SMTL ID : 7zog.1 (1 other biounit)

Crystal structure of Cryptosporidium parvum -Plasmodium falciparum mutant lysyl tRNA synthetase in complex with inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x JE5: 8-[[4-[2-[2-[2-[2-[(azanylidene-$l^{4}-azanylidene)amino]ethoxy]ethoxy]ethoxy]ethylcarbamoyl]phenyl]sulfonylamino]-~{N}-(cyclohexylmethyl)-6-fluoranyl-4-oxidanylidene-chromene-2-carboxamide(Non-covalent)

JE5.1: 25 residues within 4Å: Chain A: A.227, A.228, R.229, R.271, E.273, G.274, T.278, H.279, N.280, P.281, F.283, S.285, E.440, L.441, C.442, N.443, E.471, G.494, L.495, G.496, R.499, I.510 Chain B: N.236, E.237 Ligands: LYS.4 20 PLIP interactions: 19 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:R.271, A:E.273, A:H.279, A:F.283, A:F.283, A:N.443 Hydrogen bonds: A:R.229, A:R.271, A:E.273, A:E.273, A:N.280, B:E.237 Water bridges: A:A.227, A:H.279, A:R.499, A:R.499, A:R.499 pi-Stacking: A:H.279, A:F.283 Halogen bonds: A:R.271 JE5.6: 25 residues within 4Å: Chain A: N.236, E.237, E.239 Chain B: A.227, A.228, R.271, E.273, G.274, T.278, H.279, N.280, P.281, F.283, S.285, E.440, L.441, C.442, N.443, E.471, G.494, L.495, G.496, R.499, I.510 Ligands: LYS.7 20 PLIP interactions: 18 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:R.271, B:E.273, B:H.279, B:F.283, B:F.283, B:N.443 Hydrogen bonds: B:R.271, B:E.273, B:G.274, B:N.280, A:E.237, A:E.239 Water bridges: B:A.227, B:H.279, B:R.499, B:R.499, B:R.499 pi-Stacking: B:H.279, B:F.283 Halogen bonds: B:R.271

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 8 residues within 4Å: Chain A: T.80, F.95, K.100, M.183, L.184, N.185, E.186, R.189 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.80, A:K.100, A:M.183, A:E.186, A:R.189, A:R.189 Water bridges: A:L.184 GOL.3: 3 residues within 4Å: Chain A: N.61, V.62, E.63 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.63, A:E.63 Water bridges: A:E.63, A:E.63 GOL.5: 8 residues within 4Å: Chain B: T.80, F.95, K.100, M.183, L.184, N.185, E.186, R.189 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:T.80, B:T.80, B:K.100, B:M.183, B:E.186, B:R.189, B:R.189

2 x LYS: LYSINE(Non-covalent)

LYS.4: 14 residues within 4Å: Chain A: G.225, 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: JE5.1 5 PLIP interactions: 5 interactions with chain A, Hydrophobic interactions: A:Y.445 Hydrogen bonds: A:G.225, A:N.443, A:E.447 Water bridges: A:R.271 LYS.7: 14 residues within 4Å: Chain B: G.225, 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: JE5.6 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:Y.445 Hydrogen bonds: B:G.225, B:E.249, B:Y.289, B:N.443, B:E.447 Water bridges: B:R.271, B:Y.445

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Milne, R. et al., Toolkit of Approaches To Support Target-Focused Drug Discovery for Plasmodium falciparum Lysyl tRNA Synthetase. Acs Infect Dis. (2022)

Release Date

2022-09-07

Peptides

Lysine-tRNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Lysine-tRNA ligase

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