› 7y3s

X-ray diffraction
2.6Å resolution

Controlling fibrosis using compound with novel binding mode to prolyl-tRNA synthetase 1

Released:
DOI: 10.2210/pdb7y3s/pdb
Model geometry
Fit model/data
PDB entry 7y3s coloured by chain, front view.
PDB entry 7y3s coloured by chain, side view.
PDB entry 7y3s coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Control of fibrosis with enhanced safety via asymmetric inhibition of prolyl-tRNA synthetase 1.
Yoon I, Kim S, Cho M, You KA, Son J, Lee C, Suh JH, Bae DJ, Kim JM, Oh S, Park S, Kim S, Cho SH, Park S, Bang K, Seo M, Kim JH, Lee B, Park JS, Hwang KY, Kim S
OpenAccess logo EMBO Mol Med 15 e16940 (2023)
PMID: 37212275

Function and Biology Details

Reactions catalysed: 
ATP + L-proline + tRNA(Pro) = AMP + diphosphate + L-prolyl-tRNA(Pro)
ATP + L-glutamate + tRNA(Glu) = AMP + diphosphate + L-glutamyl-tRNA(Glu)
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-139773 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Bifunctional glutamate/proline--tRNA ligase Chains: A, B
Molecule details ›
Chains: A, B
Length: 498 amino acids
Theoretical weight: 56.68 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P07814 (Residues: 1015-1512; Coverage: 33%)
Gene names: EPRS, EPRS1, GLNS, PARS, PIG32, QARS, QPRS
Sequence domains:

Ligands and Environments

4 bound ligands:
Ligand F9C 2 x F9C
Ligand ATP 2 x ATP
Ligand MG 4 x MG
Ligand ZN 1 x ZN
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: PAL/PLS BEAMLINE 11C
Spacegroup: P21
Unit cell:
a: 71.897Å b: 92.017Å c: 87.326Å
α: 90° β: 108.16° γ: 90°
R-values:
R R work R free
0.206 0.203 0.25
Expression system: Escherichia coli

Quick links

Citations

2 citation in other articles

Control of fibrosis with enhanced safety via asymmetric inhibition of prolyl-tRNA synthetase 1.
Yoon et al. (2023)
1 more