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First crystal structure of an endo-inulinase, from aspergillus ficuum: structural analysis and comparison with other GH32 enzymes.
Analyse First crystal structure of an endo-inulinase, from aspergillus ficuum… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3RWK
- Type
- protein
- Length
- 493 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inulinase
- EC
- 3.2.1.7
- UniProt
- O94220
- Ligands
- MAN, NAG, FRU, BMA, NA, SO4
- Pockets
- 4 · best druggability 0.59
Structure
x-ray diffraction · 1 distinct chain · 5% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| X | Inulinase (EC 3.2.1.7) | protein | 493 | 5% helix, 49% strand | O94220 |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 3 copies · chains X
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains X
- FRU · beta-D-fructofuranose · sugar · 2 copies · chains X
- BMA · beta-D-mannopyranose · sugar
- NA · Sodium ion · metal · chains X
- SO4 · Sulfate ion · ion · chains X
- ACT · Acetate ion · additive · chains X
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 330 | 0.59 | 0.77 | 34 | FRU |
| 2 | 239 | 0.52 | 0.76 | 34 | SO4 |
| 3 | 85 | 0.43 | 0.80 | 26 | ACT |
| 4 | 66 | 0.40 | 0.79 | 16 | empty |
Modifications
Observed in the structure: 1 glycan (N-glycosylation).
Compared structures
- 3RWK · First crystal structure of an endo-inulinase, from Aspergillus ficuum: structural… · the same entry in another collection · chain X against X, TM-score 1.00
- O94220 · AlphaFold monomer V2.0 prediction for extracellular endo-inulinase INU2 (O94220) · a predicted model of the same protein · chain X against A, TM-score 0.99
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 O94220
- Elsewhere: RCSB PDB 3RWK · PDBe 3RWK · UniProt O94220
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