SMTL ID : 5ifu.3 (2 other biounits)

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

homo-tetramer

Ligands

4 x GBM: 5-chloro-N-(2-{4-[(cyclohexylcarbamoyl)sulfamoyl]phenyl}ethyl)-2-methoxybenzamide(Non-covalent)

GBM.1: 15 residues within 4Å: Chain A: F.22, S.23, Y.26, I.36, Y.45, L.47, E.164, T.273, R.274, I.276, G.277, I.280, M.281, Y.506 Ligands: FMT.4 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.22, A:Y.26, A:Y.26, A:I.36, A:L.47, A:I.276, A:I.280 Hydrogen bonds: A:Y.45, A:E.164, A:R.274 GBM.14: 10 residues within 4Å: Chain B: Y.26, I.36, Y.45, L.47, E.164, T.273, R.274, I.276, G.277 Ligands: FMT.16 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:Y.26, B:I.36, B:L.47, B:I.276 Hydrogen bonds: B:Y.26, B:E.164, B:E.164, B:E.164 GBM.20: 15 residues within 4Å: Chain C: F.22, S.23, Y.26, I.36, Y.45, L.47, E.164, T.273, R.274, I.276, G.277, I.280, M.281, Y.506 Ligands: FMT.23 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:F.22, C:Y.26, C:Y.26, C:I.36, C:L.47, C:I.276, C:I.280 Hydrogen bonds: C:Y.26, C:Y.45, C:Y.45, C:E.164, C:R.274, C:Y.506 GBM.33: 10 residues within 4Å: Chain D: Y.26, I.36, Y.45, L.47, E.164, T.273, R.274, I.276, G.277 Ligands: FMT.35 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:Y.26, D:I.36, D:L.47, D:I.276 Hydrogen bonds: D:E.164, D:E.164

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

CL.2: 6 residues within 4Å: Chain A: I.123, M.124, Y.125, S.126 Chain D: D.40, I.41 Ligand excluded by PLIP CL.21: 6 residues within 4Å: Chain B: D.40, I.41 Chain C: I.123, M.124, Y.125, S.126 Ligand excluded by PLIP

28 x FMT: FORMIC ACID(Non-functional Binders)

FMT.3: 5 residues within 4Å: Chain A: L.291, S.296, K.297, Y.298, I.355 Ligand excluded by PLIP FMT.4: 3 residues within 4Å: Chain A: Y.38, T.162 Ligands: GBM.1 Ligand excluded by PLIP FMT.5: 4 residues within 4Å: Chain A: F.185, D.186, D.189, K.205 Ligand excluded by PLIP FMT.6: 4 residues within 4Å: Chain A: S.228, S.415, K.432, K.433 Ligand excluded by PLIP FMT.7: 3 residues within 4Å: Chain A: C.382, E.392, M.396 Ligand excluded by PLIP FMT.8: 2 residues within 4Å: Chain A: P.485, N.486 Ligand excluded by PLIP FMT.9: 3 residues within 4Å: Chain A: P.484, P.485, N.486 Ligand excluded by PLIP FMT.10: 3 residues within 4Å: Chain A: E.164, T.272, R.274 Ligand excluded by PLIP FMT.11: 5 residues within 4Å: Chain A: Q.418, T.420, P.484, M.487, W.499 Ligand excluded by PLIP FMT.12: 2 residues within 4Å: Chain A: L.436, D.479 Ligand excluded by PLIP FMT.15: 4 residues within 4Å: Chain B: S.296, K.297, Y.298, I.355 Ligand excluded by PLIP FMT.16: 3 residues within 4Å: Chain B: Y.38, Y.45 Ligands: GBM.14 Ligand excluded by PLIP FMT.17: 7 residues within 4Å: Chain A: Q.59, N.63, W.145 Chain B: Y.52, E.56, Q.59 Ligands: EDO.13 Ligand excluded by PLIP FMT.18: 3 residues within 4Å: Chain B: E.164, T.272, R.274 Ligand excluded by PLIP FMT.22: 5 residues within 4Å: Chain C: L.291, S.296, K.297, Y.298, I.355 Ligand excluded by PLIP FMT.23: 3 residues within 4Å: Chain C: Y.38, T.162 Ligands: GBM.20 Ligand excluded by PLIP FMT.24: 4 residues within 4Å: Chain C: F.185, D.186, D.189, K.205 Ligand excluded by PLIP FMT.25: 4 residues within 4Å: Chain C: S.228, S.415, K.432, K.433 Ligand excluded by PLIP FMT.26: 3 residues within 4Å: Chain C: C.382, E.392, M.396 Ligand excluded by PLIP FMT.27: 2 residues within 4Å: Chain C: P.485, N.486 Ligand excluded by PLIP FMT.28: 3 residues within 4Å: Chain C: P.484, P.485, N.486 Ligand excluded by PLIP FMT.29: 3 residues within 4Å: Chain C: E.164, T.272, R.274 Ligand excluded by PLIP FMT.30: 5 residues within 4Å: Chain C: Q.418, T.420, P.484, M.487, W.499 Ligand excluded by PLIP FMT.31: 2 residues within 4Å: Chain C: L.436, D.479 Ligand excluded by PLIP FMT.34: 4 residues within 4Å: Chain D: S.296, K.297, Y.298, I.355 Ligand excluded by PLIP FMT.35: 3 residues within 4Å: Chain D: Y.38, Y.45 Ligands: GBM.33 Ligand excluded by PLIP FMT.36: 7 residues within 4Å: Chain C: Q.59, N.63, W.145 Chain D: Y.52, E.56, Q.59 Ligands: EDO.32 Ligand excluded by PLIP FMT.37: 3 residues within 4Å: Chain D: E.164, T.272, R.274 Ligand excluded by PLIP

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

EDO.13: 6 residues within 4Å: Chain A: E.56, Q.59, A.60, N.63 Ligands: FMT.17, EDO.19 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.56, A:N.63 EDO.19: 5 residues within 4Å: Chain B: E.56, Q.59, A.60, N.63 Ligands: EDO.13 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.56, B:N.63 EDO.32: 6 residues within 4Å: Chain C: E.56, Q.59, A.60, N.63 Ligands: FMT.36, EDO.38 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.56, C:N.63 EDO.38: 5 residues within 4Å: Chain D: E.56, Q.59, A.60, N.63 Ligands: EDO.32 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:E.56, D:E.56, D:N.63

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hewitt, S.N. et al., Biochemical and Structural Characterization of Selective Allosteric Inhibitors of the Plasmodium falciparum Drug Target, Prolyl-tRNA-synthetase. ACS Infect Dis (2017)

Release Date

2016-11-16

Peptides

Proline--tRNA ligase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Proline--tRNA ligase

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