MolNFT v1 · #163196 · protein
NADH-dependent coenzyme a disulfide reductase soaked with menadione
6RVH · NADH oxidase: “NADH-dependent coenzyme a disulfide reductase soaked with menadione”. X-ray diffraction, 3 ligands (FAD, COA, VK3), 12 pockets (best druggability 0.84). MolNFT v1 #163196 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6RVH
- Type
- protein
- Length
- 1,772 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NADH oxidase
- EC
- 1.6.-.-
- UniProt
- Q72HK3
- Ligands
- FAD, COA, VK3
- Pockets
- 12 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | NADH oxidase (EC 1.6.-.-) | protein | 443 | 26% helix, 28% strand | Q72HK3 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- COA · Coenzyme A · 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
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 | 1046 | 0.84 | 0.85 | 115 | VK3, FAD, COA |
| 2 | 1138 | 0.83 | 0.84 | 122 | FAD, COA, VK3 |
| 3 | 1118 | 0.78 | 0.80 | 107 | FAD, COA |
| 4 | 1124 | 0.78 | 0.80 | 106 | FAD |
| 5 | 223 | 0.60 | 0.81 | 26 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2704 Ų buried · 26 hydrogen bonds · protein-protein
- A–D · 281 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 216 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 6RVH · NADH-dependent Coenzyme A Disulfide Reductase soaked with Menadione · 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 Q72HK3
- Elsewhere: RCSB PDB 6RVH · PDBe 6RVH · UniProt Q72HK3
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