SMTL ID : 7evu.1

Co-crystal Structure of Toxoplasma gondii Prolyl tRNA Synthetase (TgPRS) in complex with HFG and JE6

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x HFG: 7-bromo-6-chloro-3-{3-[(2R,3S)-3-hydroxypiperidin-2-yl]-2-oxopropyl}quinazolin-4(3H)-one(Non-covalent)

HFG.1: 17 residues within 4Å: Chain A: P.87, E.88, V.89, P.108, T.109, E.111, R.140, W.157, E.159, H.161, F.204, T.228, H.230, S.258, W.259, G.260 Ligands: JE6.2 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:P.108, A:T.109, A:W.157, A:E.159, A:F.204 Hydrogen bonds: A:T.109, A:R.140 Water bridges: A:R.140 HFG.3: 17 residues within 4Å: Chain B: P.87, E.88, V.89, P.108, T.109, E.111, R.140, W.157, E.159, H.161, F.204, T.228, H.230, S.258, W.259, G.260 Ligands: JE6.4 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:W.157, B:E.159, B:F.204 Hydrogen bonds: B:T.109, B:T.109, B:R.140 Water bridges: B:R.140, B:R.140, B:R.140 Halogen bonds: B:E.88

2 x JE6: ~{N}-[4-[(3~{S})-3-cyano-3-cyclopropyl-2-oxidanylidene-pyrrolidin-1-yl]-6-methyl-pyridin-2-yl]-2-phenyl-ethanamide(Non-covalent)

JE6.2: 18 residues within 4Å: Chain A: R.140, E.142, K.144, Q.145, F.149, L.150, R.151, T.152, R.153, F.155, Q.225, A.226, A.227, T.228, G.260, T.262, R.264 Ligands: HFG.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:R.140, A:E.142, A:E.142, A:F.155, A:T.228, A:T.262 Hydrogen bonds: A:T.152, A:T.152 Water bridges: A:E.142 pi-Stacking: A:F.155 JE6.4: 20 residues within 4Å: Chain B: R.140, E.142, K.144, Q.145, P.146, F.149, L.150, R.151, T.152, R.153, F.155, Q.225, A.226, A.227, T.228, G.260, C.261, T.262, R.264 Ligands: HFG.3 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:E.142, B:E.142, B:R.153, B:F.155, B:T.228, B:T.262 Hydrogen bonds: B:R.151, B:T.152, B:T.152, B:T.262 pi-Stacking: B:F.155

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.5: 11 residues within 4Å: Chain A: Q.49, Y.65, R.107, W.135, S.137 Chain B: Q.49, Y.65, W.135, C.136, S.137, L.156 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Q.49, B:R.107, B:S.137, A:Q.49 Water bridges: B:W.135, B:C.136, A:R.107

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Manickam, Y. et al., Double drugging of prolyl-tRNA synthetase provides a new paradigm for anti-infective drug development. Plos Pathog. (2022)

Release Date

2022-03-09

Peptides

Prolyl-tRNA synthetase (ProRS): AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Prolyl-tRNA synthetase (ProRS)

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