MolNFT v1 · #110446 · protein
The crystal structure of fructosyl amine: oxygen oxidoreductase (amadoriase I) from aspergillus fumigatus in complex with the substrate fructosyl lysine
4XWZ · Fructosyl AMINE:OXYGEN oxidoreductase: “The crystal structure of fructosyl amine: oxygen oxidoreductase (amadoriase I) from aspergillus fumigatus in…”. X-ray diffraction, 3 ligands (FAD, LYS, BDF), 8 pockets (best druggability…
- PDB
- 4XWZ
- Type
- protein
- Length
- 874 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fructosyl AMINE:OXYGEN oxidoreductase
- UniProt
- O42629
- Ligands
- FAD, LYS, BDF
- Pockets
- 8 · best druggability 0.85
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 | 438 | 26% helix, 27% strand | O42629 |
| B | Fructosyl AMINE:OXYGEN oxidoreductase | protein | 436 | 28% helix, 27% strand | O42629 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- LYS · Lysine · ligand · 2 copies · chains A, B
- BDF · beta-D-fructopyranose · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1043 | 0.85 | 0.86 | 100 | FAD, LYS, BDF |
| 2 | 1063 | 0.85 | 0.86 | 104 | FAD, LYS, BDF |
| 3 | 96 | 0.59 | 0.87 | 25 | empty |
| 4 | 154 | 0.56 | 0.82 | 29 | empty |
| 5 | 78 | 0.39 | 0.78 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 581 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4XWZ · The crystal structure of Fructosyl amine: oxygen oxidoreductase (Amadoriase I) from… · the same entry in another collection · chain B against B, 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 O42629
- Elsewhere: RCSB PDB 4XWZ · PDBe 4XWZ · UniProt O42629
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