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Structure of D80A-fructofuranosidase from Xanthophyllomyces dendrorhous complexed with Raffinose
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
- 5FKC
- Type
- protein
- Length
- 1,248 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.82
- Source
- Xanthophyllomyces dendrorhous
- Molecule
- Beta-fructofuranosidase
- EC
- 3.2.1.26
- UniProt
- J7HDY4
- Ligands
- NAG, MAN, BMA, FRU, GLC, GLA
- Pockets
- 15 · best druggability 0.71
Structure
x-ray diffraction · resolution 1.82 · 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
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains A, B
- FRU · beta-D-fructofuranose · sugar · 2 copies · chains A, B
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A, B
- GLA · alpha-D-galactopyranose · sugar · 2 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 | 209 | 0.71 | 0.88 | 52 | empty |
| 2 | 230 | 0.70 | 0.86 | 52 | empty |
| 3 | 423 | 0.66 | 0.79 | 36 | FRU, GLC, GLA |
| 4 | 436 | 0.66 | 0.78 | 40 | FRU, GLC, GLA |
| 5 | 579 | 0.65 | 0.76 | 62 | empty |
Interfaces
1 interface between chains.
- A–B · 383 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 33 glycan, 2 disulfide (N-glycosylation, disulfide).
Compared structures
- 5FKC · 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 5FKC · PDBe 5FKC · UniProt J7HDY4
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