SMTL ID : 6kct.1 (1 other biounit)

Crystal structure of plasmodium lysyl-tRNA synthetase in complex with a cladosporin derivative 5

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.25 Å

Oligo State

homo-dimer

Ligands

2 x D5O: 3-(cyclohexylmethyl)-6,8-bis(oxidanyl)isochromen-1-one(Non-covalent)

D5O.1: 15 residues within 4Å: Chain A: R.255, E.257, T.262, H.263, N.264, F.267, E.425, V.426, L.427, N.428, G.479, G.481, R.484, I.495 Ligands: LYS.2 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:H.263, A:E.425, A:N.428 Hydrogen bonds: A:E.257, A:N.264, 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 D5O.3: 15 residues within 4Å: Chain B: R.255, E.257, T.262, H.263, N.264, F.267, E.425, V.426, L.427, N.428, G.479, G.481, R.484, I.495 Ligands: LYS.4 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:H.263, B:F.267, B:E.425 Hydrogen bonds: B:N.264, B:N.264 Salt bridges: B:R.484 pi-Stacking: B:H.263, B:F.267, B:F.267 pi-Cation interactions: B:R.484

2 x LYS: LYSINE(Non-covalent)

LYS.2: 14 residues within 4Å: Chain A: G.209, A.210, A.231, E.233, R.255, E.271, Y.273, N.428, Y.430, E.432, G.477, L.478, G.479 Ligands: D5O.1 8 PLIP interactions: 8 interactions with chain A, Hydrophobic interactions: A:E.271, A:N.428, A:Y.430 Hydrogen bonds: A:G.209, A:E.233, A:Y.273, A:N.428 Salt bridges: A:R.255 LYS.4: 14 residues within 4Å: Chain B: G.209, A.210, A.231, E.233, R.255, E.271, Y.273, N.428, Y.430, E.432, G.477, L.478, G.479 Ligands: D5O.3 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:Y.430 Hydrogen bonds: B:G.209, B:N.428, B:E.432 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
A

B
B

Lysine--tRNA ligase

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