MolNFT v1 · #103518 · protein
Structure of human MR1-ac-6-fp in complex with human mait TRBV6-1 TCR
4PJ5 · Major histocompatibility complex class I-related gene…: “Structure of human MR1-ac-6-fp in complex with human mait TRBV6-1 TCR”. X-ray diffraction, 1 ligand (30W), 17 pockets (best druggability 0.75). MolNFT v1 #103518 on GenesisL1…
- PDB
- 4PJ5
- Type
- protein
- Length
- 1,592 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
- 30W
- Pockets
- 17 · best druggability 0.75
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 | 263 | 29% helix, 41% strand | Q95460 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 52% strand | P61769 |
| C | Major histocompatibility complex class I-related gene protein | protein | 258 | 28% helix, 40% strand | Q95460 |
| D | TCR-alpha | protein | 200 | 5% helix, 45% strand | — |
| E | TCR-beta | protein | 243 | 7% helix, 50% strand | — |
| F | Beta-2-microglobulin | protein | 97 | 0% helix, 51% strand | P61769 |
| G | TCR-alpha | protein | 190 | 3% helix, 47% strand | — |
| H | TCR-beta | protein | 242 | 6% helix, 50% strand | — |
Ligands and binding sites
- 30W · N-(6-formyl-4-oxo-3,4-dihydropteridin-2-yl)acetamide · ligand · 2 copies · chains A, G, H, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 782 | 0.75 | 0.80 | 72 | empty |
| 2 | 68 | 0.73 | 0.97 | 21 | 30W |
| 3 | 1065 | 0.73 | 0.76 | 97 | empty |
| 4 | 61 | 0.72 | 0.98 | 19 | 30W |
| 5 | 987 | 0.71 | 0.75 | 81 | empty |
Interfaces
11 interfaces between chains.
- D–E · 2000 Ų buried · 18 hydrogen bonds · protein-protein
- G–H · 1909 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1292 Ų buried · 18 hydrogen bonds · protein-protein
- C–F · 1222 Ų buried · 15 hydrogen bonds · protein-protein
- A–H · 702 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 2 covalent (disulfide, covalent ligand).
Compared structures
- 4PJ5 · Structure of human MR1-Ac-6-FP in complex with human MAIT TRBV6-1 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 4PJ5 · PDBe 4PJ5 · UniProt Q95460 · UniProt P61769
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