Actinobacterial 2-hydroxyacyl-CoA lyase (achacl) structure in complex with a covalently bound reaction intermediate as well as products formyl-CoA and acetone

Structure

x-ray diffraction · 2 distinct chains · 44% helix, 17% strand (DSSP).

Ligands and binding sites

• TPP · Thiamine diphosphate · ligand · chains A
• ACN · Acetone · ligand · chains A
• FYN · S-{(9R,13S,15R)-17-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-9,13,15-trihydroxy-10,10-dimethyl-13,15-dioxido-4,8-dioxo-12,14,16-trioxa-3,7-diaza-13,15-diphosphaheptadec-1-yl} thioformate · ligand · chains A
• 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 · chains B
• MG · Magnesium ion · metal · 4 copies · chains A, B
• SO4 · Sulfate ion · ion · 19 copies · chains A, B

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

Pockets

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

Interfaces

1 interface between chains.

• A–B · 2234 Ų buried · 36 hydrogen bonds · protein-protein

Compared structures

• 7PT4 · Actinobacterial 2-hydroxyacyl-CoA lyase (AcHACL) structure in complex with a covalently… · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

• Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
• Elsewhere: RCSB PDB 7PT4 · PDBe 7PT4