Research workbench
Structure of E230A-fructofuranosidase from schwanniomyces occidentalis complexed with fructosylnystose
Analyse Structure of E230A-fructofuranosidase from schwanniomyces occidentalis… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3U75
- Type
- protein
- Length
- 2,048 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fructofuranosidase
- EC
- 3.2.1.26
- Ligands
- FRU, NAG, GLC
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 3% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Fructofuranosidase (EC 3.2.1.26) | protein | 512 | 3% helix, 50% strand | — |
Ligands and binding sites
- FRU · beta-D-fructofuranose · sugar · 16 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A, B, C, D
- GLC · alpha-D-glucopyranose · sugar · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 301 | 0.82 | 0.93 | 44 | empty |
| 2 | 294 | 0.81 | 0.92 | 45 | empty |
| 3 | 631 | 0.79 | 0.84 | 77 | FRU |
| 4 | 664 | 0.78 | 0.83 | 80 | FRU, GLC |
| 5 | 59 | 0.68 | 0.96 | 21 | empty |
Interfaces
3 interfaces between chains.
- C–D · 2103 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 2094 Ų buried · 32 hydrogen bonds · protein-protein
- A–D · 440 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 glycan (N-glycosylation).
Compared structures
- 3U75 · Structure of E230A-fructofuranosidase from Schwanniomyces occidentalis 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
- Elsewhere: RCSB PDB 3U75 · PDBe 3U75
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