SMTL ID : 5znk.1

Crystal structure of a bacterial ProRS with ligands

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.07 Å

Oligo State

homo-dimer

Ligands

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

ANP.1: 19 residues within 4Å: Chain A: R.140, E.142, L.149, L.150, R.151, G.152, F.155, M.157, E.406, V.407, G.408, Q.409, F.411, G.443, R.446 Ligands: MG.2, MG.3, GOL.4, 9G3.5 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:R.140, A:E.142, A:E.142, A:R.151, A:R.151, A:G.152, A:E.406, A:E.406, A:E.406, A:G.408, A:G.443, A:R.446, A:R.446 Water bridges: A:Q.409 Salt bridges: A:R.140 pi-Stacking: A:F.155, A:F.155 pi-Cation interactions: A:R.446, A:R.446 ANP.6: 19 residues within 4Å: Chain B: R.140, E.142, L.149, L.150, R.151, G.152, F.155, M.157, E.406, V.407, G.408, Q.409, F.411, G.443, R.446 Ligands: MG.7, MG.8, GOL.9, 9G3.10 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:R.140, B:E.142, B:R.151, B:R.151, B:G.152, B:E.406, B:E.406, B:G.408, B:G.443, B:R.446, B:R.446 Salt bridges: B:R.140 pi-Stacking: B:F.155, B:F.155 pi-Cation interactions: B:R.446, B:R.446

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: R.140, R.151 Ligands: ANP.1 No protein-ligand interaction detected (PLIP) MG.3: 3 residues within 4Å: Chain A: E.406, Q.409 Ligands: ANP.1 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.406, H2O.3, H2O.4 MG.7: 3 residues within 4Å: Chain B: R.140, R.151 Ligands: ANP.6 No protein-ligand interaction detected (PLIP) MG.8: 3 residues within 4Å: Chain B: E.406, Q.409 Ligands: ANP.6 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.406, H2O.8, H2O.9

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain A: E.209, D.219, N.232, E.234, E.406 Ligands: ANP.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.209, A:D.219, A:N.232 Water bridges: A:E.209, A:E.209, A:E.234 GOL.9: 6 residues within 4Å: Chain B: E.209, D.219, N.232, E.234, E.406 Ligands: ANP.6 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.209, B:D.219, B:N.232, B:E.406

2 x 9G3: 7-chloro-6-fluoro-3-{2-oxo-3-[(2S)-piperidin-2-yl]propyl}quinazolin-4(3H)-one(Non-covalent)

9G3.5: 17 residues within 4Å: Chain A: W.80, R.85, Y.89, E.92, L.93, P.108, T.109, E.111, R.140, M.157, D.159, Y.161, F.411, C.439, Y.440, G.441 Ligands: ANP.1 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:T.109, A:D.159, A:F.411, A:F.411 Hydrogen bonds: A:T.109, A:T.109, A:R.140 Water bridges: A:R.140 pi-Stacking: A:Y.89 9G3.10: 17 residues within 4Å: Chain B: W.80, R.85, Y.89, E.92, L.93, P.108, T.109, E.111, R.140, M.157, D.159, Y.161, F.411, C.439, Y.440, G.441 Ligands: ANP.6 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:T.109, B:D.159, B:F.411, B:F.411 Hydrogen bonds: B:T.109, B:R.140 Water bridges: B:R.140 pi-Stacking: B:Y.89

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cheng, B. et al., Structure-Guided Design of Halofuginone Derivatives as ATP-Aided Inhibitors Against Bacterial Prolyl-tRNA Synthetase. J.Med.Chem. (2022)

Release Date

2019-05-29

Peptides

Proline--tRNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Proline--tRNA ligase

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