Research workbench
Structure of human MR1-2-oh-1-na in complex with human mait a-F7 TCR
Analyse Structure of human MR1-2-oh-1-na 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
- 5U16
- Type
- protein
- Length
- 1,593 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
- 7WO, NA, CL
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 8 distinct chains · 13% 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 | 96 | 0% helix, 51% strand | P61769 |
| C | Major histocompatibility complex class I-related gene protein | protein | 265 | 28% helix, 42% strand | Q95460 |
| D | Beta-2-microglobulin | protein | 99 | 0% helix, 52% strand | P61769 |
| E | Mait T-cell receptor alpha chain | protein | 185 | 5% helix, 48% strand | — |
| F | Mait T-cell receptor beta chain | protein | 240 | 6% helix, 52% strand | — |
| G | Mait T-cell receptor alpha chain | protein | 200 | 5% helix, 46% strand | — |
| H | Mait T-cell receptor beta chain | protein | 243 | 7% helix, 50% strand | — |
Ligands and binding sites
- 7WO · 2-hydroxynaphthalene-1-carbaldehyde · ligand · 2 copies · chains A, G, C
- NA · Sodium ion · metal · 3 copies · chains D, F, H
- CL · Chloride ion · ion · 3 copies · chains A, G, C
- GOL · Glycerol · additive · 5 copies · chains A, G, H, B, C, E, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1148 | 0.81 | 0.83 | 98 | empty |
| 2 | 109 | 0.78 | 0.97 | 24 | 7WO, GOL, CL |
| 3 | 406 | 0.77 | 0.86 | 55 | 7WO, GOL, CL |
| 4 | 995 | 0.72 | 0.76 | 78 | empty |
| 5 | 1157 | 0.71 | 0.75 | 82 | empty |
Interfaces
12 interfaces between chains.
- G–H · 2051 Ų buried · 18 hydrogen bonds · protein-protein
- E–F · 1924 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1316 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1253 Ų buried · 14 hydrogen bonds · protein-protein
- C–H · 954 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 2 covalent (disulfide, covalent ligand).
Compared structures
- 5U16 · Structure of human MR1-2-OH-1-NA in complex with human MAIT A-F7 TCR · the same entry in another collection · chain H against H, 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 A 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 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 5U16 · PDBe 5U16 · UniProt Q95460 · UniProt P61769
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