SMTL ID : 7qhn.1

CRYSTAL STRUCTURE OF LYSYL-TRNA SYNTHETASE FROM Mycobacterium tuberculosis COMPLEXED WITH L-LYSINE and an inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.58 Å

Oligo State

homo-dimer

Ligands

2 x LYS: LYSINE(Non-covalent)

LYS.1: 15 residues within 4Å: Chain A: G.232, A.233, A.254, E.256, R.278, M.292, E.294, Y.296, T.446, Y.448, E.450, G.495, T.496, G.497 Ligands: C6I.2 10 PLIP interactions: 9 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:E.294, A:T.446, A:Y.448 Hydrogen bonds: A:G.232, A:G.232, A:E.256, A:Y.296, A:E.450, K.1 Salt bridges: A:R.278 LYS.3: 15 residues within 4Å: Chain B: G.232, A.233, A.254, E.256, R.278, M.292, E.294, Y.296, T.446, Y.448, E.450, G.495, T.496, G.497 Ligands: C6I.4 8 PLIP interactions: 7 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:E.294, B:T.446, B:Y.448 Hydrogen bonds: B:G.232, B:G.232, B:E.450, K.3 Salt bridges: B:R.278

2 x C6I: 6-azanyl-2-cyclohexyl-4-fluoranyl-1~{H}-pyrrolo[3,4-c]pyridin-3-one(Non-covalent)

C6I.2: 16 residues within 4Å: Chain A: R.278, T.285, H.286, S.287, F.290, M.292, E.443, L.444, A.445, T.446, G.497, M.498, G.499, R.502, I.512 Ligands: LYS.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.287, A:S.287 pi-Stacking: A:H.286, A:F.290, A:F.290 pi-Cation interactions: A:R.502 C6I.4: 16 residues within 4Å: Chain B: R.278, T.285, H.286, S.287, F.290, M.292, E.443, L.444, A.445, T.446, G.497, M.498, G.499, R.502, I.512 Ligands: LYS.3 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.287, B:S.287 pi-Stacking: B:H.286, B:F.290, B:F.290 pi-Cation interactions: B:R.502

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Green, S.R. et al., Lysyl-tRNA synthetase, a target for urgently needed M. tuberculosis drugs. Nat Commun (2022)

Release Date

2022-10-19

Peptides

Lysine--tRNA ligase 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Lysine--tRNA ligase 1

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