Research workbench
Crystal structure of TCR-MR1 ternary complex and covalently bound 5- (2-oxopropylideneamino)-6-D-ribitylaminouracil
Analyse Crystal structure of TCR-MR1 ternary complex and covalently bound 5… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NQC
- Type
- protein
- Length
- 1,577 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; TCR…
- UniProt
- Q95460, P61769
- Ligands
- 2LJ, NA
- Pockets
- 15 · best druggability 0.80
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 | 255 | 29% helix, 39% strand | Q95460 |
| B | Beta-2-microglobulin | protein | 96 | 0% helix, 51% strand | P61769 |
| C | Major histocompatibility complex class I-related gene protein | protein | 263 | 27% helix, 41% strand | Q95460 |
| D | TCR alpha chain | protein | 185 | 5% helix, 48% strand | — |
| E | TCR beta chain | protein | 240 | 6% helix, 51% strand | — |
| F | Beta-2-microglobulin | protein | 97 | 0% helix, 53% strand | P61769 |
| G | TCR alpha chain | protein | 198 | 5% helix, 46% strand | — |
| H | TCR beta chain | protein | 243 | 7% helix, 49% strand | — |
Ligands and binding sites
- 2LJ · 1-deoxy-1-({2,6-dioxo-5-[(E)-propylideneamino]-1,2,3,6-tetrahydropyrimidin-4-yl}amino)-D-ribitol · ligand · 2 copies · chains A, G, H, C, D, E
- NA · Sodium ion · metal · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1118 | 0.80 | 0.82 | 108 | empty |
| 2 | 378 | 0.74 | 0.84 | 56 | 2LJ |
| 3 | 312 | 0.73 | 0.85 | 52 | 2LJ |
| 4 | 1003 | 0.71 | 0.75 | 82 | empty |
| 5 | 944 | 0.70 | 0.75 | 68 | empty |
Interfaces
12 interfaces between chains.
- G–H · 2000 Ų buried · 17 hydrogen bonds · protein-protein
- D–E · 1822 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1255 Ų buried · 18 hydrogen bonds · protein-protein
- C–F · 1194 Ų buried · 19 hydrogen bonds · protein-protein
- C–H · 851 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 2 covalent (disulfide, covalent ligand).
Compared structures
- 4NQC · Crystal structure of TCR-MR1 ternary complex and covalently bound… · 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 A 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 B 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 4NQC · PDBe 4NQC · UniProt Q95460 · UniProt P61769
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