Research workbench
Structure of human mait a-F7 TCR in complex with human MR1-2`OH-ethyl- 5-op-U
Analyse Structure of human mait a-F7 TCR in complex with human MR1-2`OH-ethyl- 5-op-U in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PUG
- Type
- protein
- Length
- 1,611 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
- OZD, NA, CL
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 8 distinct chains · 12% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Major histocompatibility complex class I-related gene protein | protein | 264 | 28% helix, 41% strand | Q95460 |
| B | Beta-2-microglobulin | protein | 98 | 0% helix, 50% strand | P61769 |
| C | Major histocompatibility complex class I-related gene protein | protein | 267 | 27% helix, 41% strand | Q95460 |
| D | Human TCR alpha chain | protein | 196 | 3% helix, 47% strand | — |
| E | Human TCR beta chain | protein | 242 | 7% helix, 51% strand | — |
| F | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| G | Human TCR alpha chain | protein | 200 | 5% helix, 45% strand | — |
| H | Human TCR beta chain | protein | 244 | 7% helix, 50% strand | — |
Ligands and binding sites
- OZD · 6-[(2-hydroxyethyl)amino]-5-[(E)-(2-oxopropylidene) amino]pyrimidine-2,4(1H,3H)-dione · ligand · 2 copies · chains A, G, C, D
- NA · Sodium ion · metal · chains H
- CL · Chloride ion · ion · chains E
- GOL · Glycerol · additive · 3 copies · chains A, H, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1183 | 0.81 | 0.82 | 95 | empty |
| 2 | 103 | 0.78 | 0.97 | 23 | OZD |
| 3 | 109 | 0.77 | 0.96 | 25 | OZD |
| 4 | 1087 | 0.72 | 0.76 | 80 | empty |
| 5 | 916 | 0.70 | 0.75 | 82 | empty |
Interfaces
11 interfaces between chains.
- G–H · 2078 Ų buried · 23 hydrogen bonds · protein-protein
- D–E · 1957 Ų buried · 23 hydrogen bonds · protein-protein
- C–F · 1307 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1273 Ų buried · 16 hydrogen bonds · protein-protein
- C–H · 854 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 2 covalent (disulfide, covalent ligand).
Compared structures
- 6PUG · Structure of human MAIT A-F7 TCR in complex with human MR1-2`OH-Ethyl-5-OP-U · 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 6PUG · PDBe 6PUG · UniProt Q95460 · UniProt P61769
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