› 4zt3

X-ray diffraction
2.8Å resolution

Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor N-(3,5-dichlorobenzyl)-N'-(5-fluoro-1H-imidazo[4,5-b]pyridin-2-yl)propane-1,3-diamine (Chem 1614)

Released:
DOI: 10.2210/pdb4zt3/pdb
PDB entry 4zt3 coloured by chain, front view.
PDB entry 4zt3 coloured by chain, side view.
PDB entry 4zt3 coloured by chain, top view.
Source organism: Trypanosoma brucei brucei TREU927
Primary publication:
5-Fluoroimidazo[4,5-b]pyridine Is a Privileged Fragment That Conveys Bioavailability to Potent Trypanosomal Methionyl-tRNA Synthetase Inhibitors.
Zhang Z, Koh CY, Ranade RM, Shibata S, Gillespie JR, Hulverson MA, Huang W, Nguyen J, Pendem N, Gelb MH, Verlinde CL, Hol WG, Buckner FS, Fan E
ACS Infect Dis 2 399-404 (2016)
PMID: 27627628

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 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 MET 1 x MET
Ligand GOL 3 x GOL
Ligand DMS 7 x DMS
Ligand SO4 1 x SO4
Ligand 4RQ 1 x 4RQ
1 modified residue:
Ligand CAS 2 x CAS

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007
Spacegroup: P212121
Unit cell:
a: 86.696Å b: 106.054Å c: 207.453Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.211 0.209 0.249
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

7 review citations

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