MolNFT v1 · #170717 · protein
TRNA-guanine transglycosylase (tgt) in co-crystallized complex with (E)-N-ethyl-4-oxo-4-phenylbut-2-enamide
6YGV · Queuine tRNA-ribosyltransferase: “TRNA-guanine transglycosylase (tgt) in co-crystallized complex with (E)-N-ethyl-4-oxo-4-phenylbut-2-enamide”. X-ray diffraction, 2 ligands (OQH, ZN), 4 pockets (best druggability 0.66). MolNFT v1…
- PDB
- 6YGV
- Type
- protein
- Length
- 367 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Queuine tRNA-ribosyltransferase
- EC
- 2.4.2.29
- UniProt
- P28720
- Ligands
- OQH, ZN
- Pockets
- 4 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Queuine tRNA-ribosyltransferase (EC 2.4.2.29) | protein | 367 | 47% helix, 18% strand | P28720 |
Ligands and binding sites
- OQH · ~{N}-ethyl-4-oxidanylidene-4-phenyl-butanamide · ligand · chains A
- ZN · Zinc ion · metal · chains A
- GOL · Glycerol · additive · 5 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 280 | 0.66 | 0.82 | 45 | GOL |
| 2 | 76 | 0.41 | 0.79 | 14 | empty |
| 3 | 78 | 0.39 | 0.77 | 19 | empty |
| 4 | 60 | 0.34 | 0.78 | 12 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6YGV · tRNA-Guanine Transglycosylase (TGT) in co-crystallized complex with… · the same entry in another collection · chain A against A, TM-score 1.00
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 P28720
- Elsewhere: RCSB PDB 6YGV · PDBe 6YGV · UniProt P28720
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.