MolNFT v1 · #51546 · protein
Structure of the octameric flavoenzyme vanillyl-alcohol oxidase in complex with isoeugenol
2VAO: “Structure of the octameric flavoenzyme vanillyl-alcohol oxidase in complex with isoeugenol”. X-ray diffraction, 2 ligands (FAD, EUG), 15 pockets (best druggability 0.88). MolNFT v1 #51546 on GenesisL1: 3D structure, binding sites…
- PDB
- 2VAO
- Type
- protein
- Length
- 1,110 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vanillyl-alcohol oxidase
- EC
- 1.1.3.13
- UniProt
- P56216
- Ligands
- FAD, EUG
- Pockets
- 15 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Vanillyl-alcohol oxidase (EC 1.1.3.13) | protein | 555 | 39% helix, 18% strand | P56216 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- EUG · 2-methoxy-4-[(1E)-prop-1-en-1-yl]phenol · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 505 | 0.88 | 0.95 | 65 | FAD, EUG |
| 2 | 619 | 0.88 | 0.92 | 75 | FAD, EUG |
| 3 | 1137 | 0.87 | 0.87 | 96 | empty |
| 4 | 50 | 0.52 | 0.88 | 15 | empty |
| 5 | 57 | 0.50 | 0.86 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 3919 Ų buried · 46 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (flavinylation).
Compared structures
- 2VAO · Structure of the octameric flavoenzyme vanillyl-alcohol oxidase in complex with isoeugenol · the same entry in another collection · chain A against A, TM-score 1.00
- P56216 · AlphaFold monomer V2.0 prediction for vanillyl-alcohol oxidase (P56216) · a predicted model of the same protein · 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 P56216
- Elsewhere: RCSB PDB 2VAO · PDBe 2VAO · UniProt P56216
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