SMTL ID : 9dpb.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

2 x LYS: LYSINE(Non-covalent)

LYS.1: 11 residues within 4Å: Chain A: E.301, K.305, E.339, Y.341, L.472, N.497, Y.499, E.501, G.546, W.547, G.548 7 PLIP interactions: 7 interactions with chain A, Hydrophobic interactions: A:Y.499, A:Y.499 Hydrogen bonds: A:E.301, A:E.301, A:K.305, A:N.497, A:E.501 LYS.5: 10 residues within 4Å: Chain B: E.301, E.339, Y.341, N.497, Y.499, E.501, G.546, W.547, G.548 Ligands: MG.7 7 PLIP interactions: 7 interactions with chain B, Hydrophobic interactions: B:Y.499, B:Y.499 Hydrogen bonds: B:E.339, B:Y.341, B:Y.499, B:E.501, B:G.546

2 x APC: DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER(Non-covalent)

APC.2: 9 residues within 4Å: Chain A: R.323, E.325, H.331, N.332, F.335, E.494, G.550, R.553 Ligands: MG.3 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.325, A:H.331, A:N.332, A:E.494, A:R.553 pi-Stacking: A:F.335, A:F.335 APC.6: 10 residues within 4Å: Chain B: R.323, T.330, H.331, N.332, F.335, E.494, G.550, R.553, I.564 Ligands: MG.7 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.332, B:N.332, B:R.553, B:R.553 Salt bridges: B:H.331 pi-Stacking: B:F.335, B:F.335

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: E.494, I.495, N.497 Ligands: APC.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.494 MG.4: 2 residues within 4Å: Chain A: E.487, E.494 No protein-ligand interaction detected (PLIP) MG.7: 5 residues within 4Å: Chain B: E.494, I.495, N.497 Ligands: LYS.5, APC.6 No protein-ligand interaction detected (PLIP) MG.8: 2 residues within 4Å: Chain B: E.487, E.494 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.487

1 x NA: SODIUM ION(Non-functional Binders)

NA.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Devarkar, S.C. et al., Structural basis for aminoacylation of cellular modified tRNALys3 by human lysyl-tRNA synthetase. Nucleic Acids Res. (2025)

Release Date

2025-03-12

Peptides

Lysine--tRNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Lysine--tRNA ligase

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