SMTL ID : 9yon.1

Crystal structure of Prolyl-tRNA synthetase (ProRS, Proline--tRNA ligase) from Plasmodium falciparum in complex with inhibitor YNW69

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.43 Å

Oligo State

homo-dimer

Ligands

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

CL.1: 3 residues within 4Å: Chain A: R.161, Q.235, R.274 Ligand excluded by PLIP CL.2: 1 residues within 4Å: Chain A: R.375 Ligand excluded by PLIP CL.3: 1 residues within 4Å: Chain A: S.42 Ligand excluded by PLIP CL.4: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.5: 2 residues within 4Å: Chain A: Y.341, S.342 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain B: R.161, Q.235, R.274 Ligand excluded by PLIP CL.13: 1 residues within 4Å: Chain B: R.375 Ligand excluded by PLIP CL.14: 1 residues within 4Å: Chain B: S.42 Ligand excluded by PLIP CL.15: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.16: 2 residues within 4Å: Chain B: Y.341, S.342 Ligand excluded by PLIP

10 x SO4: SULFATE ION(Non-functional Binders)

SO4.6: 5 residues within 4Å: Chain A: Y.38, S.42, G.43, Y.45, P.156 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.43, A:Y.45 SO4.7: 4 residues within 4Å: Chain A: R.338, A.339, S.340 Chain B: R.136 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Salt bridges: B:R.136 Hydrogen bonds: A:A.339, A:S.340, A:S.340 SO4.8: 1 residues within 4Å: Chain A: R.455 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.455 SO4.9: 2 residues within 4Å: Chain A: N.378, N.403 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.378, A:N.403, A:N.403 SO4.10: 3 residues within 4Å: Chain A: N.70, P.139, K.141 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.70 Salt bridges: A:K.141 SO4.17: 5 residues within 4Å: Chain B: Y.38, S.42, G.43, Y.45, P.156 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.43 SO4.18: 4 residues within 4Å: Chain A: R.136 Chain B: R.338, A.339, S.340 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:A.339, B:S.340, B:S.340 Salt bridges: A:R.136 SO4.19: 1 residues within 4Å: Chain B: R.455 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.455 SO4.20: 2 residues within 4Å: Chain B: N.378, N.403 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.378, B:N.403, B:N.403 SO4.21: 3 residues within 4Å: Chain B: N.70, P.139, K.141 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.70, B:E.179 Salt bridges: B:K.141

2 x 01: N-[(3M)-3-(4-aminothieno[3,2-d]pyrimidin-6-yl)benzene-1-sulfonyl]-L-prolinamide

01.11: 20 residues within 4Å: Chain A: F.95, T.119, E.121, R.150, E.152, I.160, R.161, T.162, F.165, W.167, E.169, H.171, F.214, T.238, H.240, S.268, W.269, G.270, T.272, R.274 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:W.167, A:E.169, A:T.272 Hydrogen bonds: A:E.121, A:R.150, A:R.150, A:E.152, A:T.162, A:H.240 Water bridges: A:R.161 pi-Stacking: A:F.165, A:F.165, A:W.167 pi-Cation interactions: A:R.274, A:R.274 01.22: 20 residues within 4Å: Chain B: F.95, T.119, E.121, R.150, E.152, I.160, R.161, T.162, F.165, W.167, E.169, H.171, F.214, T.238, H.240, S.268, W.269, G.270, T.272, R.274 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:W.167, B:E.169, B:T.272 Hydrogen bonds: B:T.119, B:E.121, B:R.150, B:R.150, B:E.152, B:T.162, B:H.240 Water bridges: B:R.161 pi-Stacking: B:F.165, B:F.165, B:W.167 pi-Cation interactions: B:R.274, B:R.274

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, L. et al., Crystal structure of Prolyl-tRNA synthetase (ProRS, Proline--tRNA ligase) from Plasmodium falciparum in complex with inhibitor YNW69. To be published

Release Date

2025-10-22

Peptides

Proline--tRNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Proline--tRNA ligase

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