Crystal structure of 2-deoxy-scyllo-inosose synthase complexed with carbaglucose-6-phosphate, NAD+ and CO2+

Structure

x-ray diffraction · 2 distinct chains · 45% helix, 21% strand (DSSP).

Ligands and binding sites

• NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
• EXO · (1R,2S,3S,4R)-5-methylenecyclohexane-1,2,3,4-tetraol · ligand · chains A
• CAK · [(1R,2R,3S,4S,5R)-2,3,4,5-tetrahydroxycyclohexyl]methyl dihydrogen phosphate · ligand · chains A, B
• CO · Cobalt (II) ion · metal · 2 copies · chains A, B
• SO3 · Sulfite ion · ion · 2 copies · chains A, B
• PO4 · Phosphate ion · ion · chains A, B
• MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A, B

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

Pockets

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

Interfaces

1 interface between chains.

• A–B · 1319 Ų buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

• 2GRU · Crystal structure of 2-deoxy-scyllo-inosose synthase complexed with… · the same entry in another collection · chain A against A, TM-score 1.00
• Q9S5E2 · AlphaFold monomer V2.0 prediction for 2-deoxy-scyllo-inosose synthase (Q9S5E2) · a predicted model of the same protein · chain B 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 Q9S5E2
• Elsewhere: RCSB PDB 2GRU · PDBe 2GRU · UniProt Q9S5E2