Research workbench
Crystal structure of the deglycating enzyme fructosamine oxidase from aspergillus fumigatus (amadoriase II)
Analyse Crystal structure of the deglycating enzyme fructosamine oxidase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DJD
- Type
- protein
- Length
- 835 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fructosyl amine: oxygen oxidoreductase
- UniProt
- P78573
- Ligands
- FAD
- Pockets
- 4 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fructosyl amine: oxygen oxidoreductase | protein | 418 | 27% helix, 27% strand | P78573 |
| B | Fructosyl amine: oxygen oxidoreductase | protein | 417 | 27% helix, 27% strand | P78573 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1009 | 0.84 | 0.85 | 110 | FAD |
| 2 | 992 | 0.84 | 0.85 | 107 | FAD |
| 3 | 499 | 0.69 | 0.79 | 46 | empty |
| 4 | 349 | 0.58 | 0.76 | 41 | empty |
Interfaces
1 interface between chains.
- A–B · 555 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified, 2 cofactor (engineered, flavinylation).
Compared structures
- 3DJD · Crystal structure of the deglycating enzyme fructosamine oxidase from Aspergillus… · 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 P78573
- Elsewhere: RCSB PDB 3DJD · PDBe 3DJD · UniProt P78573
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