› 3zju

X-ray diffraction
2.4Å resolution

Ternary complex of E .coli leucyl-tRNA synthetase, tRNA(Leu) and the benzoxaborole AN3016 in the editing conformation

Released:
DOI: 10.2210/pdb3zju/pdb
PDB entry 3zju coloured by chain, front view.
PDB entry 3zju coloured by chain, side view.
PDB entry 3zju coloured by chain, top view.
Source organisms:
Primary publication:
Discovery of a novel class of boron-based antibacterials with activity against gram-negative bacteria.
Hernandez V, Crépin T, Palencia A, Cusack S, Akama T, Baker SJ, Bu W, Feng L, Freund YR, Liu L, Meewan M, Mohan M, Mao W, Rock FL, Sexton H, Sheoran A, Zhang Y, Zhang YK, Zhou Y, Nieman JA, Anugula MR, Keramane el M, Savariraj K, Reddy DS, Sharma R, Subedi R, Singh R, O'Leary A, Simon NL, De Marsh PL, Mushtaq S, Warner M, Livermore DM, Alley MR, Plattner JJ
Antimicrob Agents Chemother 57 1394-403 (2013)
PMID: 23295920

Function and Biology Details

Reaction catalysed: 
ATP + L-leucine + tRNA(Leu) = AMP + diphosphate + L-leucyl-tRNA(Leu)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-139770 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct RNA molecule
Macromolecules (2 distinct):
Leucine--tRNA ligase Chain: A
Molecule details ›
Chain: A
Length: 880 amino acids
Theoretical weight: 99.52 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P07813 (Residues: 1-860; Coverage: 100%)
Gene names: JW0637, b0642, leuS
Sequence domains:
Structure domains:
TRNALEU5 UAA ISOACCEPTOR Chain: B
Molecule details ›
Chain: B
Length: 87 nucleotides
Theoretical weight: 28.24 KDa
Source organism: Escherichia coli K-12
Expression system: Not provided
Sequence domains: tRNA

Ligands and Environments

1 bound ligand:
Ligand MG 2 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-3
Spacegroup: P212121
Unit cell:
a: 76.72Å b: 120.03Å c: 142.81Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.21 0.207 0.261
Expression systems:
  • Escherichia coli BL21
  • Not provided

Quick links

Citations

18 review citations

ESKAPEing the labyrinth of antibacterial discovery.
Tommasi et al. (2015)
17 more

4 mentions without citation

Personalized Medicine in Mitochondrial Health and Disease: Molecular Basis of Therapeutic Approaches Based on Nutritional Supplements and Their Analogs.
Tragni et al. (2022)
3 more