MolNFT v1 · #109801 · protein
Crystal structure of quinone reductase II in complex with a 2-(4- methoxy-phenyl)-5-methoxy-indol-3-one molecule
4XDH · Ribosyldihydronicotinamide dehydrogenase [quinone]: “Crystal structure of quinone reductase II in complex with a 2-(4- methoxy-phenyl)-5-methoxy-indol-3-one…”. X-ray diffraction, 4 ligands (FAD, 3ZV, ZN), 2 pockets (best…
- PDB
- 4XDH
- Type
- protein
- Length
- 459 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
- FAD, 3ZV, ZN, SO4
- Pockets
- 2 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribosyldihydronicotinamide dehydrogenase [quinone] (EC 1.10.99.2) | protein | 229 | 40% helix, 17% strand | P16083 |
| B | Ribosyldihydronicotinamide dehydrogenase [quinone] (EC 1.10.99.2) | protein | 230 | 40% helix, 16% strand | P16083 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- 3ZV · 5-methoxy-2-(4-methoxyphenyl)-3H-indol-3-one · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
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 | 516 | 0.78 | 0.85 | 43 | FAD, 3ZV |
| 2 | 544 | 0.78 | 0.84 | 45 | FAD, 3ZV |
Interfaces
1 interface between chains.
- A–B · 2101 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 4XDH · Crystal Structure of Qui Reductase II in complex with a… · 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 4XDH · PDBe 4XDH · UniProt P16083
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