Research workbench
Crystal structure of the deglycating enzyme fructosamine oxidase from aspergillus fumigatus (amadoriase II) in complex with fsa
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
- 3DJE
- Type
- protein
- Length
- 873 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fructosyl amine: oxygen oxidoreductase
- UniProt
- P78573
- Ligands
- FAD, FSA
- Pockets
- 4 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fructosyl amine: oxygen oxidoreductase | protein | 436 | 29% helix, 25% strand | P78573 |
| B | Fructosyl amine: oxygen oxidoreductase | protein | 437 | 28% helix, 25% strand | P78573 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- FSA · 1-S-(carboxymethyl)-1-thio-beta-D-fructopyranose · ligand · 2 copies · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains 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 | 805 | 0.86 | 0.89 | 112 | FAD, FSA |
| 2 | 840 | 0.86 | 0.88 | 113 | FAD, FSA |
| 3 | 459 | 0.64 | 0.77 | 34 | empty |
| 4 | 315 | 0.56 | 0.76 | 38 | empty |
Interfaces
1 interface between chains.
- A–B · 543 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified, 2 cofactor (engineered, flavinylation).
Compared structures
- 3DJE · 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 3DJE · PDBe 3DJE · UniProt P78573
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