SMTL ID : 6a88.2 (1 other biounit)

Crystal Structure of T. gondii prolyl tRNA synthetase with Febrifugine and ATP Analog

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-dimer

Ligands

2 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.1: 15 residues within 4Å: Chain A: R.140, E.142, K.144, F.149, L.150, R.151, T.152, F.155, Q.225, A.227, T.228, T.262, R.264 Ligands: MG.2, 9SF.3 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:R.140, A:E.142, A:K.144, A:R.151, A:R.151, A:T.152, A:Q.225, A:Q.225 Water bridges: A:K.144, A:K.144 Salt bridges: A:R.140 pi-Stacking: A:F.155, A:F.155 ANP.4: 14 residues within 4Å: Chain B: R.140, E.142, F.149, L.150, R.151, T.152, F.155, Q.225, A.226, T.228, T.262, R.264 Ligands: MG.5, 9SF.6 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:R.140, B:E.142, B:R.151, B:R.151, B:T.152, B:Q.225, B:Q.225, B:R.264, B:R.264 Water bridges: B:E.142, B:E.142, B:K.144 Salt bridges: B:R.140 pi-Stacking: B:F.155, B:F.155 pi-Cation interactions: B:R.264

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: R.140, K.144 Ligands: ANP.1 No protein-ligand interaction detected (PLIP) MG.5: 3 residues within 4Å: Chain B: E.88, R.140 Ligands: ANP.4 No protein-ligand interaction detected (PLIP)

2 x 9SF: 3-{3-[(2R,3S)-3-hydroxypiperidin-2-yl]-2-oxopropyl}quinazolin-4(3H)-one(Non-covalent)

9SF.3: 13 residues within 4Å: Chain A: F.85, P.108, T.109, E.111, R.140, E.159, H.161, F.204, T.228, H.230, W.259, G.260 Ligands: ANP.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.85, A:P.108, A:P.108, A:T.109, A:E.159, A:F.204 Hydrogen bonds: A:T.109, A:R.140 Water bridges: A:R.140 pi-Stacking: A:F.85, A:F.85 9SF.6: 15 residues within 4Å: Chain B: F.85, E.88, P.108, T.109, E.111, R.140, W.157, E.159, H.161, F.204, T.228, H.230, W.259, G.260 Ligands: ANP.4 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:F.85, B:P.108, B:P.108, B:T.109, B:W.157, B:E.159, B:F.204 Hydrogen bonds: B:R.140 pi-Stacking: B:F.85, B:F.85

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mishra, S. et al., Conformational heterogeneity in apo and drug-bound structures of Toxoplasma gondii prolyl-tRNA synthetase. Acta Crystallogr.,Sect.F (2019)

Release Date

2019-10-23

Peptides

Prolyl-tRNA synthetase (ProRS): AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Prolyl-tRNA synthetase (ProRS)

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