SMTL ID : 7f9u.1 (1 other biounit)

Toxoplasma gondii Prolyl-tRNA Synthetase (TgPRS) in Complex with inhibitor T35 and Halofuginone

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 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: 14 residues within 4Å: Chain A: V.89, P.108, T.109, E.111, R.140, W.157, E.159, H.161, F.204, T.228, H.230, W.259, G.260 Ligands: BR.3 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:T.109, A:W.157, A:W.157, A:E.159, A:F.204 Hydrogen bonds: A:T.109, A:T.109, A:R.140 HFG.9: 15 residues within 4Å: Chain B: E.88, V.89, P.108, T.109, E.111, R.140, W.157, E.159, H.161, F.204, T.228, H.230, W.259, G.260 Ligands: BR.11 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:P.108, B:P.108, B:W.157, B:E.159, B:F.204 Hydrogen bonds: B:T.109, B:T.109, B:R.140

2 x 1TI: 4-[(3S)-3-cyano-3-(1-methylcyclopropyl)-2-oxidanylidene-pyrrolidin-1-yl]-N-[[3-fluoranyl-5-(1-methylpyrazol-4-yl)phenyl]methyl]-6-methyl-pyridine-2-carboxamide(Non-covalent)

1TI.2: 21 residues within 4Å: Chain A: R.140, E.142, K.144, Q.145, P.146, F.149, L.150, R.151, T.152, R.153, F.155, W.157, Q.225, A.226, A.227, T.228, G.260, C.261, T.262, R.264 Ligands: BR.3 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:E.142, A:R.151, A:F.155, A:W.157, A:T.228, A:T.262 Hydrogen bonds: A:E.142, A:T.152, A:T.152, A:T.262, A:R.264 Water bridges: A:Y.185 pi-Stacking: A:F.155 pi-Cation interactions: A:R.151 1TI.10: 21 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, W.157, Q.225, A.226, A.227, T.228, G.260, C.261, T.262, R.264 Ligands: BR.11 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:E.142, B:E.142, B:K.144, B:R.151, B:F.155, B:W.157, B:T.228 Hydrogen bonds: B:T.152, B:T.152, B:T.262, B:R.264 Water bridges: B:T.262 pi-Stacking: B:F.155 pi-Cation interactions: B:R.151

2 x BR: BROMIDE ION(Non-covalent)

BR.3: 3 residues within 4Å: Chain A: R.140 Ligands: HFG.1, 1TI.2 Ligand excluded by PLIP BR.11: 3 residues within 4Å: Chain B: R.140 Ligands: HFG.9, 1TI.10 Ligand excluded by PLIP

2 x CA: CALCIUM ION(Non-covalent)

CA.4: 2 residues within 4Å: Chain A: E.172, D.176 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.176 CA.5: 1 residues within 4Å: Chain A: H.423 No protein-ligand interaction detected (PLIP)

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 3 residues within 4Å: Chain A: Q.289, D.320, R.322 Ligand excluded by PLIP CL.7: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain A: N.301, T.302, G.303, E.304 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Malhotra, N. et al., TgPRS with double inhibitors. To Be Published

Release Date

2022-07-06

Peptides

Prolyl-tRNA synthetase (ProRS): AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

Prolyl-tRNA synthetase (ProRS)

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