SMTL ID : 6l4q.1

Crystal Structure of Lysyl-tRNA Synthetase from Plasmodium falciparum complexed with L-lysine and Clado-B

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

homo-dimer

Ligands

2 x E5R: (3R)-3-[[(3R)-3-methylpiperidin-1-yl]methyl]-6,8-bis(oxidanyl)-3,4-dihydroisochromen-1-one(Non-covalent)

E5R.1: 14 residues within 4Å: Chain A: R.254, E.256, T.261, H.262, N.263, F.266, E.424, N.427, G.478, L.479, G.480, R.483, I.494 Ligands: LYS.2 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:H.262, A:N.427 Hydrogen bonds: A:E.256, A:N.263, A:N.263, A:N.263 Salt bridges: A:E.424, A:R.483 pi-Stacking: A:H.262, A:F.266 E5R.3: 14 residues within 4Å: Chain B: R.254, E.256, T.261, H.262, N.263, F.266, E.424, V.425, L.426, G.478, L.479, G.480, R.483 Ligands: LYS.4 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:H.262, B:F.266 Hydrogen bonds: B:N.263, B:N.263 Salt bridges: B:E.424, B:R.483 pi-Cation interactions: B:H.262

2 x LYS: LYSINE(Non-covalent)

LYS.2: 12 residues within 4Å: Chain A: G.208, A.230, E.232, R.254, E.270, Y.272, N.427, Y.429, E.431, G.476, G.478 Ligands: E5R.1 7 PLIP interactions: 7 interactions with chain A, Hydrophobic interactions: A:Y.429 Hydrogen bonds: A:G.208, A:E.232, A:Y.272, A:N.427, A:E.431 Salt bridges: A:R.254 LYS.4: 11 residues within 4Å: Chain B: A.230, E.232, E.270, Y.272, N.427, Y.429, E.431, G.476, L.477, G.478 Ligands: E5R.3 7 PLIP interactions: 1 Ligand-Ligand interactions, 6 interactions with chain B Hydrogen bonds: K.4, B:G.208, B:R.254, B:E.270, B:N.427, B:E.431 Hydrophobic interactions: B:Y.429

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Babbar, P. et al., Crystal Structure of Lysyl-tRNA Synthetase from Plasmodium falciparum complexed with L-lysine and Cladosporin inhibitor, Cla-B. Chembiochem (2021)

Release Date

2021-05-19

Peptides

Lysine--tRNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

Lysine--tRNA ligase

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