› 5ekd

X-ray diffraction
1.82Å resolution

Human mitochondrial tryptophanyl-tRNA synthetase bound by indolmycin and Mn*ATP.

Released:
DOI: 10.2210/pdb5ekd/pdb
PDB entry 5ekd coloured by chain, front view.
PDB entry 5ekd coloured by chain, side view.
PDB entry 5ekd coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Williams TL, Carter Jr CW

Function and Biology Details

Reaction catalysed: 
ATP + L-tryptophan + tRNA(Trp) = AMP + diphosphate + L-tryptophyl-tRNA(Trp)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-193719 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Tryptophan--tRNA ligase, mitochondrial Chains: A, B
Molecule details ›
Chains: A, B
Length: 343 amino acids
Theoretical weight: 38.04 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9UGM6 (Residues: 18-360; Coverage: 95%)
Gene name: WARS2
Sequence domains: tRNA synthetases class I (W and Y)
Structure domains:

Ligands and Environments

4 bound ligands:
Ligand 5BX 2 x 5BX
Ligand ATP 2 x ATP
Ligand MN 4 x MN
Ligand GOL 2 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: C2
Unit cell:
a: 58.289Å b: 78.087Å c: 153.996Å
α: 90° β: 96.55° γ: 90°
R-values:
R R work R free
0.172 0.17 0.207
Expression system: Escherichia coli

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