Research workbench
Crystal structure of partially deglycosylated acid beta-glucosidase
Analyse Crystal structure of partially deglycosylated acid beta-glucosidase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2F61
- Type
- protein
- Length
- 994 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acid beta-glucosidase
- EC
- 3.2.1.45
- Ligands
- NAG, SO4
- Pockets
- 7 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Acid beta-glucosidase (EC 3.2.1.45) | protein | 497 | 27% helix, 27% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains B, A
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 416 | 0.65 | 0.79 | 52 | empty |
| 2 | 219 | 0.59 | 0.80 | 40 | empty |
| 3 | 119 | 0.49 | 0.80 | 22 | empty |
| 4 | 96 | 0.45 | 0.80 | 21 | empty |
| 5 | 68 | 0.38 | 0.79 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 390 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 2F61 · Crystal structure of partially deglycosylated acid beta-glucosidase · 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 2F61 · PDBe 2F61
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