Structure of the NDI1 protein from saccharomyces cerevisiae in complex with the competitive inhibitor, stigmatellin.

Structure

x-ray diffraction · 1 distinct chain · 36% helix, 25% strand (DSSP).

Ligands and binding sites

• SMA · Stigmatellin A · ligand · 2 copies · chains A
• FAD · Flavin-adenine dinucleotide · ligand · chains A
• MG · Magnesium ion · metal · 4 copies · chains A
• GOL · Glycerol · additive · 7 copies · chains A
• PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A
• PGE · Triethylene glycol · additive · 3 copies · chains A
• PG4 · Tetraethylene glycol · additive · 2 copies · chains A
• MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains A
• PE4 · 2-{2-[2-(2-{2-[2-(2-ethoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethoxy]-ethoxy}-ethanol · additive · chains A
• P6G · Hexaethylene glycol · additive · chains A

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

Pockets

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

Compared structures

• 5YJW · Structure of the Ndi1 protein from Saccharomyces cerevisiae in complex with the… · the same entry in another collection · chain A against A, TM-score 1.00
• P32340 · AlphaFold monomer V2.0 prediction for rotenone-insensitive NADH- ubiquinone… · a predicted model of the same protein · chain A against A, TM-score 0.97

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 P32340
• Elsewhere: RCSB PDB 5YJW · PDBe 5YJW · UniProt P32340