› 4q4p

X-ray diffraction
1.54Å resolution

tRNA-Guanine Transglycosylase (TGT) in Complex with 2-{[2-(PIPERIDIN-1-YL)ETHYL]AMINO}-3,5-DIHYDRO-8H-IMIDAZO[4,5-G]QUINAZOLIN-8-ONE

Released:
DOI: 10.2210/pdb4q4p/pdb
PDB entry 4q4p coloured by chain, front view.
PDB entry 4q4p coloured by chain, side view.
PDB entry 4q4p coloured by chain, top view.
Source organism: Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821
Primary publication:
Beyond affinity: enthalpy-entropy factorization unravels complexity of a flat structure-activity relationship for inhibition of a tRNA-modifying enzyme.
Neeb M, Betz M, Heine A, Barandun LJ, Hohn C, Diederich F, Klebe G
J Med Chem 57 5566-78 (2014)
PMID: 24960372

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 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 subsp. mobilis ZM4 = ATCC 31821
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

5 bound ligands:
Ligand ZN 1 x ZN
Ligand GOL 1 x GOL
Ligand DMS 1 x DMS
Ligand CL 1 x CL
Ligand 2YO 1 x 2YO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: BESSY BEAMLINE 14.3
Spacegroup: C2
Unit cell:
a: 89.985Å b: 64.853Å c: 70.741Å
α: 90° β: 93.32° γ: 90°
R-values:
R R work R free
0.153 0.152 0.17
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

3 review citations

Molecular recognition in chemical and biological systems.
Persch et al. (2015)
2 more