MolNFT v1 · #135511 · protein
Structure of human MR1-da-6-fp in complex with human mait a-F7 TCR
5U17 · Major histocompatibility complex class I-related gene…: “Structure of human MR1-da-6-fp in complex with human mait a-F7 TCR”. X-ray diffraction, 2 ligands (7WP, NA), 20 pockets (best druggability 0.83). MolNFT v1 #135511 on…
- PDB
- 5U17
- Type
- protein
- Length
- 1,602 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
- 7WP, NA
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 8 distinct chains · 13% 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 | Mait T-cell receptor alpha chain | protein | 195 | 3% helix, 48% strand | — |
| C | Major histocompatibility complex class I-related gene protein | protein | 262 | 30% helix, 40% strand | Q95460 |
| D | Mait T-cell receptor alpha chain | protein | 200 | 5% helix, 47% strand | — |
| E | Mait T-cell receptor beta chain | protein | 244 | 7% helix, 49% strand | — |
| F | Beta-2-microglobulin | protein | 97 | 0% helix, 51% strand | P61769 |
| G | Mait T-cell receptor beta chain | protein | 241 | 7% helix, 51% strand | — |
| H | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P61769 |
Ligands and binding sites
- 7WP · 2,4-diaminopteridine-6-carbaldehyde · ligand · 2 copies · chains A, B, C, D
- NA · Sodium ion · metal · 3 copies · chains E, G, H
- GOL · Glycerol · additive · 9 copies · chains A, B, E, C, D, H
- ACT · Acetate ion · additive · 2 copies · chains C, D, 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, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 972 | 0.83 | 0.84 | 87 | GOL |
| 2 | 352 | 0.75 | 0.86 | 49 | 7WP |
| 3 | 1134 | 0.73 | 0.76 | 85 | empty |
| 4 | 343 | 0.72 | 0.84 | 50 | 7WP |
| 5 | 1051 | 0.72 | 0.76 | 69 | empty |
Interfaces
13 interfaces between chains.
- B–G · 2023 Ų buried · 22 hydrogen bonds · protein-protein
- D–E · 1995 Ų buried · 21 hydrogen bonds · protein-protein
- A–H · 1239 Ų buried · 15 hydrogen bonds · protein-protein
- C–F · 1212 Ų buried · 17 hydrogen bonds · protein-protein
- A–E · 802 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 2 covalent (disulfide, covalent ligand).
Compared structures
- 5U17 · Structure of human MR1-DA-6-FP 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 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 5U17 · PDBe 5U17 · UniProt Q95460 · UniProt P61769
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