Crystal structure of E. coli threonyl tRNA synthetase in complex with a TM84 analogue

Structure

x-ray diffraction · resolution 2.05 · 2 distinct chains · 37% helix, 29% strand (DSSP).

Ligands and binding sites

• W0U · [(2~{S},4~{S},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-oxolan-2-yl]methoxy-~{N}-[(2~{S},3~{S})-2-azanyl-3-oxidanyl-butanoyl]phosphonamidic acid · ligand · 2 copies · chains D, A
• ZN · Zinc ion · metal · 2 copies · chains D, A
• DMS · Dimethyl sulfoxide · additive · 2 copies · chains D, A
• EDO · 1,2-ethanediol · additive · 2 copies · chains D, A

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

Pockets

6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• D–A · 2169 Ų buried · 37 hydrogen bonds · protein-protein

Compared structures

• B7M1C7 · AlphaFold monomer V2.0 prediction for threonine--tRNA ligase (B7M1C7) · a predicted model of the same protein · chain D 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 B7M1C7
• Elsewhere: RCSB PDB 8OU8 · PDBe 8OU8 · UniProt B7M1C7