› 4mw4

X-ray diffraction
2.5Å resolution

Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor 1-{3-[(5-chloro-2-hydroxy-3-iodobenzyl)amino]propyl}-3-thiophen-3-ylurea (Chem 1473)

Released:
DOI: 10.2210/pdb4mw4/pdb
PDB entry 4mw4 coloured by chain, front view.
PDB entry 4mw4 coloured by chain, side view.
PDB entry 4mw4 coloured by chain, top view.
Source organism: Trypanosoma brucei
Primary publication:
Structures of Trypanosoma brucei methionyl-tRNA synthetase with urea-based inhibitors provide guidance for drug design against sleeping sickness.
Koh CY, Kim JE, Wetzel AB, de van der Schueren WJ, Shibata S, Ranade RM, Liu J, Zhang Z, Gillespie JR, Buckner FS, Verlinde CL, Fan E, Hol WG
PLoS Negl Trop Dis 8 e2775 (2014)
PMID: 24743796

Function and Biology Details

Reaction catalysed: 
ATP + L-methionine + tRNA(Met) = AMP + diphosphate + L-methionyl-tRNA(Met)
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-174405 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
methionine--tRNA ligase Chains: A, B
Molecule details ›
Chains: A, B
Length: 542 amino acids
Theoretical weight: 61.43 KDa
Source organism: Trypanosoma brucei
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q38C91 (Residues: 237-773; Coverage: 70%)
Gene name: Tb10.70.6470
Sequence domains:
Structure domains:

Ligands and Environments

5 bound ligands:
Ligand GOL 9 x GOL
Ligand DMS 5 x DMS
Ligand SO4 3 x SO4
Ligand MET 1 x MET
Ligand 2EB 1 x 2EB
1 modified residue:
Ligand CAS 2 x CAS

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL12-2
Spacegroup: P212121
Unit cell:
a: 87.829Å b: 106.063Å c: 207.642Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.206 0.204 0.231
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

6 review citations

Evolutionary Limitation and Opportunities for Developing tRNA Synthetase Inhibitors with 5-Binding-Mode Classification.
Fang et al. (2015)
5 more

2 mentions without citation

The Potential of Secondary Metabolites from Plants as Drugs or Leads against Protozoan Neglected Diseases-Part III: In-Silico Molecular Docking Investigations.
Ogungbe et al. (2016)
1 more