MolNFT v1 · #135529 · protein
Structure of human MR1-diclofenac in complex with human mait a-F7 TCR
5U1R · Major histocompatibility complex class I-related gene…: “Structure of human MR1-diclofenac in complex with human mait a-F7 TCR”. X-ray diffraction, 2 ligands (DIF, NA), 19 pockets (best druggability 0.81). MolNFT v1 #135529 on…
- PDB
- 5U1R
- Type
- protein
- Length
- 1,605 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Major histocompatibility complex class I-related gene protein; Mait T-cell receptor alpha…
- UniProt
- Q95460, P61769
- Ligands
- DIF, NA
- Pockets
- 19 · best druggability 0.81
Structure
x-ray diffraction · 8 distinct chains · 12% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Major histocompatibility complex class I-related gene protein | protein | 263 | 27% helix, 40% strand | Q95460 |
| D | Mait T-cell receptor alpha chain | protein | 199 | 3% helix, 45% strand | — |
| E | Mait T-cell receptor beta chain | protein | 243 | 7% helix, 51% strand | — |
| F | Beta-2-microglobulin | protein | 97 | 0% helix, 51% strand | P61769 |
| A | Major histocompatibility complex class I-related gene protein | protein | 262 | 27% helix, 43% strand | Q95460 |
| B | Mait T-cell receptor alpha chain | protein | 200 | 3% helix, 46% strand | — |
| G | Mait T-cell receptor beta chain | protein | 241 | 7% helix, 51% strand | — |
| H | Beta-2-microglobulin | protein | 100 | 0% helix, 51% strand | P61769 |
Ligands and binding sites
- DIF · 2-[2,6-dichlorophenyl)amino]benzeneacetic acid · ligand · 2 copies · chains C, D, E, A, B, G
- NA · Sodium ion · metal · 2 copies · chains C, E
- ACT · Acetate ion · additive · 3 copies · chains C, D, A, H, E, B
- GOL · Glycerol · additive · 3 copies · chains C, E, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 130 | 0.81 | 0.98 | 27 | DIF |
| 2 | 123 | 0.80 | 0.98 | 26 | DIF |
| 3 | 769 | 0.78 | 0.82 | 71 | ACT |
| 4 | 1091 | 0.73 | 0.76 | 73 | empty |
| 5 | 1079 | 0.72 | 0.76 | 86 | empty |
Interfaces
11 interfaces between chains.
- D–E · 2073 Ų buried · 20 hydrogen bonds · protein-protein
- B–G · 1984 Ų buried · 22 hydrogen bonds · protein-protein
- A–H · 1312 Ų buried · 13 hydrogen bonds · protein-protein
- C–F · 1252 Ų buried · 16 hydrogen bonds · protein-protein
- E–A · 875 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 5U1R · Structure of human MR1-diclofenac 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 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 F 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 5U1R · PDBe 5U1R · UniProt Q95460 · UniProt P61769
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