Research workbench
Xylosidase from aspergillus niger
Analyse Xylosidase from aspergillus niger in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DRU
- Type
- protein
- Length
- 1,435 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycosyl hydrolases family 31 family protein
- UniProt
- A0A254U0T8
- Ligands
- MAN, NAG, BGC, BMA, XYS, GAL
- Pockets
- 11 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycosyl hydrolases family 31 family protein | protein | 718 | 24% helix, 26% strand | A0A254U0T8 |
| B | Glycosyl hydrolases family 31 family protein | protein | 717 | 24% helix, 26% strand | A0A254U0T8 |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 28 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 19 copies · chains A, B
- BGC · beta-D-glucopyranose · sugar · 9 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 5 copies · chains A, B
- XYS · alpha-D-xylopyranose · sugar · 5 copies · chains A, B
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 883 | 0.83 | 0.85 | 74 | empty |
| 2 | 636 | 0.72 | 0.79 | 78 | MAN, BGC, XYS |
| 3 | 403 | 0.66 | 0.79 | 55 | MAN |
| 4 | 210 | 0.56 | 0.79 | 32 | BGC, XYS |
| 5 | 276 | 0.55 | 0.76 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 2458 Ų buried · 32 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 glycan, 4 disulfide (N-glycosylation, disulfide).
Compared structures
- 6DRU · Xylosidase from Aspergillus niger · 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 A0A254U0T8
- Elsewhere: RCSB PDB 6DRU · PDBe 6DRU · UniProt A0A254U0T8
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