› 6l4q

X-ray diffraction
3.1Å resolution

Crystal Structure of Lysyl-tRNA Synthetase from Plasmodium falciparum complexed with L-lysine and Clado-B

Released:
DOI: 10.2210/pdb6l4q/pdb
PDB entry 6l4q coloured by chain, front view.
PDB entry 6l4q coloured by chain, side view.
PDB entry 6l4q coloured by chain, top view.
Source organism: Plasmodium falciparum 3D7
Primary publication:
Crystal Structure of Lysyl-tRNA Synthetase from Plasmodium falciparum complexed with L-lysine and Cladosporin inhibitor, Cla-B
Babbar P, Sato M, Manickam Y, Mishra S, Harlos K, Gupta S, Parvez S, Kikuchi H, Sharma A
Chembiochem (2021)

Function and Biology Details

Reaction catalysed: 
ATP + L-lysine + tRNA(Lys) = AMP + diphosphate + L-lysyl-tRNA(Lys)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-184744 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Lysine--tRNA ligase Chains: A, B
Molecule details ›
Chains: A, B
Length: 507 amino acids
Theoretical weight: 58.71 KDa
Source organism: Plasmodium falciparum 3D7
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8IDJ8 (Residues: 77-583; Coverage: 87%)
Gene name: PF3D7_1350100
Sequence domains:

Ligands and Environments

2 bound ligands:
Ligand E5R 2 x E5R
Ligand LYS 2 x LYS
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04
Spacegroup: P212121
Unit cell:
a: 52.181Å b: 121.833Å c: 179.695Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.235 0.232 0.286
Expression system: Escherichia coli

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