SMTL ID : 7fak.1

Co-crystal Structure of Toxoplasma gondii Prolyl tRNA Synthetase (TgPRS) in complex with L96 and L-pro

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 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: 19 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 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:E.142, A:K.144, A:R.151, A:F.155, A:W.157, A:W.157, A:T.228, A:T.262 Hydrogen bonds: A:Q.145, A:T.152, A:T.152, A:T.262 Water bridges: A:R.151 pi-Stacking: A:F.155 pi-Cation interactions: A:R.151 Halogen bonds: A:R.153 1UI.17: 19 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 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:E.142, B:K.144, B:R.151, B:F.155, B:W.157, B:W.157, B:T.228, B:T.262 Hydrogen bonds: B:E.142, B:Q.145, B:T.152, B:T.152 Water bridges: B:R.151 pi-Stacking: B:F.155 pi-Cation interactions: B:R.151 Halogen bonds: B:R.153

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 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.18: 12 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 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.18 Water bridges: B:R.140, B:R.140 Salt bridges: B:R.140, B:H.230

2 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.3: 17 residues within 4Å: Chain A: Q.49, Y.65, R.107, W.135, C.136, S.137, L.156 Chain B: Q.49, Y.65, R.107, W.135, C.136, S.137, L.156 Ligands: FMT.6, MES.19, FMT.22 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:Q.49, A:R.107, A:S.137, B:Q.49, B:S.137 Water bridges: B:R.107 MES.19: 17 residues within 4Å: Chain A: Q.49, Y.65, R.107, W.135, C.136, S.137, L.156 Chain B: Q.49, Y.65, R.107, W.135, C.136, S.137, L.156 Ligands: MES.3, FMT.6, FMT.22 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:Q.49, A:S.137, B:Q.49, B:Y.65, B:R.107, B:S.137 Water bridges: A:R.107

24 x FMT: FORMIC ACID(Non-functional Binders)

FMT.4: 4 residues within 4Å: Chain A: S.13, T.147, M.271, Y.500 Ligand excluded by PLIP FMT.5: 2 residues within 4Å: Chain A: E.350, D.355 Ligand excluded by PLIP FMT.6: 7 residues within 4Å: Chain A: E.46, Q.49 Chain B: Q.49, D.53 Ligands: MES.3, MES.19, FMT.22 Ligand excluded by PLIP FMT.7: 6 residues within 4Å: Chain A: E.186, E.187, A.190, R.284, Q.391, F.395 Ligand excluded by PLIP FMT.8: 6 residues within 4Å: Chain A: E.197, I.470, P.471, F.472, Q.474, R.492 Ligand excluded by PLIP FMT.9: 6 residues within 4Å: Chain A: Y.35, M.37, E.154, F.155, L.156, T.263 Ligand excluded by PLIP FMT.10: 8 residues within 4Å: Chain A: K.198, E.202, K.203, F.204, T.210, Q.225, T.228, H.230 Ligand excluded by PLIP FMT.11: 3 residues within 4Å: Chain A: E.46, K.47, R.50 Ligand excluded by PLIP FMT.12: 2 residues within 4Å: Chain A: D.275, D.276 Ligand excluded by PLIP FMT.13: 5 residues within 4Å: Chain A: R.324, I.325, D.326, R.328, W.340 Ligand excluded by PLIP FMT.14: 2 residues within 4Å: Chain A: T.109, R.140 Ligand excluded by PLIP FMT.15: 2 residues within 4Å: Chain A: R.252, L.253 Ligand excluded by PLIP FMT.20: 4 residues within 4Å: Chain B: S.13, T.147, M.271, Y.500 Ligand excluded by PLIP FMT.21: 2 residues within 4Å: Chain B: E.350, D.355 Ligand excluded by PLIP FMT.22: 7 residues within 4Å: Chain A: Q.49, D.53 Chain B: E.46, Q.49 Ligands: MES.3, FMT.6, MES.19 Ligand excluded by PLIP FMT.23: 6 residues within 4Å: Chain B: E.186, E.187, A.190, R.284, Q.391, F.395 Ligand excluded by PLIP FMT.24: 6 residues within 4Å: Chain B: E.197, I.470, P.471, F.472, Q.474, R.492 Ligand excluded by PLIP FMT.25: 6 residues within 4Å: Chain B: Y.35, M.37, E.154, F.155, L.156, T.263 Ligand excluded by PLIP FMT.26: 8 residues within 4Å: Chain B: K.198, E.202, K.203, F.204, T.210, Q.225, T.228, H.230 Ligand excluded by PLIP FMT.27: 3 residues within 4Å: Chain B: E.46, K.47, R.50 Ligand excluded by PLIP FMT.28: 2 residues within 4Å: Chain B: D.275, D.276 Ligand excluded by PLIP FMT.29: 5 residues within 4Å: Chain B: R.324, I.325, D.326, R.328, W.340 Ligand excluded by PLIP FMT.30: 2 residues within 4Å: Chain B: T.109, R.140 Ligand excluded by PLIP FMT.31: 2 residues within 4Å: Chain B: R.252, L.253 Ligand excluded by PLIP

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.16: 2 residues within 4Å: Chain A: P.471, D.473 No protein-ligand interaction detected (PLIP) ACT.32: 2 residues within 4Å: Chain B: P.471, D.473 No protein-ligand interaction detected (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

2023-02-08

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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