SMTL ID : 9dpl.1

Human LysRS bound to cellular modified tRNA-Lys3 and AIMP2

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-mer

Ligands

2 x LYS: LYSINE(Non-covalent)

LYS.1: 11 residues within 4Å: Chain A: E.301, E.339, Y.341, N.497, Y.499, E.501, G.546, W.547, G.548 Chain C: A.76 Ligands: AMP.2 6 PLIP interactions: 6 interactions with chain A, Hydrophobic interactions: A:E.339, A:Y.499 Hydrogen bonds: A:E.301, A:E.339, A:Y.341, A:N.497 LYS.3: 11 residues within 4Å: Chain B: G.277, A.299, E.301, E.339, Y.341, N.497, Y.499, E.501, G.546, W.547 Ligands: AMP.4 4 PLIP interactions: 4 interactions with chain B, Hydrophobic interactions: B:Y.499 Hydrogen bonds: B:E.301, B:Y.341, B:N.497

2 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.2: 13 residues within 4Å: Chain A: R.323, T.330, H.331, N.332, F.335, T.337, E.494, I.495, N.497, G.550, R.553 Chain C: A.76 Ligands: LYS.1 13 PLIP interactions: 10 interactions with chain A, 3 Ligand-Ligand interactions Hydrogen bonds: A:R.323, A:N.332, A:N.332, A:E.494, A:N.497, A:G.550, K.1, K.1, K.1 Salt bridges: A:R.323 pi-Stacking: A:F.335, A:F.335 pi-Cation interactions: A:R.553 AMP.4: 10 residues within 4Å: Chain B: R.323, E.325, H.331, N.332, F.335, E.494, G.550, R.553, I.564 Ligands: LYS.3 10 PLIP interactions: 8 interactions with chain B, 2 Ligand-Ligand interactions Hydrogen bonds: B:E.325, B:N.332, B:G.550, B:R.553, B:R.553, K.3, K.3 Salt bridges: B:R.323 pi-Stacking: B:F.335, B:F.335

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

NA.5: 1 residues within 4Å: Chain C: G.45 No protein-ligand interaction detected (PLIP) NA.6: 2 residues within 4Å: Chain C: U.8, U.12 No protein-ligand interaction detected (PLIP)

2 x MG: MAGNESIUM ION(Non-functional Binders)

MG.7: 1 residues within 4Å: Chain C: A.29 No protein-ligand interaction detected (PLIP) MG.8: 5 residues within 4Å: Chain C: G.5, G.6, A.7, U.66, U.67 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
Aminoacyl tRNA synthase complex-interacting multifunctional protein 2: DE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

D
D

E
E

Lysine--tRNA ligase

Aminoacyl tRNA synthase complex-interacting multifunctional protein 2

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