MolNFT v1 · #119480 · protein
Crystal structure of eugenol oxidase in complex with benzoate
5FXF: “Crystal structure of eugenol oxidase in complex with benzoate”. X-ray diffraction, 2 ligands (FAD, BEZ), 9 pockets (best druggability 0.88). MolNFT v1 #119480 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5FXF
- 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, BEZ
- Pockets
- 9 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Eugenol oxidase (EC 1.1.3.38) | protein | 525 | 39% helix, 20% strand | Q0SBK1 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- BEZ · Benzoic acid · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 5 copies · 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 482 | 0.88 | 0.96 | 64 | FAD, BEZ |
| 2 | 485 | 0.88 | 0.95 | 63 | FAD, BEZ |
| 3 | 1183 | 0.87 | 0.88 | 102 | GOL |
| 4 | 79 | 0.52 | 0.85 | 18 | empty |
| 5 | 63 | 0.51 | 0.86 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 3533 Ų buried · 43 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (flavinylation).
Compared structures
- 5FXF · Crystal structure of eugenol oxidase in complex with benzoate · 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 5FXF · PDBe 5FXF · UniProt Q0SBK1
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