› 1n2v

X-ray diffraction
2.1Å resolution

Crystal Structure of TGT in complex with 2-Butyl-5,6-dihydro-1H-imidazo[4,5-d]pyridazine-4,7-dione

Released:
DOI: 10.2210/pdb1n2v/pdb
PDB entry 1n2v coloured by chain, front view.
PDB entry 1n2v coloured by chain, side view.
PDB entry 1n2v coloured by chain, top view.
Source organism: Zymomonas mobilis
Primary publication:
Virtual screening for submicromolar leads of tRNA-guanine transglycosylase based on a new unexpected binding mode detected by crystal structure analysis.
Brenk R, Naerum L, Grädler U, Gerber HD, Garcia GA, Reuter K, Stubbs MT, Klebe G
J Med Chem 46 1133-43 (2003)
PMID: 12646024

Function and Biology Details

Reaction catalysed: 
Guanine(34) in tRNA + 7-aminomethyl-7-carbaguanine = 7-aminomethyl-7-carbaguanine(34) in tRNA + guanine
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-151274 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Queuine tRNA-ribosyltransferase Chain: A
Molecule details ›
Chain: A
Length: 386 amino acids
Theoretical weight: 42.93 KDa
Source organism: Zymomonas mobilis
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P28720 (Residues: 1-386; Coverage: 100%)
Gene names: ZMO0363, tgt
Sequence domains: Queuine tRNA-ribosyltransferase
Structure domains: Queuine tRNA-ribosyltransferase-like

Ligands and Environments

2 bound ligands:
Ligand ZN 1 x ZN
Ligand BDI 1 x BDI
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU300
Spacegroup: C2
Unit cell:
a: 91.06Å b: 64.38Å c: 70.77Å
α: 90° β: 96.5° γ: 90°
R-values:
R R work R free
0.188 0.188 0.233
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

9 review citations

Docking and scoring in virtual screening for drug discovery: methods and applications.
Kitchen et al. (2004)
8 more

9 mentions without citation

CB-Dock: a web server for cavity detection-guided protein-ligand blind docking.
Liu et al. (2020)
8 more