SMTL ID : 7vc3.1

Toxoplasma gondii Prolyl-tRNA Synthetase (TgPRS) in Complex with inhibitor L97 and L-proline at 1.97 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.97 Å

Oligo State

homo-dimer

Ligands

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

1XK.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 Ligands: PRO.2 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:E.142, A:K.144, A:R.151, A:R.153, A:F.155, A:W.157, A:T.262 Hydrogen bonds: A:T.152, A:T.152, A:Q.225, A:Q.225, A:T.262 Water bridges: A:R.151 pi-Stacking: A:F.155 pi-Cation interactions: A:R.151 1XK.20: 20 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 Ligands: PRO.21 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:E.142, B:K.144, B:R.151, B:R.153, B:F.155, B:W.157, B:T.262 Hydrogen bonds: B:T.152, B:T.152, B:Q.225, B:Q.225, B:T.228 Water bridges: B:R.151 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, H.230, S.258, W.259, G.260 Ligands: 1XK.1 10 PLIP interactions: 9 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:W.157, A:E.159 Hydrogen bonds: A:T.109, 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.21: 12 residues within 4Å: Chain B: T.109, E.111, R.140, W.157, E.159, H.161, F.204, H.230, S.258, W.259, G.260 Ligands: 1XK.20 9 PLIP interactions: 8 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:W.157, B:E.159 Hydrogen bonds: B:T.109, B:S.258, P.21 Water bridges: B:R.140, B:R.140 Salt bridges: B:R.140, B:H.230

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: E.243, K.251, R.252, L.253 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.251, A:L.253 GOL.4: 7 residues within 4Å: Chain A: Y.28, Y.29, S.32, G.33, C.34, Y.35, P.146 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.29, A:Y.29, A:G.33, A:C.34 GOL.5: 6 residues within 4Å: Chain A: Y.35, M.37, T.152, F.155, L.156, T.263 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.35, A:Y.35, A:L.156, A:T.263, A:T.263 Water bridges: A:M.37 GOL.22: 4 residues within 4Å: Chain B: E.243, K.251, R.252, L.253 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.251, B:L.253 GOL.23: 7 residues within 4Å: Chain B: Y.28, Y.29, 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:C.34 GOL.24: 6 residues within 4Å: Chain B: Y.35, M.37, T.152, F.155, L.156, T.263 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Y.35, B:Y.35, B:L.156, B:T.263 Water bridges: B:M.37, B:T.152, B:T.263

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

CL.6: 2 residues within 4Å: Chain A: S.13, Y.500 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain A: K.198, Q.225, H.230 Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain A: W.171, K.209 Ligand excluded by PLIP CL.9: 1 residues within 4Å: Chain A: K.277 Ligand excluded by PLIP CL.10: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.11: 1 residues within 4Å: Chain A: R.324 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain A: E.350, D.355 Ligand excluded by PLIP CL.13: 1 residues within 4Å: Chain B: E.46 Ligand excluded by PLIP CL.14: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.15: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.16: 1 residues within 4Å: Chain A: W.335 Ligand excluded by PLIP CL.25: 2 residues within 4Å: Chain B: S.13, Y.500 Ligand excluded by PLIP CL.26: 3 residues within 4Å: Chain B: K.198, Q.225, H.230 Ligand excluded by PLIP CL.27: 2 residues within 4Å: Chain B: W.171, K.209 Ligand excluded by PLIP CL.28: 1 residues within 4Å: Chain B: K.277 Ligand excluded by PLIP CL.29: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.30: 1 residues within 4Å: Chain B: R.324 Ligand excluded by PLIP CL.31: 2 residues within 4Å: Chain B: E.350, D.355 Ligand excluded by PLIP CL.32: 1 residues within 4Å: Chain A: E.46 Ligand excluded by PLIP CL.33: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.34: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.35: 1 residues within 4Å: Chain B: W.335 Ligand excluded by PLIP

2 x NA: SODIUM ION(Non-functional Binders)

NA.17: 3 residues within 4Å: Chain A: E.479, T.481, A.490 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.490 NA.36: 3 residues within 4Å: Chain B: E.479, T.481, A.490 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.490

2 x SO3: SULFITE ION(Non-covalent)

SO3.18: 7 residues within 4Å: Chain A: F.42, W.45, Q.49, W.135, L.156 Chain B: W.135 Ligands: SO3.37 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Water bridges: B:W.135 Hydrogen bonds: A:W.45, A:Q.49 SO3.37: 7 residues within 4Å: Chain A: W.135 Chain B: F.42, W.45, Q.49, W.135, L.156 Ligands: SO3.18 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:W.45, B:Q.49 Water bridges: A:W.135

2 x ETA: ETHANOLAMINE(Non-covalent)

ETA.19: 9 residues within 4Å: Chain A: Y.65, R.107, C.136, S.137 Chain B: Y.65, R.107, C.136, S.137 Ligands: ETA.38 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.107, A:S.137, B:Y.65, B:Y.65 ETA.38: 9 residues within 4Å: Chain A: Y.65, R.107, C.136, S.137 Chain B: Y.65, R.107, C.136, S.137 Ligands: ETA.19 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Y.65, B:R.107, B:S.137

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
A

Prolyl-tRNA synthetase (ProRS)

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