› 4yrt

X-ray diffraction
2.05Å resolution

Crystal structure of T. cruzi Histidyl-tRNA synthetase in complex with N-(5-hydroxynaphthalen-2-yl)propanamide (Chem 1781)

Released:
DOI: 10.2210/pdb4yrt/pdb
PDB entry 4yrt coloured by chain, front view.
PDB entry 4yrt coloured by chain, side view.
PDB entry 4yrt coloured by chain, top view.
Source organism: Trypanosoma cruzi strain CL Brener
Primary publication:
A binding hotspot in Trypanosoma cruzi histidyl-tRNA synthetase revealed by fragment-based crystallographic cocktail screens.
Koh CY, Siddaramaiah LK, Ranade RM, Nguyen J, Jian T, Zhang Z, Gillespie JR, Buckner FS, Verlinde CL, Fan E, Hol WG
Acta Crystallogr D Biol Crystallogr 71 1684-98 (2015)
PMID: 26249349

Function and Biology Details

Reaction catalysed: 
ATP + L-histidine + tRNA(His) = AMP + diphosphate + L-histidyl-tRNA(His)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-175465 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
histidine--tRNA ligase Chain: A
Molecule details ›
Chain: A
Length: 456 amino acids
Theoretical weight: 51.19 KDa
Source organism: Trypanosoma cruzi strain CL Brener
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q4DA54 (Residues: 45-478; Coverage: 91%)
Gene name: Tc00.1047053507019.40
Sequence domains:
Structure domains:

Ligands and Environments

4 bound ligands:
Ligand HIS 1 x HIS
Ligand 781 1 x 781
Ligand SO4 1 x SO4
Ligand EDO 1 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007
Unit cell:
a: 65.432Å b: 119.34Å c: 66.302Å
α: 90° β: 93.39° γ: 90°
R-values:
R R work R free
0.187 0.185 0.226
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

8 review citations

Twenty years on: the impact of fragments on drug discovery.
Erlanson et al. (2016)
7 more

1 mention without citation

A binding hotspot in Trypanosoma cruzi histidyl-tRNA synthetase revealed by fragment-based crystallographic cocktail screens.
Koh et al. (2015)