SMTL ID : 6kcn.2 (1 other biounit)

Crystal structure of plasmodium lysyl-tRNA synthetase in complex with a cladosporin derivative 4

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

2 x D5F: 3-[[(1~{S},3~{S})-3-methylcyclohexyl]methyl]-6,8-bis(oxidanyl)isochromen-1-one(Non-covalent)

D5F.1: 17 residues within 4Å: Chain A: R.255, E.257, T.262, H.263, N.264, F.267, S.269, E.425, V.426, L.427, N.428, G.479, L.480, G.481, R.484, I.495 Ligands: LYS.4 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:H.263, A:F.267, A:E.425, A:N.428 Hydrogen bonds: A:E.257, A:N.264, A:N.264 Water bridges: A:R.255, A:N.264 Salt bridges: A:R.484 pi-Stacking: A:H.263, A:F.267, A:F.267 pi-Cation interactions: A:R.484 D5F.5: 17 residues within 4Å: Chain B: R.255, E.257, T.262, H.263, N.264, F.267, S.269, E.425, V.426, L.427, N.428, G.479, L.480, G.481, R.484, I.495 Ligands: LYS.6 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:H.263, B:F.267 Hydrogen bonds: B:E.257, B:N.264, B:N.264 Water bridges: B:R.255, B:E.257 Salt bridges: B:R.484 pi-Stacking: B:H.263, B:F.267, B:F.267 pi-Cation interactions: B:R.484

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: K.246, W.274, A.275, Y.276 Chain B: E.32, R.33 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:E.32, B:R.33, A:K.246, A:K.246 GOL.3: 7 residues within 4Å: Chain A: R.187, E.197, E.199, I.250 Chain B: I.183, R.187, I.250 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:E.197, A:E.199, A:I.250, B:R.187, B:R.187, B:I.250

2 x LYS: LYSINE(Non-covalent)

LYS.4: 14 residues within 4Å: Chain A: G.209, A.210, A.231, E.233, R.255, E.271, Y.273, N.428, A.429, Y.430, E.432, G.477, G.479 Ligands: D5F.1 8 PLIP interactions: 8 interactions with chain A, Hydrophobic interactions: A:Y.430 Hydrogen bonds: A:G.209, A:E.233, A:N.428, A:E.432 Water bridges: A:R.255, A:R.255 Salt bridges: A:R.255 LYS.6: 14 residues within 4Å: Chain B: G.209, A.210, A.231, E.233, R.255, E.271, Y.273, N.428, A.429, Y.430, E.432, G.477, G.479 Ligands: D5F.5 10 PLIP interactions: 9 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:Y.430 Hydrogen bonds: B:G.209, B:G.209, B:Y.273, B:N.428, B:E.432, K.6 Water bridges: B:R.255, B:R.255 Salt bridges: B:R.255

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhou, J. et al., Atomic Resolution Analyses of Isocoumarin Derivatives for Inhibition of Lysyl-tRNA Synthetase. Acs Chem.Biol. (2020)

Release Date

2020-04-08

Peptides

Lysine--tRNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Lysine--tRNA ligase

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