MolNFT v1 · #119044 · protein
Structure of D80A-fructofuranosidase from xanthophyllomyces dendrorhous complexed with neokestose
5FK7 · Beta-fructofuranosidase: “Structure of D80A-fructofuranosidase from xanthophyllomyces dendrorhous complexed with neokestose”. X-ray diffraction, 5 ligands (NAG, MAN, FRU), 11 pockets (best druggability 0.78). MolNFT v1 #119044 on…
- PDB
- 5FK7
- Type
- protein
- Length
- 1,248 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-fructofuranosidase
- EC
- 3.2.1.26
- UniProt
- J7HDY4
- Ligands
- NAG, MAN, FRU, BMA, GLC
- Pockets
- 11 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 7% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-fructofuranosidase (EC 3.2.1.26) | protein | 624 | 7% helix, 43% strand | J7HDY4 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 38 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 18 copies · chains A, B
- FRU · beta-D-fructofuranose · sugar · 4 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains A, B
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1053 | 0.78 | 0.80 | 158 | empty |
| 2 | 457 | 0.67 | 0.79 | 40 | GLC, FRU |
| 3 | 432 | 0.67 | 0.79 | 36 | GLC, FRU |
| 4 | 415 | 0.61 | 0.77 | 50 | NAG |
| 5 | 61 | 0.44 | 0.83 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 389 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 glycan, 2 disulfide (N-glycosylation, disulfide).
Compared structures
- 5FK7 · 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 5FK7 · PDBe 5FK7 · UniProt J7HDY4
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