SMTL ID : 7evv.1

Co-crystal Structure of Toxoplasma gondii Prolyl tRNA Synthetase (TgPRS) in complex with JE6 and L-pro

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

1 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: 18 residues within 4Å: Chain A: R.140, E.142, K.144, Q.145, 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: PRO.2 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:R.140, A:E.142, 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 pi-Stacking: A:F.155

1 x PRO: PROLINE(Non-covalent)

PRO.2: 13 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 Ligands: JE6.1 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

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

CL.3: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

2 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.4: 9 residues within 4Å: Chain A: I.26, Y.35, M.37, P.148, F.149, T.152, E.154, F.155, T.263 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.26, A:Y.35, A:F.149, A:T.152 Hydrogen bonds: A:F.149, A:T.263 MPD.5: 4 residues within 4Å: Chain A: E.167, E.168, W.171, K.209 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:E.167, A:E.168, A:W.171, A:W.171

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Manickam, Y. et al., Double drugging of prolyl-tRNA synthetase provides a new paradigm for anti-infective drug development. Plos Pathog. (2022)

Release Date

2022-03-09

Peptides

Prolyl-tRNA synthetase (ProRS): A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Prolyl-tRNA synthetase (ProRS)

Related Entries With Identical Sequence