Research workbench
Structure of human MR1-hmb in complex with human mait a-F7 TCR
Analyse Structure of human MR1-hmb in complex with human mait a-F7 TCR in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5U2V
- Type
- protein
- Length
- 1,598 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; Mait…
- UniProt
- Q95460, P61769
- Ligands
- 7WQ, PRO
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 7 distinct chains · 13% helix, 45% 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 | 99 | 0% helix, 52% strand | P61769 |
| G | Mait T-cell receptor alpha chain | protein | 193 | 5% helix, 48% strand | — |
| H, F | Mait T-cell receptor beta chain | protein | 242 | 7% helix, 51% strand | — |
| C | Major histocompatibility complex class I-related gene protein | protein | 262 | 28% helix, 38% strand | Q95460 |
| D | Beta-2-microglobulin | protein | 96 | 0% helix, 51% strand | P61769 |
| E | Mait T-cell receptor alpha chain | protein | 200 | 4% helix, 46% strand | — |
Ligands and binding sites
- 7WQ · 2-hydroxy-5-methoxybenzaldehyde · ligand · 2 copies · chains A, C, E
- PRO · Proline · ligand · chains A
- GOL · Glycerol · additive · 2 copies · chains A, G, C, E, 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 | 1187 | 0.80 | 0.82 | 101 | empty |
| 2 | 118 | 0.78 | 0.97 | 26 | 7WQ, GOL |
| 3 | 376 | 0.76 | 0.86 | 49 | 7WQ, GOL |
| 4 | 1101 | 0.72 | 0.76 | 87 | empty |
| 5 | 1129 | 0.71 | 0.75 | 86 | empty |
Interfaces
12 interfaces between chains.
- E–F · 2063 Ų buried · 20 hydrogen bonds · protein-protein
- G–H · 1998 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1266 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1189 Ų buried · 17 hydrogen bonds · protein-protein
- A–F · 861 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 2 covalent (disulfide, covalent ligand).
Compared structures
- 5U2V · Structure of human MR1-HMB in complex with human MAIT A-F7 TCR · the same entry in another collection · chain F against F, TM-score 1.00
- Q95460 · AlphaFold monomer V2.0 prediction for major histocompatibility complex class I-related… · a predicted model of the same protein · chain C against A, TM-score 0.99
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain D 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 5U2V · PDBe 5U2V · UniProt Q95460 · UniProt P61769
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