SMTL ID : 7f9p.1

Toxoplasma gondii Prolyl-tRNA Synthetase (TgPRS) in Complex with inhibitor L95 and azetidine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.57 Å

Oligo State

homo-dimer

Ligands

2 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: 19 residues within 4Å: Chain A: R.140, E.142, K.144, Q.145, P.146, 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: 02A.2 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:R.140, A:E.142, A:K.144, A:P.146, A:R.151, A:F.155, A:W.157, A:W.157, A:T.228, A:T.262 Hydrogen bonds: A:T.152, A:T.152, A:T.262 Water bridges: A:R.140 pi-Stacking: A:F.155 JE6.14: 19 residues within 4Å: Chain B: R.140, E.142, K.144, Q.145, P.146, 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: 02A.15 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:R.140, B:E.142, B:K.144, B:P.146, B:R.151, B:F.155, B:W.157, B:W.157, B:T.228, B:T.262 Hydrogen bonds: B:T.152, B:T.152 Water bridges: B:R.140 pi-Stacking: B:F.155

2 x 02A: (2S)-azetidine-2-carboxylic acid(Non-covalent)

02A.2: 12 residues within 4Å: Chain A: T.109, E.111, R.140, W.157, E.159, F.204, T.228, H.230, S.258, W.259, G.260 Ligands: JE6.1 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.109, A:T.109, A:T.109 Water bridges: A:R.140, A:R.140 Salt bridges: A:R.140, A:H.230 02A.15: 12 residues within 4Å: Chain B: T.109, E.111, R.140, W.157, E.159, F.204, T.228, H.230, S.258, W.259, G.260 Ligands: JE6.14 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.109, B:T.109 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: 14 residues within 4Å: Chain A: Q.49, Y.65, 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.16 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Q.49, B:R.107, B:S.137, A:Q.49 Water bridges: A:R.107 MES.16: 14 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, W.135, C.136, S.137, L.156 Ligands: MES.3 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:Q.49, A:Q.49, A:R.107, A:S.137 Water bridges: B:R.107

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

EDO.4: 7 residues within 4Å: Chain A: Y.35, M.37, E.154, F.155, L.156, T.263 Chain B: Y.65 Ligand excluded by PLIP EDO.5: 7 residues within 4Å: Chain A: F.12, S.13, Y.16, T.147, N.220, M.271, Y.500 Ligand excluded by PLIP EDO.6: 6 residues within 4Å: Chain A: E.197, I.470, P.471, F.472, Q.474, R.492 Ligand excluded by PLIP EDO.7: 3 residues within 4Å: Chain A: W.171, L.175, F.472 Ligand excluded by PLIP EDO.8: 4 residues within 4Å: Chain A: W.171, K.208, K.209, L.231 Ligand excluded by PLIP EDO.9: 6 residues within 4Å: Chain A: D.275, K.277, R.366, D.367, T.368, G.369 Ligand excluded by PLIP EDO.10: 2 residues within 4Å: Chain A: K.399, H.403 Ligand excluded by PLIP EDO.11: 2 residues within 4Å: Chain A: K.58, M.59 Ligand excluded by PLIP EDO.12: 2 residues within 4Å: Chain A: R.252, L.253 Ligand excluded by PLIP EDO.13: 5 residues within 4Å: Chain A: P.283, R.284, Q.289, M.387, E.388 Ligand excluded by PLIP EDO.17: 7 residues within 4Å: Chain A: Y.65 Chain B: Y.35, M.37, E.154, F.155, L.156, T.263 Ligand excluded by PLIP EDO.18: 7 residues within 4Å: Chain B: F.12, S.13, Y.16, T.147, N.220, M.271, Y.500 Ligand excluded by PLIP EDO.19: 6 residues within 4Å: Chain B: E.197, I.470, P.471, F.472, Q.474, R.492 Ligand excluded by PLIP EDO.20: 3 residues within 4Å: Chain B: W.171, L.175, F.472 Ligand excluded by PLIP EDO.21: 4 residues within 4Å: Chain B: W.171, K.208, K.209, L.231 Ligand excluded by PLIP EDO.22: 6 residues within 4Å: Chain B: D.275, K.277, R.366, D.367, T.368, G.369 Ligand excluded by PLIP EDO.23: 2 residues within 4Å: Chain B: K.399, H.403 Ligand excluded by PLIP EDO.24: 2 residues within 4Å: Chain B: K.58, M.59 Ligand excluded by PLIP EDO.25: 2 residues within 4Å: Chain B: R.252, L.253 Ligand excluded by PLIP EDO.26: 5 residues within 4Å: Chain B: P.283, R.284, Q.289, M.387, E.388 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Malhotra, N. et al., TgPRS with double inhibitors. To Be Published

Release Date

2022-10-05

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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