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

Structure

x-ray diffraction · 1 distinct chain · 30% helix, 23% strand (DSSP).

Ligands and binding sites

• 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 · ligand · chains A
• SO4 · Sulfate ion · ion · 4 copies · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Compared structures

• 4K47 · Structure of the Streptococcus pneumoniae leucyl-tRNA synthetase editing domain bound to… · the same entry in another collection · chain A against A, TM-score 1.00
• B8ZKS5 · AlphaFold monomer V2.0 prediction for leucine--tRNA ligase (B8ZKS5) · a predicted model of the same protein · chain A against A, TM-score 0.98

Analyse

• Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
• Every structure of UniProt B8ZKS5
• Elsewhere: RCSB PDB 4K47 · PDBe 4K47 · UniProt B8ZKS5