Structure of pyrrolysyl-tRNA synthetase in complex with adenylated propargyloxycarbonyl lysine

Structure

x-ray diffraction · 1 distinct chain · 38% helix, 22% strand (DSSP).

Ligands and binding sites

• YLA · (S)-2-amino-6-(((prop-2-yn-1-yloxy)carbonyl)amino)hexanoic (((2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl)methyl phosphoric)anhydride · ligand · chains A
• MG · Magnesium ion · metal · chains A
• EDO · 1,2-ethanediol · additive · 5 copies · chains A

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

Pockets

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

Compared structures

• 4CH6 · Structure of pyrrolysyl-tRNA synthetase in complex with adenylated propargyloxycarbonyl… · the same entry in another collection · chain A against A, TM-score 1.00
• Q8PWY1 · AlphaFold monomer V2.0 prediction for pyrrolysine--tRNA ligase (Q8PWY1) · 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 Q8PWY1
• Elsewhere: RCSB PDB 4CH6 · PDBe 4CH6 · UniProt Q8PWY1