X-ray structure of oxalyl-CoA decarboxylase with covalent reaction intermediate

Structure

x-ray diffraction · 1 distinct chain · 45% helix, 18% strand (DSSP).

Ligands and binding sites

• OXT · 3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-2-{(1R,11R, 15S,17R)-19-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-1,11, 15,17-tetrahydroxy-12,12-dimethyl-15,17-dioxido-6,10-dioxo-14,16,18-trioxa-2-thia-5,9-diaza-15,17-diphosphanonadec-1-yl}-5-(2-{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1, 3-thiazol-3-ium · ligand · 2 copies · chains A, B
• ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
• MG · Magnesium ion · metal · 2 copies · chains A, B
• B3P · 2-[3-(2-hydroxy-1,1-dihydroxymethyl-ethylamino)-propylamino]-2-hydroxymethyl-propane-1,3-diol · additive · 6 copies · chains A, B
• PGE · Triethylene glycol · additive · 2 copies · chains A, B

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

Pockets

6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 3878 Ų buried · 47 hydrogen bonds · protein-protein

Compared structures

• 2JI7 · X-ray structure of Oxalyl-CoA decarboxylase with covalent reaction intermediate · the same entry in another collection · chain A against A, TM-score 1.00
• P40149 · AlphaFold monomer V2.0 prediction for oxalyl-CoA decarboxylase (P40149) · 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 P40149
• Elsewhere: RCSB PDB 2JI7 · PDBe 2JI7 · UniProt P40149