SMTL ID : 5xih.2 (1 other biounit)

Crystal Structure of Toxoplasma gondii Prolyl-tRNA Synthetase (TgPRS) in complex with inhibitor 5

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

2 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.1: 15 residues within 4Å: Chain A: R.140, E.142, F.149, L.150, R.151, T.152, F.155, Q.225, A.226, T.228, T.262, R.264 Ligands: MG.2, MG.3, 86U.4 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:R.140, A:R.151, A:R.151, A:T.152, A:T.152, A:Q.225, A:R.264 Water bridges: A:K.144, A:K.144, A:K.144, A:K.144, A:Q.225, A:T.262, A:R.264 Salt bridges: A:R.140 pi-Stacking: A:F.155, A:F.155 ANP.8: 17 residues within 4Å: Chain B: R.140, E.142, K.144, F.149, L.150, R.151, T.152, F.155, Q.225, A.226, A.227, T.228, T.262, R.264 Ligands: MG.9, MG.10, 86U.11 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:R.140, B:K.144, B:K.144, B:R.151, B:R.151, B:T.152, B:T.152, B:A.226 Water bridges: B:K.144, B:K.144, B:K.144, B:K.144, B:K.144, B:T.262, B:R.264, B:R.264 Salt bridges: B:R.140 pi-Stacking: B:F.155, B:F.155

4 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.2: 2 residues within 4Å: Chain A: E.202 Ligands: ANP.1 No protein-ligand interaction detected (PLIP) MG.3: 3 residues within 4Å: Chain A: R.140, R.151 Ligands: ANP.1 No protein-ligand interaction detected (PLIP) MG.9: 1 residues within 4Å: Ligands: ANP.8 No protein-ligand interaction detected (PLIP) MG.10: 4 residues within 4Å: Chain B: R.140, K.144, R.151 Ligands: ANP.8 No protein-ligand interaction detected (PLIP)

2 x 86U: 6,7-bis(fluoranyl)-3-[3-[(2R)-3-oxidanylidenepiperidin-2-yl]propyl]quinazolin-4-one(Non-covalent)

86U.4: 16 residues within 4Å: Chain A: F.85, E.88, V.89, P.108, T.109, E.111, R.140, W.157, H.161, F.204, T.228, H.230, S.258, W.259, G.260 Ligands: ANP.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:P.108, A:T.109, A:W.157, A:F.204 Hydrogen bonds: A:E.111 Water bridges: A:R.140 pi-Stacking: A:F.85, A:F.85 86U.11: 15 residues within 4Å: Chain B: F.85, E.88, V.89, P.108, T.109, E.111, R.140, H.161, F.204, T.228, H.230, S.258, W.259, G.260 Ligands: ANP.8 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:F.85, B:T.109 Hydrogen bonds: B:E.111 Water bridges: B:R.140 pi-Stacking: B:F.85, B:F.85

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

CL.5: 1 residues within 4Å: Chain A: S.13 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain A: W.141, R.153 Chain B: L.100 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain A: V.21, R.22 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain B: S.13, Y.500 Ligand excluded by PLIP CL.13: 2 residues within 4Å: Chain B: V.21, R.22 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jain, V. et al., Targeting Prolyl-tRNA Synthetase to Accelerate Drug Discovery against Malaria, Leishmaniasis, Toxoplasmosis, Cryptosporidiosis, and Coccidiosis. Structure (2017)

Release Date

2018-03-07

Peptides

Prolyl-tRNA synthetase (ProRS): AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Prolyl-tRNA synthetase (ProRS)

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