MolNFT v2 · #152327 · protein
wild-type NuoEF from Aquifex aeolicus - reduced form
6HL4 · NADH-quinone oxidoreductase subunit E: “wild-type NuoEF from Aquifex aeolicus - reduced form”. X-ray diffraction at 2.06, 4 ligands (FES, SF4, FMN), 11 pockets (best druggability 0.74). MolNFT v2 #152327 on GenesisL1: 3D structure…
- PDB
- 6HL4
- Type
- protein
- Length
- 1,141 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.06
- Source
- Aquifex aeolicus VF5
- Molecule
- NADH-quinone oxidoreductase subunit E; NADH-quinone oxidoreductase subunit F
- EC
- 1.6.5.11
- UniProt
- O66842, O66841
- Ligands
- FES, SF4, FMN, CL
- Pockets
- 11 · best druggability 0.74
Structure
x-ray diffraction · resolution 2.06 · 3 distinct chains · 46% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | NADH-quinone oxidoreductase subunit E (EC 1.6.5.11) | protein | 155 | 51% helix, 14% strand | O66842 |
| B | NADH-quinone oxidoreductase subunit F (EC 1.6.5.11) | protein | 416 | 45% helix, 15% strand | O66841 |
| D | NADH-quinone oxidoreductase subunit F (EC 1.6.5.11) | protein | 415 | 45% helix, 15% 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
- CL · Chloride ion · ion · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 504 | 0.74 | 0.82 | 41 | FMN |
| 2 | 472 | 0.74 | 0.83 | 39 | FMN |
| 3 | 328 | 0.69 | 0.82 | 38 | empty |
| 4 | 79 | 0.55 | 0.87 | 30 | empty |
| 5 | 87 | 0.52 | 0.84 | 25 | empty |
Interfaces
4 interfaces between chains.
- C–D · 2173 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 2165 Ų buried · 22 hydrogen bonds · protein-protein
- B–D · 528 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 351 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6HL4 · Wild-type nuoef from aquifex aeolicus - reduced form · 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 6HL4 · PDBe 6HL4 · UniProt O66842 · UniProt O66841
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