MolNFT v1 · #127470 · protein
Structure of the Y108F mutant of vanillyl alcohol oxidase
5MXJ · Vanillyl-alcohol oxidase: “Structure of the Y108F mutant of vanillyl alcohol oxidase”. X-ray diffraction, 1 ligand (FAD), 10 pockets (best druggability 0.88). MolNFT v1 #127470 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5MXJ
- Type
- protein
- Length
- 1,106 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vanillyl-alcohol oxidase
- EC
- 1.1.3.38
- UniProt
- P56216
- Ligands
- FAD
- Pockets
- 10 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Vanillyl-alcohol oxidase (EC 1.1.3.38) | protein | 553 | 36% helix, 18% strand | P56216 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 464 | 0.88 | 0.95 | 65 | FAD |
| 2 | 494 | 0.87 | 0.93 | 73 | FAD |
| 3 | 1195 | 0.86 | 0.87 | 98 | GOL |
| 4 | 65 | 0.46 | 0.83 | 15 | empty |
| 5 | 147 | 0.46 | 0.77 | 41 | empty |
Interfaces
1 interface between chains.
- A–B · 4006 Ų buried · 44 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (flavinylation).
Compared structures
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 5MXJ · PDBe 5MXJ · UniProt P56216
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