Research workbench
Structure of beta-fructofuranosidase from schwanniomyces occidentalis complexed with fructosyl-erythritol
Analyse Structure of beta-fructofuranosidase from schwanniomyces occidentalis complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6S2B
- Type
- protein
- Length
- 1,024 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fructofuranosidase
- EC
- 3.2.1.26
- UniProt
- E5D0X5
- Ligands
- KTE, NAG, BMA, ZN
- Pockets
- 8 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 4% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Fructofuranosidase (EC 3.2.1.26) | protein | 512 | 4% helix, 50% strand | E5D0X5 |
Ligands and binding sites
- KTE · (2~{S},3~{R})-4-[(2~{R},3~{S},4~{S},5~{R})-2,5-bis(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]oxybutane-1,2,3-triol · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · chains A
- ZN · Zinc ion · metal · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 355 | 0.83 | 0.93 | 66 | EDO |
| 2 | 713 | 0.78 | 0.83 | 83 | KTE |
| 3 | 391 | 0.60 | 0.76 | 50 | KTE |
| 4 | 294 | 0.58 | 0.77 | 32 | empty |
| 5 | 263 | 0.58 | 0.78 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 2192 Ų buried · 37 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 glycan (N-glycosylation).
Compared structures
- 6S2B · Structure of beta-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
- Every structure of UniProt E5D0X5
- Elsewhere: RCSB PDB 6S2B · PDBe 6S2B · UniProt E5D0X5
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