› 4eg4

X-ray diffraction
3.15Å resolution

Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor Chem 1289

Released:
DOI: 10.2210/pdb4eg4/pdb
PDB entry 4eg4 coloured by chain, front view.
PDB entry 4eg4 coloured by chain, side view.
PDB entry 4eg4 coloured by chain, top view.
Source organism: Trypanosoma brucei brucei TREU927
Primary publication:
Distinct states of methionyl-tRNA synthetase indicate inhibitor binding by conformational selection.
Koh CY, Kim JE, Shibata S, Ranade RM, Yu M, Liu J, Gillespie JR, Buckner FS, Verlinde CL, Fan E, Hol WG
Structure 20 1681-91 (2012)
PMID: 22902861

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: 61.54 KDa
Source organism: Trypanosoma brucei brucei TREU927
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 20 x GOL
Ligand DMS 6 x DMS
Ligand MET 1 x MET
Ligand SO4 1 x SO4
Ligand 0OT 1 x 0OT
1 modified residue:
Ligand CAS 4 x CAS

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007
Spacegroup: P212121
Unit cell:
a: 87.478Å b: 105.892Å c: 207.553Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.194 0.191 0.24
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

12 review citations

Multiple conformational selection and induced fit events take place in allosteric propagation.
Nussinov et al. (2014)
11 more

6 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)
5 more