MolNFT v1 · #151360 · protein
Variant G129D of nuoef from aquifex aeolicus bound to NAD+
6HLM · NADH-quinone oxidoreductase subunit E: “Variant G129D of nuoef from aquifex aeolicus bound to NAD+”. X-ray diffraction, 5 ligands (FES, SF4, FMN), 9 pockets (best druggability 0.81). MolNFT v1 #151360 on GenesisL1: 3D structure…
- PDB
- 6HLM
- Type
- protein
- Length
- 1,143 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, NA
- Pockets
- 9 · best druggability 0.81
Structure
x-ray diffraction · 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, 16% strand | O66841 |
| D | NADH-quinone oxidoreductase subunit F (EC 1.6.5.11) | protein | 417 | 46% 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
- NA · Sodium ion · metal · chains 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
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 970 | 0.81 | 0.83 | 94 | FMN, NAD |
| 2 | 481 | 0.75 | 0.83 | 42 | FMN, NAD |
| 3 | 147 | 0.56 | 0.82 | 24 | empty |
| 4 | 133 | 0.56 | 0.83 | 22 | empty |
| 5 | 89 | 0.43 | 0.79 | 17 | MPO |
Interfaces
3 interfaces between chains.
- A–B · 2155 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 2149 Ų buried · 25 hydrogen bonds · protein-protein
- B–D · 473 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6HLM · Variant G129D of NuoEF from Aquifex aeolicus 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 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 6HLM · PDBe 6HLM · UniProt O66842 · UniProt O66841
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