Research workbench
Structure of human mait TCR in complex with human MR1-rl-6-me-7-oh
Analyse Structure of human mait TCR in complex with human MR1-rl-6-me-7-oh in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4L4V
- Type
- protein
- Length
- 1,584 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
- 1VY
- Pockets
- 15 · best druggability 0.79
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 | 262 | 28% 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 | 256 | 29% helix, 41% strand | Q95460 |
| D | Mait T-cell receptor alpha chain | protein | 200 | 5% helix, 45% strand | — |
| E | Mait T-cell receptor beta chain | protein | 243 | 7% helix, 49% strand | — |
| F | Beta-2-microglobulin | protein | 96 | 0% helix, 51% strand | P61769 |
| G | Mait T-cell receptor alpha chain | protein | 188 | 5% helix, 48% strand | — |
| H | Mait T-cell receptor beta chain | protein | 240 | 6% helix, 50% strand | — |
Ligands and binding sites
- 1VY · 1-deoxy-1-(7-hydroxy-6-methyl-2,4-dioxo-3,4-dihydropteridin-8(2H)-yl)-D-ribitol · ligand · 2 copies · chains A, G, H, C, D, E
- GOL · Glycerol · additive · 3 copies · chains B, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 740 | 0.79 | 0.83 | 75 | GOL |
| 2 | 399 | 0.76 | 0.85 | 49 | 1VY |
| 3 | 407 | 0.73 | 0.83 | 53 | 1VY |
| 4 | 998 | 0.72 | 0.76 | 80 | empty |
| 5 | 1034 | 0.71 | 0.75 | 85 | empty |
Interfaces
11 interfaces between chains.
- D–E · 2013 Ų buried · 18 hydrogen bonds · protein-protein
- G–H · 1856 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1269 Ų buried · 15 hydrogen bonds · protein-protein
- C–F · 1222 Ų buried · 17 hydrogen bonds · protein-protein
- A–G · 692 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 4L4V · Structure of human MAIT TCR in complex with human MR1-RL-6-Me-7-OH · 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 4L4V · PDBe 4L4V · UniProt Q95460 · UniProt P61769
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