Wild-type nuoef from aquifex aeolicus - oxidized form bound to NAD+

Structure

x-ray diffraction · 3 distinct chains · 46% helix, 16% 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
• NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains B, D
• NA · Sodium ion · metal · 2 copies · chains B, D
• SO4 · Sulfate ion · ion · 6 copies · chains A, B, D, C
• CL · Chloride ion · ion · 2 copies · chains A, B
• MPO · 3[N-morpholino]propane sulfonic acid · additive · 2 copies · chains B, D

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

Pockets

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

Interfaces

4 interfaces between chains.

• C–D · 2150 Ų buried · 21 hydrogen bonds · protein-protein
• A–B · 2139 Ų buried · 20 hydrogen bonds · protein-protein
• A–D · 386 Ų buried · 4 hydrogen bonds · protein-protein
• B–D · 312 Ų buried · 1 hydrogen bond · protein-protein

Compared structures

• 6HL3 · wild-type NuoEF from Aquifex aeolicus - oxidized form bound to NAD+ · 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 0.97

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 O66842
• Every structure of UniProt O66841
• Elsewhere: RCSB PDB 6HL3 · PDBe 6HL3 · UniProt O66842 · UniProt O66841