 0.70 | 0.75 | 86 | empty |
Interfaces
12 interfaces between chains.
- G–H · 2021 Ų buried · 17 hydrogen bonds · protein-protein
- D–E · 1854 Ų buried · 18 hydrogen bonds · protein-protein
- C–F · 1356 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1261 Ų buried · 16 hydrogen bonds · protein-protein
- C–H · 915 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 2 covalent (disulfide, covalent ligand).
Compared structures
- 6W9U · Structure of human MAIT A-F7 TCR in complex with patient MR1-R9H-Ac-6-FP · the same entry in another collection · chain H against H, 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 Q95460
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 6W9U · PDBe 6W9U · UniProt Q95460 · UniProt P61769
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