Research workbench
Crystal structure of eugenol oxidase in complex with vanillin
Analyse Crystal structure of eugenol oxidase in complex with vanillin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FXP
- Type
- protein
- Length
- 1,050 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Eugenol oxidase
- EC
- 1.1.3.38
- UniProt
- Q0SBK1
- Ligands
- FAD, V55
- Pockets
- 9 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Eugenol oxidase (EC 1.1.3.38) | protein | 525 | 38% helix, 19% strand | Q0SBK1 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- V55 · 4-hydroxy-3-methoxybenzaldehyde · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 510 | 0.88 | 0.95 | 64 | FAD, V55 |
| 2 | 489 | 0.88 | 0.95 | 64 | FAD, V55 |
| 3 | 1170 | 0.87 | 0.88 | 91 | empty |
| 4 | 69 | 0.47 | 0.83 | 15 | empty |
| 5 | 53 | 0.47 | 0.85 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 3604 Ų buried · 42 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (flavinylation).
Compared structures
- 5FXP · Crystal structure of eugenol oxidase in complex with vanillin · 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 5FXP · PDBe 5FXP · UniProt Q0SBK1
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