SMTL ID : 7qh8.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.92 Å

Oligo State

homo-dimer

Ligands

2 x LYS: LYSINE(Non-covalent)

LYS.1: 13 residues within 4Å: Chain A: G.232, A.233, A.254, E.256, R.278, M.292, E.294, Y.296, Y.448, E.450, G.495, T.496, G.497 8 PLIP interactions: 7 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:Y.448 Hydrogen bonds: A:G.232, A:G.232, A:E.256, A:Y.296, A:Y.296, K.1 Salt bridges: A:R.278 LYS.3: 13 residues within 4Å: Chain B: G.232, A.233, A.254, E.256, R.278, M.292, E.294, Y.296, Y.448, E.450, G.495, T.496, G.497 6 PLIP interactions: 5 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:Y.448 Hydrogen bonds: B:G.232, B:G.232, B:Y.296, K.3 Salt bridges: B:R.278

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: A.306, V.307, R.310, E.339, W.340, F.410 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.310, A:R.310, A:W.340, A:W.340 GOL.4: 6 residues within 4Å: Chain B: A.306, V.307, R.310, E.339, W.340, F.410 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.310, B:R.310, B:W.340, B:W.340 Water bridges: B:T.342

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