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Structure of D80A-fructofuranosidase from xanthophyllomyces dendrorhous complexed with nystose
Analyse Structure of D80A-fructofuranosidase from xanthophyllomyces dendrorhous… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FMD
- 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
- 14 · best druggability 0.74
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 · 39 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 20 copies · chains A, B
- FRU · beta-D-fructofuranose · sugar · 6 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 5 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
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 818 | 0.74 | 0.79 | 115 | empty |
| 2 | 207 | 0.73 | 0.89 | 48 | empty |
| 3 | 417 | 0.67 | 0.79 | 37 | GLC, FRU |
| 4 | 442 | 0.67 | 0.79 | 38 | GLC, FRU |
| 5 | 422 | 0.61 | 0.77 | 51 | NAG |
Interfaces
1 interface between chains.
- A–B · 386 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 33 glycan, 2 disulfide (N-glycosylation, disulfide).
Compared structures
- 5FMD · 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 5FMD · PDBe 5FMD · UniProt J7HDY4
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