SMTL ID : 5znj.1

Crystal structure of a bacterial ProRS with ligands

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.84 Å

Oligo State

homo-dimer

Ligands

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

ANP.1: 17 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, G.443, R.446 Ligands: HFG.2, MG.3, GOL.5 18 PLIP interactions: 18 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.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: 17 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, G.443, R.446 Ligands: HFG.7, MG.8, GOL.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.443, B:R.446, B:R.446 Water bridges: B:Q.409 Salt bridges: B:R.140 pi-Stacking: B:F.155, B:F.155 pi-Cation interactions: B:R.446, B:R.446

2 x HFG: 7-bromo-6-chloro-3-{3-[(2R,3S)-3-hydroxypiperidin-2-yl]-2-oxopropyl}quinazolin-4(3H)-one(Non-covalent)

HFG.2: 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, Q.409, C.439, Y.440, G.441 Ligands: ANP.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.89, A:T.109, A:D.159 Hydrogen bonds: A:T.109, A:T.109, A:R.140, A:Q.409 Water bridges: A:Y.89, A:R.140, A:Q.409, A:Y.417 HFG.7: 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, Q.409, C.439, Y.440, G.441 Ligands: ANP.6 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:Y.89, B:T.109, B:D.159 Hydrogen bonds: B:T.109, B:R.140, B:Q.409 Water bridges: B:Y.89, B:R.140, B:Q.409

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: R.140, R.151 Ligands: ANP.1 No protein-ligand interaction detected (PLIP) MG.8: 3 residues within 4Å: Chain B: R.140, R.151 Ligands: ANP.6 No protein-ligand interaction detected (PLIP)

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.4: 4 residues within 4Å: Chain A: Y.89, G.90, P.91, E.92 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.90, A:E.92, B:R.99 PO4.9: 4 residues within 4Å: Chain B: Y.89, G.90, P.91, E.92 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:R.99, B:G.90, B:E.92, B:E.92

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 4 residues within 4Å: Chain A: E.209, D.219, E.406 Ligands: ANP.1 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:E.209, A:D.219, A:E.234 Water bridges: A:R.151, A:R.151, A:R.151, A:E.406, A:E.406 GOL.10: 4 residues within 4Å: Chain B: E.209, D.219, E.406 Ligands: ANP.6 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:D.219, B:E.234, B:E.406 Water bridges: B:R.151, B:R.151, B:R.151, B:E.406, B:E.406

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

Related Entries With Identical Sequence