SMTL ID : 4k47.1

Structure of the Streptococcus pneumoniae leucyl-tRNA synthetase editing domain bound to a benzoxaborole-AMP adduct

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.02 Å

Oligo State

monomer

Ligands

1 x WMP: [(1R,5R,6R,8S)-6-(6-aminopurin-9-yl)-3'-[(R)-oxidanyl(phenyl)methyl]spiro[2,4,7-trioxa-3-boranuidabicyclo[3.3.0]octane-3,9'-8-oxa-9-boranuidabicyclo[4.3.0]nona-1,3,5-triene]-8-yl]methyl dihydrogen phosphate(Non-covalent)

WMP.1: 15 residues within 4Å: Chain A: F.20, T.21, T.22, R.23, T.26, Y.101, V.102, L.103, Y.106, G.109, V.111, M.112, H.117, D.118, T.147 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:T.22, A:R.23, A:R.23, A:R.23, A:D.118 Hydrogen bonds: A:T.22, A:T.22, A:L.103, A:L.103, A:Y.106, A:Y.106, A:D.118 Water bridges: A:A.110 pi-Cation interactions: A:R.23

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

SO4.2: 3 residues within 4Å: Chain A: S.47, S.48, E.49 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.48, A:S.48 SO4.3: 2 residues within 4Å: Chain A: K.74, E.75 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.75 Water bridges: A:E.75 Salt bridges: A:K.74 SO4.4: 2 residues within 4Å: Chain A: F.17, T.18 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.18, A:T.18 Water bridges: A:E.16, A:E.40, A:E.40 SO4.5: 3 residues within 4Å: Chain A: T.13, D.14, K.15 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.14

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hu, Q.H. et al., Discovery of a potent benzoxaborole-based anti-pneumococcal agent targeting leucyl-tRNA synthetase. Sci Rep (2013)

Release Date

2013-09-04

Peptides

Leucine--tRNA ligase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Leucine--tRNA ligase

Related Entries With Identical Sequence