Research workbench
NADH-dependent coenzyme a disulfide reductase soaked with NADH
Analyse NADH-dependent coenzyme a disulfide reductase soaked with NADH in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RVB
- 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, NAD, COA
- Pockets
- 15 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | NADH oxidase (EC 1.6.-.-) | protein | 443 | 26% helix, 27% strand | Q72HK3 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- COA · Coenzyme A · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1096 | 0.83 | 0.84 | 108 | FAD, NAD, COA |
| 2 | 874 | 0.83 | 0.85 | 95 | FAD, NAD, COA |
| 3 | 1091 | 0.76 | 0.79 | 92 | FAD, NAD |
| 4 | 1168 | 0.76 | 0.79 | 102 | FAD, NAD |
| 5 | 221 | 0.61 | 0.81 | 23 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2685 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 273 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 255 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 6RVB · NADH-dependent Coenzyme A Disulfide Reductase soaked with NADH · 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 6RVB · PDBe 6RVB · UniProt Q72HK3
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