Wild-type nuoef from aquifex aeolicus bound to NADH-oh

Structure

x-ray diffraction · 3 distinct chains · 46% helix, 15% strand (DSSP).

Ligands and binding sites

• FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains A, B, C, D
• FMN · Flavin mononucleotide · ligand · 2 copies · chains B, D
• SF4 · Iron/sulfur cluster · ligand · 2 copies · chains B, D
• L3W · [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-5-[[(1~{E},3~{Z})-5-azanyl-4-oxidanyl-5-oxidanylidene-penta-1,3-dienyl]-methanoyl-amino]-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate · ligand · 2 copies · chains B, D
• GOL · Glycerol · additive · 7 copies · chains A, 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, 5 with a druggability of 0.5 or more.

Interfaces

3 interfaces between chains.

• A–B · 2139 Ų buried · 22 hydrogen bonds · protein-protein
• C–D · 2125 Ų buried · 21 hydrogen bonds · protein-protein
• B–D · 404 Ų buried · 3 hydrogen bonds · protein-protein

Compared structures

• 6SAQ · wild-type NuoEF from Aquifex aeolicus bound to NADH-OH · 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 D 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 6SAQ · PDBe 6SAQ · UniProt O66842 · UniProt O66841