SMTL ID : 6hcw.1

Crystal Structure of Lysyl-tRNA Synthetase from Cryptosporidium parvum complexed with L-lysine and a difluoro cyclohexyl chromone ligand

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.46 Å

Oligo State

homo-dimer

Ligands

2 x LYS: LYSINE(Non-covalent)

LYS.1: 15 residues within 4Å: Chain A: G.225, A.226, A.247, E.249, R.271, E.287, Y.289, N.443, A.444, Y.445, E.447, G.492, W.493, G.494 Ligands: FYB.2 12 PLIP interactions: 12 interactions with chain A, Hydrophobic interactions: A:Y.445 Hydrogen bonds: A:G.225, A:E.249, A:E.287, A:Y.289, A:N.443, A:E.447 Water bridges: A:R.271, A:R.271, A:R.271, A:R.271 Salt bridges: A:R.271 LYS.3: 15 residues within 4Å: Chain B: G.225, A.226, A.247, E.249, R.271, E.287, Y.289, N.443, A.444, Y.445, E.447, G.492, W.493, G.494 Ligands: FYB.4 12 PLIP interactions: 1 Ligand-Ligand interactions, 11 interactions with chain B Hydrogen bonds: K.3, B:G.225, B:E.287, B:N.443, B:E.447 Hydrophobic interactions: B:Y.445 Water bridges: B:R.271, B:R.271, B:R.271, B:R.271, B:Y.445 Salt bridges: B:R.271

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

FYB.2: 18 residues within 4Å: Chain A: R.271, E.273, T.278, H.279, N.280, F.283, A.285, E.287, E.440, L.441, C.442, N.443, G.494, L.495, G.496, R.499, I.510 Ligands: LYS.1 15 PLIP interactions: 14 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:R.271, A:E.273, A:H.279, A:F.283, A:F.283, A:F.283, A:N.443 Hydrogen bonds: A:N.280 Water bridges: A:R.271, A:R.499, K.1 pi-Stacking: A:H.279, A:F.283 Halogen bonds: A:R.271, A:E.287 FYB.4: 17 residues within 4Å: Chain B: R.271, E.273, T.278, H.279, N.280, F.283, A.285, E.440, L.441, C.442, N.443, G.494, L.495, G.496, R.499, I.510 Ligands: LYS.3 15 PLIP interactions: 14 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:R.271, B:H.279, B:F.283, B:F.283, B:F.283, B:F.283, B:N.443 Hydrogen bonds: B:N.280 Water bridges: B:R.271, B:R.499, B:R.499, K.3 pi-Stacking: B:H.279, B:F.283 Halogen bonds: B:R.271

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

TRS.5: 2 residues within 4Å: Chain B: S.350, G.353 No protein-ligand interaction detected (PLIP)

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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