MolNFT v1 · #128895 · protein
Structure of D80A-fructofuranosidase from xanthophyllomyces dendrorhous complexed with fructosyl-hydroxytyrosol
5O47 · Beta-fructofuranosidase: “Structure of D80A-fructofuranosidase from xanthophyllomyces dendrorhous complexed with…”. X-ray diffraction, 6 ligands (9OK, 9WZ, 975), 15 pockets (best druggability 0.73). MolNFT v1 #128895 on GenesisL1…
- PDB
- 5O47
- Type
- protein
- Length
- 1,248 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-fructofuranosidase
- UniProt
- J7HDY4
- Ligands
- 9OK, 9WZ, 975, NAG, MAN, BMA
- Pockets
- 15 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 7% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-fructofuranosidase | protein | 624 | 7% helix, 43% strand | J7HDY4 |
Ligands and binding sites
- 9OK · 2-(3,4-dihydroxyphenyl)ethyl beta-D-fructofuranoside · ligand · 2 copies · chains A, B
- 9WZ · 2-hydroxy-4-(2-hydroxyethyl)phenyl beta-D-fructofuranoside · ligand · 2 copies · chains A, B
- 975 · 4-(2-hydroxyethyl)benzene-1,2-diol · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 39 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 20 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 22 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 206 | 0.73 | 0.89 | 52 | empty |
| 2 | 186 | 0.72 | 0.89 | 48 | empty |
| 3 | 491 | 0.69 | 0.79 | 40 | 9OK, 9WZ, EDO |
| 4 | 490 | 0.69 | 0.79 | 41 | 9OK, 9WZ, EDO |
| 5 | 412 | 0.64 | 0.78 | 54 | empty |
Interfaces
1 interface between chains.
- A–B · 390 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 33 glycan, 2 disulfide (N-glycosylation, disulfide).
Compared structures
- 5O47 · Structure of D80A-fructofuranosidase from Xanthophyllomyces dendrorhous complexed with… · 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 J7HDY4
- Elsewhere: RCSB PDB 5O47 · PDBe 5O47 · UniProt J7HDY4
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.