Research workbench
Structure of human MR1-ac-6-fp in complex with human mait B-B10 TCR
Analyse Structure of human MR1-ac-6-fp in complex with human mait B-B10 TCR in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PJE
- Type
- protein
- Length
- 1,575 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, NA, CL
- Pockets
- 16 · best druggability 0.74
Structure
x-ray diffraction · 7 distinct chains · 14% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Major histocompatibility complex class I-related gene protein | protein | 261 | 29% helix, 42% strand | Q95460 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P61769 |
| C | Major histocompatibility complex class I-related gene protein | protein | 252 | 29% helix, 40% strand | Q95460 |
| D | Beta-2-microglobulin | protein | 97 | 0% helix, 51% strand | P61769 |
| E | TCR-alpha | protein | 189 | 5% helix, 46% strand | — |
| F, H | TCR-beta | protein | 240 | 6% helix, 51% strand | — |
| G | TCR-alpha | protein | 197 | 5% helix, 46% strand | — |
Ligands and binding sites
- 30W · N-(6-formyl-4-oxo-3,4-dihydropteridin-2-yl)acetamide · ligand · 2 copies · chains A, E, F, C, G, H
- NA · Sodium ion · metal · 2 copies · chains F, H
- CL · Chloride ion · ion · 3 copies · chains A, E, C, F
- GOL · Glycerol · additive · 8 copies · chains A, F, B, C, D, E, H
- ACT · Acetate ion · additive · 3 copies · chains A, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 73 | 0.74 | 0.97 | 19 | 30W |
| 2 | 74 | 0.74 | 0.97 | 18 | 30W |
| 3 | 902 | 0.73 | 0.77 | 87 | GOL |
| 4 | 1013 | 0.71 | 0.75 | 89 | empty |
| 5 | 608 | 0.69 | 0.78 | 89 | empty |
Interfaces
9 interfaces between chains.
- G–H · 1944 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 1744 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1280 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1258 Ų buried · 18 hydrogen bonds · protein-protein
- A–E · 700 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 2 covalent (disulfide, covalent ligand).
Compared structures
- 4PJE · Structure of human MR1-Ac-6-FP in complex with human MAIT B-B10 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 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 4PJE · PDBe 4PJE · UniProt Q95460 · UniProt P61769
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