MolNFT v1 · #151356 · protein
Wild-type nuoef from aquifex aeolicus - reduced form bound to NAD+
6HLI · NADH-quinone oxidoreductase subunit E: “Wild-type nuoef from aquifex aeolicus - reduced form bound to NAD+”. X-ray diffraction, 4 ligands (FES, SF4, FMN), 13 pockets (best druggability 0.76). MolNFT v1 #151356 on GenesisL1: 3D…
- PDB
- 6HLI
- Type
- protein
- Length
- 1,145 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NADH-quinone oxidoreductase subunit E; NADH-quinone oxidoreductase subunit F
- EC
- 1.6.5.11
- UniProt
- O66842, O66841
- Ligands
- FES, SF4, FMN, NAD
- Pockets
- 13 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | NADH-quinone oxidoreductase subunit E (EC 1.6.5.11) | protein | 155 | 50% helix, 14% strand | O66842 |
| B | NADH-quinone oxidoreductase subunit F (EC 1.6.5.11) | protein | 417 | 44% helix, 16% strand | O66841 |
| D | NADH-quinone oxidoreductase subunit F (EC 1.6.5.11) | protein | 418 | 44% helix, 16% strand | O66841 |
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
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 586 | 0.76 | 0.82 | 48 | FMN, NAD |
| 2 | 517 | 0.76 | 0.83 | 60 | empty |
| 3 | 569 | 0.74 | 0.82 | 51 | FMN, NAD |
| 4 | 324 | 0.61 | 0.78 | 33 | empty |
| 5 | 92 | 0.56 | 0.85 | 22 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2156 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 2139 Ų buried · 23 hydrogen bonds · protein-protein
- A–D · 386 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 363 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6HLI · wild-type NuoEF from Aquifex aeolicus - reduced 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 6HLI · PDBe 6HLI · UniProt O66842 · UniProt O66841
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