Crystal structure of reduced aquifex aeolicus NADH-quinone oxidoreductase subunits nuoe G129D and nuof bound to NADH

Structure

x-ray diffraction · 2 distinct chains · 46% helix, 15% strand (DSSP).

Ligands and binding sites

• FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains A, B, C, D
• SF4 · Iron/sulfur cluster · ligand · 2 copies · chains B, D
• FMN · Flavin mononucleotide · ligand · 2 copies · chains B, D
• NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 2 copies · chains B, D
• NA · Sodium ion · metal · 3 copies · chains B, D
• SO4 · Sulfate ion · ion · 5 copies · chains A, C, D
• GOL · Glycerol · additive · 2 copies · chains B, D

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

Pockets

10 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Interfaces

4 interfaces between chains.

• C–D · 2137 Ų buried · 25 hydrogen bonds · protein-protein
• A–B · 2116 Ų buried · 23 hydrogen bonds · protein-protein
• B–C · 387 Ų buried · 6 hydrogen bonds · protein-protein
• B–D · 303 Ų buried · 1 hydrogen bond · protein-protein

Compared structures

• 6Q9G · Crystal structure of reduced Aquifex aeolicus NADH-qui oxidoreductase subunits NuoE G129D… · the same entry in another collection · chain A against A, TM-score 1.00
• O66841 · AlphaFold monomer V2.0 prediction for NADH-quinone oxidoreductase subunit F (O66841) · a predicted model of the same protein · chain B against A, TM-score 1.00
• O66842 · AlphaFold monomer V2.0 prediction for NADH-quinone oxidoreductase subunit E (O66842) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 O66842
• Every structure of UniProt O66841
• Elsewhere: RCSB PDB 6Q9G · PDBe 6Q9G · UniProt O66842 · UniProt O66841