Quaternary complex of mutant T252A of E. COLI leucyl-tRNA synthetase with TRNA(LEU), leucyl-adenylate analogue, and post-transfer editing analogue of leucine in the aminoacylation conformation

Structure

x-ray diffraction · 3 distinct chains · 37% helix, 22% strand (DSSP).

Ligands and binding sites

• LSS · 5'-O-(L-leucylsulfamoyl)adenosine · ligand · 2 copies · chains A, B, D, E
• 9YN · (2~{S})-~{N}-[(2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-(hydroxymethyl)-4-oxidanyl-oxolan-3-yl]-2-azanyl-4-methyl-pentanamide · ligand · 2 copies · chains A, D
• ZN · Zinc ion · metal · chains A

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

Pockets

20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.

Interfaces

3 interfaces between chains.

• A–B · 3064 Ų buried · 52 hydrogen bonds · protein-nucleic
• D–E · 2852 Ų buried · 50 hydrogen bonds · protein-nucleic
• A–D · 564 Ų buried · 0 hydrogen bonds · protein-protein

Compared structures

• 5ON3 · Quaternary complex of mutant T252A of E. coli leucyl-tRNA synthetase with tRNA(leu)… · the same entry in another collection · chain A against A, TM-score 1.00
• P07813 · AlphaFold monomer V2.0 prediction for leucine--tRNA ligase (P07813) · a predicted model of the same protein · chain D against A, TM-score 0.90

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 P07813
• Elsewhere: RCSB PDB 5ON3 · PDBe 5ON3 · UniProt P07813