Research workbench
Sugar beet alpha-glucosidase with acarbose
Analyse Sugar beet alpha-glucosidase with acarbose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3W37
- Type
- protein
- Length
- 826 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-glucosidase
- EC
- 3.2.1.20
- Ligands
- AC1, NAG, GLC, FUC, SO4
- Pockets
- 5 · best druggability 0.52
Structure
x-ray diffraction · 1 distinct chain · 21% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-glucosidase (EC 3.2.1.20) | protein | 826 | 21% helix, 32% strand | — |
Ligands and binding sites
- AC1 · 4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A
- FUC · alpha-L-fucopyranose · sugar
- SO4 · Sulfate ion · ion · chains A
- ACY · Acetic acid · additive · 3 copies · chains A
- GOL · Glycerol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 91 | 0.52 | 0.84 | 22 | SO4 |
| 2 | 109 | 0.50 | 0.81 | 25 | AC1 |
| 3 | 58 | 0.33 | 0.77 | 18 | GOL |
| 4 | 63 | 0.29 | 0.74 | 16 | empty |
| 5 | 51 | 0.28 | 0.74 | 13 | GOL |
Modifications
Observed in the structure: 3 glycan, 1 disulfide (N-glycosylation, disulfide).
Compared structures
- 3W37 · Sugar beet alpha-glucosidase with acarbose · 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 3W37 · PDBe 3W37
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