Research workbench
tRNA-Guanine Transglycosylase (TGT) in co-crystallized complex with (E)-N-ethyl-4-oxo-4-phenylbut-2-enamide
Analyse tRNA-Guanine Transglycosylase (TGT) in co-crystallized complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YGV
- Type
- protein
- Length
- 367 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.63
- Source
- Zymomonas mobilis subsp. mobilis (strain ATCC 31821 / ZM4 / CP4)
- Molecule
- Queuine tRNA-ribosyltransferase
- EC
- 2.4.2.29
- UniProt
- P28720
- Ligands
- OQH, ZN
- Pockets
- 4 · best druggability 0.66
Structure
x-ray diffraction · resolution 1.63 · 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
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