› 9dpb

Electron Microscopy
2.9Å resolution

Human LysRS bound to unmodified tRNA-Lys3 (Undocked State, AMPCPP bound)

Released:
DOI: 10.2210/pdb9dpb/pdb
PDB entry 9dpb coloured by chain, front view.
PDB entry 9dpb coloured by chain, side view.
PDB entry 9dpb coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural basis for aminoacylation of cellular modified tRNALys3 by human lysyl-tRNA synthetase.
Devarkar SC, Budding CR, Pathirage C, Kavoor A, Herbert C, Limbach PA, Musier-Forsyth K, Xiong Y
Nucleic Acids Res 53 (2025)
PMID: 40036503
Related structures: EMD-47101

Function and Biology Details

Reaction catalysed: 
ATP + L-lysine + tRNA(Lys) = AMP + diphosphate + L-lysyl-tRNA(Lys)
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domain:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-290767 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct RNA molecule
Macromolecules (2 distinct):
Lysine--tRNA ligase Chains: A, B
Molecule details ›
Chains: A, B
Length: 597 amino acids
Theoretical weight: 68.14 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q15046 (Residues: 1-597; Coverage: 100%)
Gene names: KARS, KARS1, KIAA0070
Sequence domains:
tRNA-Lys3 (unmodified) Chain: C
Molecule details ›
Chain: C
Length: 76 nucleotides
Theoretical weight: 24.45 KDa
Source organism: Homo sapiens
Expression system: Not provided
Sequence domains: tRNA

Ligands and Environments

4 bound ligands:
Ligand LYS 2 x LYS
Ligand APC 2 x APC
Ligand MG 4 x MG
Ligand NA 1 x NA
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this EM entry.
Resolution: 2.9Å
Relevant EMDB volumes: EMD-47101
Expression systems:
  • Escherichia coli
  • Not provided

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