Crystals structure of acyl-CoA oxidase-2 in caenorhabditis elegans bound with FAD, ascaroside-CoA, and ATP

Structure

x-ray diffraction · 2 distinct chains · 56% helix, 9% strand (DSSP).

Ligands and binding sites

• FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
• ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
• 6QA · ~{S}-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethyl] 5-[(2~{R},3~{R}, 5~{R},6~{S})-6-methyl-3,5-bis(oxidanyl)oxan-2-yl]oxypentanethioate · ligand · 2 copies · chains A, B
• MG · Magnesium ion · metal · 2 copies · chains A, B

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

Pockets

20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 6091 Ų buried · 78 hydrogen bonds · protein-protein

Compared structures

• 5K3J · Crystals structure of Acyl-CoA oxidase-2 in Caenorhabditis elegans bound with FAD… · the same entry in another collection · chain A against A, TM-score 1.00
• O62137 · AlphaFold monomer V2.0 prediction for acyl-coenzyme a oxidase acox-1.2 (O62137) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 O62137
• Elsewhere: RCSB PDB 5K3J · PDBe 5K3J · UniProt O62137