Research workbench
Structure of the octameric flavoenzyme vanillyl-alcohol oxidase: GLU502GLY mutant
Analyse Structure of the octameric flavoenzyme vanillyl-alcohol oxidase: GLU502GLY… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1W1M
- Type
- protein
- Length
- 1,100 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
- 12 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Vanillyl-alcohol oxidase (EC 1.1.3.13) | protein | 550 | 38% 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
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 669 | 0.88 | 0.92 | 75 | FAD, EUG |
| 2 | 581 | 0.88 | 0.93 | 74 | FAD, EUG |
| 3 | 1140 | 0.86 | 0.86 | 98 | empty |
| 4 | 57 | 0.56 | 0.89 | 17 | empty |
| 5 | 108 | 0.46 | 0.79 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 4108 Ų buried · 44 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (flavinylation).
Compared structures
- 1W1M · STRUCTURE OF THE OCTAMERIC FLAVOENZYME VANILLYL-ALCOHOL OXIDASE: Glu502Gly Mutant · 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 1W1M · PDBe 1W1M · UniProt P56216
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