MolNFT v1 · #101409 · protein
Crystal structure of TCR-MR1 ternary complex and non-covalently bound 5-(2-oxopropylideneamino)-6-D-ribitylaminouracil
4NQD · Major histocompatibility complex class I-related gene…: “Crystal structure of TCR-MR1 ternary complex and non-covalently bound…”. X-ray diffraction, 1 ligand (2LJ), 14 pockets (best druggability 0.76). MolNFT v1 #101409 on…
- PDB
- 4NQD
- Type
- protein
- Length
- 1,576 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
- Pockets
- 14 · best druggability 0.76
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 | 260 | 29% helix, 41% strand | Q95460 |
| B | Beta-2-microglobulin | protein | 96 | 0% helix, 51% strand | P61769 |
| C | Major histocompatibility complex class I-related gene protein | protein | 248 | 29% helix, 41% strand | Q95460 |
| D | TCR alpha chain | protein | 200 | 4% helix, 46% strand | — |
| E | TCR beta chain | protein | 243 | 7% helix, 49% strand | — |
| F | Beta-2-microglobulin | protein | 97 | 0% helix, 51% strand | P61769 |
| G | TCR alpha chain | protein | 190 | 3% helix, 48% strand | — |
| H | TCR beta chain | protein | 242 | 6% helix, 50% 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
- GOL · Glycerol · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 425 | 0.76 | 0.85 | 61 | 2LJ |
| 2 | 401 | 0.75 | 0.85 | 59 | 2LJ |
| 3 | 1019 | 0.72 | 0.76 | 83 | empty |
| 4 | 991 | 0.72 | 0.76 | 79 | empty |
| 5 | 469 | 0.71 | 0.81 | 37 | empty |
Interfaces
11 interfaces between chains.
- D–E · 1985 Ų buried · 17 hydrogen bonds · protein-protein
- G–H · 1953 Ų buried · 25 hydrogen bonds · protein-protein
- C–F · 1194 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1191 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 668 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 4NQD · Crystal structure of TCR-MR1 ternary complex and non-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 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 4NQD · PDBe 4NQD · UniProt Q95460 · UniProt P61769
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