Research workbench
tRNA guanine Transglycosylase (TGT) in co-crystallized complex (space group C2) with 6-amino-2-(methylamino)-4-(2-((2R,3R,4S,5R,6S)-3,4,5,6-tetramethoxytetrahydro-2H-pyran-2-yl)ethyl)-1H-imidazo[4,5-g]quinazolin-8(7H)-one
Analyse tRNA guanine Transglycosylase (TGT) in co-crystallized complex (space group C2)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LPS
- Type
- protein
- Length
- 341 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.27
- Source
- Zymomonas mobilis subsp. mobilis (strain ATCC 31821 / ZM4 / CP4)
- Molecule
- Queuine tRNA-ribosyltransferase
- EC
- 2.4.2.29
- UniProt
- P28720
- Ligands
- 726, ZN
- Pockets
- 3 · best druggability 0.55
Structure
x-ray diffraction · resolution 1.27 · 1 distinct chain · 44% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Queuine tRNA-ribosyltransferase (EC 2.4.2.29) | protein | 341 | 44% helix, 20% strand | P28720 |
Ligands and binding sites
- 726 · 6-azanyl-2-(methylamino)-4-[2-[(2~{R},3~{R},4~{S}, 5~{R},6~{S})-3,4,5,6-tetramethoxyoxan-2-yl]ethyl]-1,7-dihydroimidazo[4,5-g]quinazolin-8-one · ligand · chains A
- ZN · Zinc ion · metal · chains A
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 185 | 0.55 | 0.80 | 29 | 726 |
| 2 | 61 | 0.31 | 0.76 | 19 | empty |
| 3 | 54 | 0.30 | 0.75 | 15 | empty |
Compared structures
- 5LPS · TRNA guanine transglycosylase (tgt) in co-crystallized complex (space group C2) 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 5LPS · PDBe 5LPS · UniProt P28720
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