D-2-hydroxyacid dehydrogenases (D2-hdh) from haloferax mediterranei in complex with a mixture of 2-ketohexanoic acid and 2-hydroxyhexanoic acid, and NADPH (1.57 a resolution)

Structure

x-ray diffraction · 1 distinct chain · 36% helix, 17% strand (DSSP).

Ligands and binding sites

• 7N5 · 2-Ketohexanoic acid · ligand · 2 copies · chains A, B
• NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
• 7N6 · (2R)-2-hydroxyhexanoic acid · ligand · chains B
• MG · Magnesium ion · metal · 7 copies · chains A, B
• SO4 · Sulfate ion · ion · chains A
• EDO · 1,2-ethanediol · additive · 8 copies · chains A, B

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

Pockets

5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 2586 Ų buried · 53 hydrogen bonds · protein-protein

Compared structures

• 5MHA · D-2-hydroxyacid dehydrogenases (D2-HDH) from Haloferax mediterranei in complex with a… · the same entry in another collection · chain A against A, TM-score 1.00
• Q2VEQ7 · AlphaFold monomer V2.0 prediction for D-2-hydroxyacid dehydrogenase (Q2VEQ7) · a predicted model of the same protein · chain B against A, TM-score 0.96

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 Q2VEQ7
• Elsewhere: RCSB PDB 5MHA · PDBe 5MHA · UniProt Q2VEQ7