Research workbench
Wild-type nuoef from aquifex aeolicus - oxidized form
Analyse Wild-type nuoef from aquifex aeolicus - oxidized form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HL2
- Type
- protein
- Length
- 1,144 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, NA, SO4, CL
- Pockets
- 12 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NADH-quinone oxidoreductase subunit E (EC 1.6.5.11) | protein | 156 | 51% helix, 13% strand | O66842 |
| B | NADH-quinone oxidoreductase subunit F (EC 1.6.5.11) | protein | 416 | 44% helix, 16% strand | O66841 |
| C | NADH-quinone oxidoreductase subunit E (EC 1.6.5.11) | protein | 155 | 51% helix, 14% strand | O66842 |
| D | NADH-quinone oxidoreductase subunit F (EC 1.6.5.11) | protein | 417 | 45% 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
- NA · Sodium ion · metal · 2 copies · chains B, D
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, D, C
- CL · Chloride ion · ion · 8 copies · chains A, B, C, D
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 4 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 493 | 0.74 | 0.83 | 47 | FMN, CL |
| 2 | 469 | 0.74 | 0.83 | 54 | SO4 |
| 3 | 509 | 0.73 | 0.82 | 45 | FMN, CL |
| 4 | 334 | 0.63 | 0.79 | 32 | empty |
| 5 | 143 | 0.54 | 0.81 | 22 | TRS |
Interfaces
4 interfaces between chains.
- A–B · 2143 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 2126 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 385 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 325 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6HL2 · wild-type NuoEF from Aquifex aeolicus - oxidized form · the same entry in another collection · chain D against D, 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 6HL2 · PDBe 6HL2 · UniProt O66842 · UniProt O66841
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