Research workbench
Crystal structure of alpha-glucosidase mutant D202N in complex with glucose and glycerol
Analyse Crystal structure of alpha-glucosidase mutant D202N in complex with glucose and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WY3
- Type
- protein
- Length
- 1,070 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-glucosidase
- EC
- 3.2.1.20
- UniProt
- H3K096
- Ligands
- BGC, MG
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 28% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Alpha-glucosidase (EC 3.2.1.20) | protein | 535 | 28% helix, 19% strand | H3K096 |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 4 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 728 | 0.77 | 0.82 | 52 | empty |
| 2 | 327 | 0.73 | 0.85 | 50 | GOL, BGC |
| 3 | 341 | 0.72 | 0.84 | 49 | GOL, BGC |
| 4 | 52 | 0.47 | 0.85 | 15 | empty |
| 5 | 59 | 0.39 | 0.80 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 572 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3WY3 · Crystal structure of alpha-glucosidase mutant D202N in complex with glucose and glycerol · 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 H3K096
- Elsewhere: RCSB PDB 3WY3 · PDBe 3WY3 · UniProt H3K096
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