SMTL ID : 7vc1.1

Toxoplasma gondii Prolyl-tRNA Synthetase (TgPRS) in Complex with inhibitor L95 and L-proline in space group P21

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

homo-dimer

Ligands

1 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)

JE6.1: 18 residues within 4Å: Chain A: R.140, E.142, K.144, Q.145, F.149, L.150, R.151, T.152, F.155, W.157, Q.225, A.226, A.227, T.228, G.260, T.262, R.264 Ligands: PRO.2 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:R.140, A:E.142, A:E.142, A:R.151, A:F.155, A:W.157, A:T.228, A:T.262, A:R.264 Hydrogen bonds: A:T.152, A:T.152 pi-Stacking: A:F.155

1 x PRO: PROLINE(Non-covalent)

PRO.2: 13 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 Ligands: JE6.1 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

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

EDO.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) EDO.4: 4 residues within 4Å: Chain A: K.399, L.402, H.403 Ligands: EDO.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.403 EDO.5: 5 residues within 4Å: Chain A: E.186, P.192, V.193, F.395 Ligands: EDO.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.186 EDO.6: 4 residues within 4Å: Chain A: E.167, W.171, K.209, L.231 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.167 EDO.7: 6 residues within 4Å: Chain A: E.27, Y.28, Y.29, I.36 Chain B: P.116, A.117 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Water bridges: B:A.117, B:A.117, A:D.30 Hydrogen bonds: A:Y.28 EDO.10: 7 residues within 4Å: Chain B: E.186, P.192, V.193, F.395, K.399, L.402, H.403 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.186 EDO.11: 8 residues within 4Å: Chain B: Y.28, Y.29, I.31, S.32, G.33, C.34, Y.35, P.146 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.29, B:Y.29, B:G.33, B:Y.35 EDO.12: 6 residues within 4Å: Chain B: E.197, I.470, P.471, F.472, Q.474, R.492 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.197, B:R.492 EDO.13: 6 residues within 4Å: Chain B: Y.35, M.37, T.152, E.154, F.155, T.263 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Y.35, B:T.152, B:T.263 Water bridges: B:Y.35, B:M.37, B:E.154 EDO.14: 2 residues within 4Å: Chain B: R.252, L.253 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.252, B:L.253 Water bridges: B:L.253

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 4 residues within 4Å: Chain A: Q.289, D.320, R.322, L.384 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.289 Water bridges: A:P.283, A:A.319, A:R.322, A:R.322 GOL.15: 7 residues within 4Å: Chain B: F.149, L.150, R.151, T.152, F.155, T.262, R.264 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.152, B:T.152, B:T.262, B:R.264

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

CL.9: 2 residues within 4Å: Chain A: E.46, K.47 Ligand excluded by PLIP CL.16: 5 residues within 4Å: Chain B: I.224, Q.225, R.264, S.499, Y.500 Ligand excluded by PLIP CL.17: 2 residues within 4Å: Chain B: E.167, L.231 Ligand excluded by PLIP CL.18: 1 residues within 4Å: Chain B: K.47 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)

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