SMTL ID : 6hcu.1

Crystal Structure of Lysyl-tRNA Synthetase from Plasmodium falciparum bound to a difluoro cyclohexyl chromone ligand

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.62 Å

Oligo State

homo-dimer

Ligands

2 x FYB: ~{N}-[[4,4-bis(fluoranyl)-1-oxidanyl-cyclohexyl]methyl]-6-fluoranyl-4-oxidanylidene-chromene-2-carboxamide(Non-covalent)

FYB.1: 17 residues within 4Å: Chain A: R.254, E.256, G.257, T.261, H.262, N.263, F.266, S.268, E.424, L.426, N.427, G.478, L.479, G.480, R.483, I.494 Ligands: TRS.6 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:R.254, A:H.262, A:F.266, A:F.266, A:F.266, A:F.266, A:N.427 Hydrogen bonds: A:N.263 Water bridges: A:R.254, A:R.483 pi-Stacking: A:H.262, A:F.266 Halogen bonds: A:R.254 FYB.7: 15 residues within 4Å: Chain B: R.254, E.256, T.261, H.262, N.263, F.266, E.424, L.426, N.427, G.478, L.479, G.480, R.483, I.494 Ligands: TRS.9 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:H.262, B:F.266, B:N.427 Hydrogen bonds: B:N.263 Water bridges: B:R.254, B:E.424, B:R.483 pi-Stacking: B:H.262, B:F.266 Halogen bonds: B:R.254

1 x LYS: LYSINE(Non-covalent)

LYS.2: 8 residues within 4Å: Chain A: K.245, W.273, A.274, Y.275, A.276 Chain B: K.29, E.31, R.32 7 PLIP interactions: 5 interactions with chain B, 1 Ligand-Ligand interactions, 1 interactions with chain A Hydrogen bonds: B:E.31, K.2 Water bridges: B:R.32, B:R.32, B:R.32 Salt bridges: B:K.29 Hydrophobic interactions: A:W.273

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 5 residues within 4Å: Chain A: R.159, F.500 Chain B: P.200, N.203, P.234 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.159 Water bridges: B:P.200

1 x HIS: HISTIDINE(Non-covalent)

HIS.4: 3 residues within 4Å: Chain A: H.359, H.379, F.380 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.380 pi-Stacking: A:H.379

4 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.5: 8 residues within 4Å: Chain A: I.182, R.186, E.196, I.249 Chain B: R.186, E.196, E.198, I.249 11 PLIP interactions: 7 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:R.186, B:E.196, B:E.198, B:I.249, A:R.186, A:R.186, A:E.196 Water bridges: B:E.198, B:E.248, B:I.249, A:I.249 TRS.6: 9 residues within 4Å: Chain A: A.230, E.232, E.270, Y.272, N.427, Y.429, L.477, G.478 Ligands: FYB.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.270, A:Y.272, A:Y.272, A:N.427, A:Y.429 TRS.8: 8 residues within 4Å: Chain A: K.29, R.32 Chain B: K.245, W.273, A.274, Y.275, A.276, D.280 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:K.245, B:W.273, A:K.29, A:K.29, A:R.32, A:R.32 TRS.9: 9 residues within 4Å: Chain B: E.232, E.270, Y.272, N.427, Y.429, G.476, L.477, G.478 Ligands: FYB.7 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.232, B:E.232, B:Y.272, B:N.427

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Baragana, B. et al., Lysyl-tRNA synthetase as a drug target in malaria and cryptosporidiosis. Proc.Natl.Acad.Sci.USA (2019)

Release Date

2019-04-03

Peptides

Lysine--tRNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Lysine--tRNA ligase

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