SMTL ID : 7v8j.1

Toxoplasma gondii Prolyl-tRNA Synthetase (TgPRS) in complex with the reaction intermediates proline-adenylate (Pro-AMP) and pyrophosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.52 Å

Oligo State

homo-dimer

Ligands

1 x PR8: 5'-O-[(R)-hydroxy{[(2S)-pyrrolidin-2-ylcarbonyl]oxy}phosphoryl]adenosine(Non-covalent)

PR8.1: 23 residues within 4Å: Chain A: T.109, E.111, R.140, F.149, L.150, R.151, T.152, F.155, W.157, E.159, H.161, F.204, Q.225, A.226, A.227, T.228, H.230, S.258, W.259, G.260, T.262, R.264 Ligands: PPV.2 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:W.157, A:E.159 Hydrogen bonds: A:T.109, A:T.109, A:R.151, A:T.152, A:T.152, A:Q.225, A:T.228, A:S.258, A:T.262, A:R.264, A:R.264 Salt bridges: A:R.140, A:R.140, A:H.230, A:H.230 pi-Stacking: A:F.155, A:F.155 pi-Cation interactions: A:R.264, A:R.264

1 x PPV: PYROPHOSPHATE(Non-covalent)

PPV.2: 5 residues within 4Å: Chain A: R.140, R.151, Q.225, R.264 Ligands: PR8.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.225 Salt bridges: A:R.140, A:R.151, A:R.264

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

EDO.3: 6 residues within 4Å: Chain A: F.12, S.13, Y.16, T.147, M.271, Y.500 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.12, A:T.147, A:T.147 EDO.4: 4 residues within 4Å: Chain A: E.111, F.204, A.205, F.236 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.111, A:A.205 Water bridges: A:E.111, A:T.112 EDO.6: 6 residues within 4Å: Chain B: F.12, Y.16, T.147, L.150, M.271, Y.500 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.500 EDO.7: 5 residues within 4Å: Chain A: K.57 Chain B: H.43, E.46, K.47, R.50 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.46, B:R.50 Water bridges: B:K.47

1 x PRO: PROLINE(Non-covalent)

PRO.5: 10 residues within 4Å: Chain B: E.111, W.157, E.159, H.161, F.204, T.228, H.230, S.258, W.259, G.260 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Ligand interactions Hydrogen bonds: B:T.228, P.5, P.5 Salt bridges: B:H.230

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Manickam, Y. et al., Toxoplasma gondii Prolyl-tRNA Synthetase (TgPRS) in complex with the reaction intermediates proline-adenylate (Pro-AMP) and pyrophosphate. To Be Published

Release Date

2022-09-07

Peptides

Prolyl-tRNA synthetase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Prolyl-tRNA synthetase

Related Entries With Identical Sequence