SMTL ID : 4wi1.2 (2 other biounits)

Crystal Structure of Prolyl-tRNA synthetase (ProRS, Proline--tRNA ligase) from Plasmodium falciparum in complex with TCMDC-124506

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

monomer

Ligands

1 x 3O6: 1-(4-fluorophenyl)-3-[4-(4-fluorophenyl)-1-methyl-3-(trifluoromethyl)-1H-pyrazol-5-yl]urea(Non-covalent)

3O6.1: 15 residues within 4Å: Chain A: Y.26, L.35, Y.45, A.51, R.163, E.164, I.234, T.273, I.276, G.277, I.278, I.280, M.281, Y.506 Ligands: EDO.4 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.234, A:I.280, A:Y.506 Hydrogen bonds: A:Y.26, A:E.164, A:E.164

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

EDO.2: 6 residues within 4Å: Chain A: D.285, K.287, D.377, N.378, N.379 Ligands: EDO.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.287 Water bridges: A:R.376 EDO.3: 5 residues within 4Å: Chain A: A.50, S.296, K.297, Y.298, I.355 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.297, A:Y.298 Water bridges: A:P.49 EDO.4: 7 residues within 4Å: Chain A: F.22, S.23, Y.26, N.230, M.281, Y.506 Ligands: 3O6.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.230, A:Y.506, A:Y.506 Water bridges: A:S.23 EDO.5: 7 residues within 4Å: Chain A: E.177, N.218, Y.241, G.243, T.244, N.245, H.265 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.177, A:N.218, A:Y.241, A:T.244, A:T.244 EDO.6: 7 residues within 4Å: Chain A: K.18, E.229, T.282, H.283, G.284, D.285, K.411 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.18, A:E.229, A:H.283 Water bridges: A:E.229 EDO.7: 3 residues within 4Å: Chain A: D.285, D.286 Ligands: EDO.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.286, A:K.287 Water bridges: A:K.18 EDO.8: 4 residues within 4Å: Chain A: P.477, L.478, Q.480, R.498 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.498

1 x IMD: IMIDAZOLE(Non-covalent)

IMD.9: 3 residues within 4Å: Chain A: Y.39, D.40, E.152 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.40, A:D.40

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nakazawa Hewitt, S. et al., Biochemical and Structural Characterization of Selective Allosteric Inhibitors of the Plasmodium falciparum Drug Target, Prolyl-tRNA-synthetase. Acs Infect Dis. (2016)

Release Date

2016-05-04

Peptides

Proline--tRNA ligase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Proline--tRNA ligase

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