› 5j59

X-ray diffraction
2.4Å resolution

Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor (Chem 1893)

Released:
DOI: 10.2210/pdb5j59/pdb
PDB entry 5j59 coloured by chain, front view.
PDB entry 5j59 coloured by chain, side view.
PDB entry 5j59 coloured by chain, top view.
Source organism: Trypanosoma brucei brucei TREU927
Primary publication:
Structure-guided design of novel Trypanosoma brucei Methionyl-tRNA synthetase inhibitors.
Huang W, Zhang Z, Barros-Álvarez X, Koh CY, Ranade RM, Gillespie JR, Creason SA, Shibata S, Verlinde CLMJ, Hol WGJ, Buckner FS, Fan E
Eur J Med Chem 124 1081-1092 (2016)
PMID: 27788467

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: 61.33 KDa
Source organism: Trypanosoma brucei brucei TREU927
Expression system: Escherichia coli
UniProt:
  • Canonical: Q38C91 (Residues: 237-773; Coverage: 70%)
Gene name: Tb10.70.6470
Sequence domains:
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand MET 1 x MET
Ligand GOL 1 x GOL
Ligand N93 1 x N93
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL12-2
Spacegroup: P212121
Unit cell:
a: 87.31Å b: 106.4Å c: 207.91Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.192 0.192 0.207
Expression system: Escherichia coli

Quick links

Citations

4 review citations

Roles of aminoacyl-tRNA synthetases in immune regulation and immune diseases.
Nie et al. (2019)
3 more

1 mention without citation

Optimization of a binding fragment targeting the "enlarged methionine pocket" leads to potent Trypanosoma brucei methionyl-tRNA synthetase inhibitors.
Huang et al. (2017)