SMTL ID : 5xii.1 (1 other biounit)

Crystal Structure of Toxoplasma gondii Prolyl-tRNA Synthetase (TgPRS) in complex with inhibitor 6

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.17 Å

Oligo State

homo-dimer

Ligands

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

ANP.1: 13 residues within 4Å: Chain A: R.140, E.142, R.151, T.152, F.155, W.157, Q.225, T.228, T.262, R.264 Ligands: MG.2, MG.3, 86X.4 16 PLIP interactions: 16 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:T.262, A:R.264 Water bridges: A:K.144, A:T.262, A:R.264, A:R.264 Salt bridges: A:R.140 pi-Stacking: A:F.155, A:F.155 pi-Cation interactions: A:R.264 ANP.11: 16 residues within 4Å: Chain B: R.140, E.142, F.149, L.150, R.151, T.152, F.155, W.157, Q.225, A.226, T.228, T.262, R.264 Ligands: MG.12, MG.13, 86X.14 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:R.140, B:R.151, B:R.151, B:T.152, B:T.152, B:Q.225, B:T.262, B:R.264 Water bridges: B:K.144, B:T.262, B:K.466, B:K.466 Salt bridges: B:R.140 pi-Stacking: B:F.155, B:F.155 pi-Cation interactions: B:R.264

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

MG.2: 1 residues within 4Å: Ligands: ANP.1 No protein-ligand interaction detected (PLIP) MG.3: 2 residues within 4Å: Chain A: R.140 Ligands: ANP.1 No protein-ligand interaction detected (PLIP) MG.12: 1 residues within 4Å: Ligands: ANP.11 No protein-ligand interaction detected (PLIP) MG.13: 2 residues within 4Å: Chain B: R.140 Ligands: ANP.11 No protein-ligand interaction detected (PLIP)

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

86X.4: 13 residues within 4Å: Chain A: F.85, E.88, V.89, P.108, T.109, E.111, R.140, W.157, F.204, T.228, H.230, S.258 Ligands: ANP.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:P.108, A:T.109, A:W.157, A:W.157, A:F.204 Hydrogen bonds: A:T.109, A:T.109 Water bridges: A:R.140 pi-Stacking: A:F.85, A:F.85 86X.14: 14 residues within 4Å: Chain B: L.75, F.85, E.88, V.89, P.108, T.109, E.111, R.140, W.157, F.204, T.228, H.230, S.258 Ligands: ANP.11 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:P.108, B:T.109, B:W.157, B:W.157, B:F.204 Hydrogen bonds: B:T.109, B:T.109, B:S.258 Water bridges: B:R.140 pi-Stacking: B:F.85, B:F.85

6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 4 residues within 4Å: Chain A: E.167, W.171, K.209, L.231 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.167, A:E.167, A:K.209 Water bridges: A:K.209 EDO.6: 5 residues within 4Å: Chain A: I.470, P.471, F.472, Q.474, R.492 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.197, A:E.197, A:R.492 EDO.7: 3 residues within 4Å: Chain A: E.46, K.47, R.50 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.43, A:K.47 EDO.8: 2 residues within 4Å: Chain A: R.252, L.253 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.252, A:L.253 Water bridges: A:L.253 EDO.9: 3 residues within 4Å: Chain A: F.51, C.188, R.284 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.284 EDO.10: 4 residues within 4Å: Chain A: W.141, R.153 Chain B: L.100, P.101 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.153, A:R.153

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

CL.15: 1 residues within 4Å: Chain B: E.46 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
A

B
C

Prolyl-tRNA synthetase (ProRS)

Related Entries With Identical Sequence