MolNFT v1 · #119478 · protein
Crystal structure of eugenol oxidase in complex with isoeugenol
5FXD · Probable vanillyl-alcohol oxidase: “Crystal structure of eugenol oxidase in complex with isoeugenol”. X-ray diffraction, 2 ligands (FAD, H7Y), 9 pockets (best druggability 0.89). MolNFT v1 #119478 on GenesisL1: 3D structure, binding…
- PDB
- 5FXD
- Type
- protein
- Length
- 1,050 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable vanillyl-alcohol oxidase
- UniProt
- Q0SBK1
- Ligands
- FAD, H7Y
- Pockets
- 9 · best druggability 0.89
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Probable vanillyl-alcohol oxidase | protein | 525 | 40% helix, 20% strand | Q0SBK1 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- H7Y · Isoeugenol · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 516 | 0.89 | 0.96 | 67 | FAD, H7Y |
| 2 | 511 | 0.89 | 0.96 | 65 | FAD, H7Y |
| 3 | 1135 | 0.88 | 0.88 | 99 | empty |
| 4 | 59 | 0.51 | 0.86 | 15 | empty |
| 5 | 87 | 0.49 | 0.82 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 3552 Ų buried · 43 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (flavinylation).
Compared structures
- 5FXD · Crystal structure of eugenol oxidase in complex with isoeugenol · 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 Q0SBK1
- Elsewhere: RCSB PDB 5FXD · PDBe 5FXD · UniProt Q0SBK1
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