› 7d5c

X-ray diffraction
1.9Å resolution

IleRS in complex with a tRNA site inhibitor

Released:
DOI: 10.2210/pdb7d5c/pdb
PDB entry 7d5c coloured by chain, front view.
PDB entry 7d5c coloured by chain, side view.
PDB entry 7d5c coloured by chain, top view.
Source organism: Saccharomyces cerevisiae S288C
Primary publication:
Inhibitory mechanism of reveromycin A at the tRNA binding site of a class I synthetase.
Chen B, Luo S, Zhang S, Ju Y, Gu Q, Xu J, Yang XL, Zhou H
Nat Commun 12 1616 (2021)
PMID: 33712620

Function and Biology Details

Reaction catalysed: 
ATP + L-isoleucine + tRNA(Ile) = AMP + diphosphate + L-isoleucyl-tRNA(Ile)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-140654 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Isoleucine--tRNA ligase, cytoplasmic Chain: A
Molecule details ›
Chain: A
Length: 992 amino acids
Theoretical weight: 114.11 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: P09436 (Residues: 1-984; Coverage: 92%)
Gene names: ILS1, YBL0734, YBL076C
Sequence domains:

Ligands and Environments

3 bound ligands:
Ligand GVU 1 x GVU
Ligand GV6 1 x GV6
Ligand EDO 3 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U1
Spacegroup: C2
Unit cell:
a: 170.649Å b: 64.758Å c: 142.229Å
α: 90° β: 107.78° γ: 90°
R-values:
R R work R free
0.178 0.177 0.194
Expression system: Escherichia coli

Quick links

Citations

5 citation in other articles

The binding mode of orphan glycyl-tRNA synthetase with tRNA supports the synthetase classification and reveals large domain movements.
Han et al. (2023)
4 more

2 mentions without citation

Inhibitory mechanism of reveromycin A at the tRNA binding site of a class I synthetase.
Chen et al. (2021)
1 more