MolNFT v1 · #91293 · protein
Complex structure of NADPH:QUINONE oxidoreductase with menadione in streptococcus mutans
4F8Y · NADPH quinone oxidoreductase: “Complex structure of NADPH:QUINONE oxidoreductase with menadione in streptococcus mutans”. X-ray diffraction, 2 ligands (FAD, VK3), 7 pockets (best druggability 0.71). MolNFT v1 #91293 on GenesisL1: 3D…
- PDB
- 4F8Y
- Type
- protein
- Length
- 768 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NADPH quinone oxidoreductase
- EC
- 1.6.5.2
- UniProt
- Q8DTD1
- Ligands
- FAD, VK3
- Pockets
- 7 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | NADPH quinone oxidoreductase (EC 1.6.5.2) | protein | 196 | 33% helix, 23% strand | Q8DTD1 |
| B, D | NADPH quinone oxidoreductase (EC 1.6.5.2) | protein | 188 | 37% helix, 22% strand | Q8DTD1 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- VK3 · Menadione · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 454 | 0.71 | 0.81 | 42 | VK3, FAD |
| 2 | 702 | 0.71 | 0.78 | 58 | empty |
| 3 | 473 | 0.70 | 0.80 | 42 | VK3, FAD |
| 4 | 419 | 0.70 | 0.81 | 40 | FAD, VK3 |
| 5 | 417 | 0.69 | 0.80 | 42 | FAD, VK3 |
Interfaces
3 interfaces between chains.
- C–D · 1667 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1644 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 425 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4F8Y · Complex structure of NADPH:qui oxidoreductase with menadione in Streptococcus mutans · the same entry in another collection · chain A against A, TM-score 1.00
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 Q8DTD1
- Elsewhere: RCSB PDB 4F8Y · PDBe 4F8Y · UniProt Q8DTD1
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