MolNFT v1 · #114593 · protein
Oxidized quinone reductase 2 in complex with ethidium
5BUC · Ribosyldihydronicotinamide dehydrogenase [quinone]: “Oxidized quinone reductase 2 in complex with ethidium”. X-ray diffraction, 4 ligands (ET, FAD, ZN), 2 pockets (best druggability 0.78). MolNFT v1 #114593 on GenesisL1: 3D…
- PDB
- 5BUC
- Type
- protein
- Length
- 460 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribosyldihydronicotinamide dehydrogenase [quinone]
- EC
- 1.10.99.2
- UniProt
- P16083
- Ligands
- ET, FAD, ZN, SO4
- Pockets
- 2 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ribosyldihydronicotinamide dehydrogenase [quinone] (EC 1.10.99.2) | protein | 230 | 41% helix, 16% strand | P16083 |
Ligands and binding sites
- ET · Ethidium · ligand · 3 copies · chains A, B
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 582 | 0.78 | 0.84 | 42 | FAD, ET |
| 2 | 556 | 0.77 | 0.83 | 47 | ET, FAD |
Interfaces
1 interface between chains.
- A–B · 2051 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 5BUC · Oxidized qui reductase 2 in complex with ethidium · 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 P16083
- Elsewhere: RCSB PDB 5BUC · PDBe 5BUC · UniProt P16083
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