› 5y6l

X-ray diffraction
2.9Å resolution

A subcomplex crystal structure of human cytosolic aspartyl-tRNA synthetase and heterotetrameric glutathione transferase-homology domains in multi-tRNA synthetase complex

Released:
DOI: 10.2210/pdb5y6l/pdb
PDB entry 5y6l coloured by chain, front view.
PDB entry 5y6l coloured by chain, side view.
PDB entry 5y6l coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Cho HY, Lee HJ, Kang BS

Function and Biology Details

Reactions catalysed: 
ATP + L-methionine + tRNA(Met) = AMP + diphosphate + L-methionyl-tRNA(Met)
ATP + L-proline + tRNA(Pro) = AMP + diphosphate + L-prolyl-tRNA(Pro)
ATP + L-glutamate + tRNA(Glu) = AMP + diphosphate + L-glutamyl-tRNA(Glu)
ATP + L-aspartate + tRNA(Asp) = AMP + diphosphate + L-aspartyl-tRNA(Asp)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero pentamer (preferred)
PDBe Complex ID:
PDB-CPX-128903 (preferred)
Entry contents:
5 distinct polypeptide molecules
Macromolecules (5 distinct):
Methionine--tRNA ligase, cytoplasmic Chain: A
Molecule details ›
Chain: A
Length: 232 amino acids
Theoretical weight: 25.96 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P56192 (Residues: 1-224; Coverage: 25%)
Gene names: MARS, MARS1
Sequence domains:
Structure domains:
Eukaryotic translation elongation factor 1 epsilon-1 Chain: B
Molecule details ›
Chain: B
Length: 186 amino acids
Theoretical weight: 21.23 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O43324 (Residues: 1-174; Coverage: 100%)
Gene names: AIMP3, EEF1E1, P18
Sequence domains: Glutathione S-transferase, C-terminal domain
Structure domains:
Bifunctional glutamate/proline--tRNA ligase Chain: C
Molecule details ›
Chain: C
Length: 175 amino acids
Theoretical weight: 19.31 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P07814 (Residues: 1-175; Coverage: 12%)
Gene names: EPRS, EPRS1, GLNS, PARS, PIG32, QARS, QPRS
Structure domains: Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2
Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 Chain: D
Molecule details ›
Chain: D
Length: 240 amino acids
Theoretical weight: 26.79 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q13155 (Residues: 89-320; Coverage: 73%)
Gene names: AIMP2, JTV1, PRO0992
Sequence domains:
Structure domains: Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2
Aspartate--tRNA ligase, cytoplasmic Chain: E
Molecule details ›
Chain: E
Length: 521 amino acids
Theoretical weight: 59.38 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P14868 (Residues: 1-501; Coverage: 100%)
Gene names: DARS, DARS1, PIG40
Sequence domains:

Ligands and Environments

1 bound ligand:
Ligand PO4 2 x PO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PAL/PLS BEAMLINE 7A (6B, 6C1)
Spacegroup: P212121
Unit cell:
a: 84.535Å b: 98.413Å c: 125.919Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.183 0.176 0.252
Expression systems:
  • Escherichia coli
  • Escherichia coli BL21(DE3)

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