SMTL ID : 7vc2.1

Toxoplasma gondii Prolyl-tRNA Synthetase (TgPRS) in Complex with inhibitor L96 and L-proline in space group P21

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

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

1UI.1: 20 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, T.262, R.264, Y.500 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:E.142, A:R.153, A:F.155, A:W.157, A:W.157, A:T.228, A:T.262 Hydrogen bonds: A:T.152, A:T.152 Water bridges: A:R.151 pi-Stacking: A:F.155 pi-Cation interactions: A:R.151 1UI.8: 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, T.262, R.264, Y.500 Ligands: PRO.9 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:E.142, B:R.151, B:F.155, B:W.157, B:T.228, B:T.262 Hydrogen bonds: B:E.142, B:R.151, B:T.152, B:T.152, B:T.262 Water bridges: B:R.140, B:T.262 pi-Stacking: B:F.155 pi-Cation interactions: B:R.151

2 x PRO: PROLINE(Non-covalent)

PRO.2: 12 residues within 4Å: Chain A: T.109, E.111, R.140, W.157, E.159, H.161, F.204, T.228, H.230, S.258, W.259, G.260 9 PLIP interactions: 8 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:W.157, A:E.159 Hydrogen bonds: A:T.109, A:S.258, P.2 Water bridges: A:R.140, A:R.140 Salt bridges: A:R.140, A:H.230 PRO.9: 13 residues within 4Å: Chain B: 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: 1UI.8 9 PLIP interactions: 7 interactions with chain B, 2 Ligand-Ligand interactions Hydrophobic interactions: B:W.157, B:E.159 Hydrogen bonds: B:T.109, B:T.109, B:T.109, P.9, P.9 Salt bridges: B:R.140, B:H.230

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

EDO.3: 4 residues within 4Å: Chain A: S.13, T.147, M.271, Y.500 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.13, A:Y.500, A:Y.500 Water bridges: A:N.220 EDO.4: 4 residues within 4Å: Chain A: I.194, I.406, P.471, D.473 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.473 EDO.5: 5 residues within 4Å: Chain A: E.186, P.192, V.193, F.395, K.399 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.193, A:V.193 EDO.6: 3 residues within 4Å: Chain A: Q.289, D.320, R.322 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.289, A:D.320 Water bridges: A:R.322, A:R.322, A:R.322 EDO.7: 4 residues within 4Å: Chain A: E.167, W.171, K.209, L.231 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.167, A:K.209 EDO.10: 6 residues within 4Å: Chain B: E.186, P.192, V.193, F.395, K.399, L.402 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.186 EDO.11: 4 residues within 4Å: Chain B: E.167, W.171, K.209, L.231 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.209, B:K.209 EDO.12: 3 residues within 4Å: Chain A: Q.49, W.135 Chain B: Q.49 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.49, A:Q.49 Water bridges: B:Q.49 EDO.13: 6 residues within 4Å: Chain B: E.197, I.470, P.471, F.472, R.492 Ligands: EDO.14 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.197, B:R.492 EDO.14: 2 residues within 4Å: Chain B: F.472 Ligands: EDO.13 No protein-ligand interaction detected (PLIP) EDO.15: 3 residues within 4Å: Chain B: E.46, K.47, R.50 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.47 Water bridges: B:R.50 EDO.16: 2 residues within 4Å: Chain B: C.188, R.284 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.284

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

CL.17: 2 residues within 4Å: Chain B: L.150, Y.500 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yogavel, M. et al., Targeting prolyl-tRNA synthetase via a series of ATP-mimetics to accelerate drug discovery against toxoplasmosis. Plos Pathog. (2023)

Release Date

2022-09-07

Peptides

Prolyl-tRNA synthetase (ProRS): AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Prolyl-tRNA synthetase (ProRS)

Related Entries With Identical Sequence