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Co-crystal structure of alpha glucosidase with compound 1
Analyse Co-crystal structure of alpha glucosidase with compound 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7JTY
- Type
- protein
- Length
- 1,876 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha glucosidase 2 alpha neutral subunit; Glucosidase 2 subunit beta
- UniProt
- A1A4T2, O08795
- Ligands
- VND, CA, SO4
- Pockets
- 20 · best druggability 0.68
Structure
x-ray diffraction · 4 distinct chains · 20% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha glucosidase 2 alpha neutral subunit | protein | 851 | 21% helix, 32% strand | A1A4T2 |
| B | Glucosidase 2 subunit beta | protein | 83 | 7% helix, 14% strand | O08795 |
| C | Alpha glucosidase 2 alpha neutral subunit | protein | 857 | 21% helix, 32% strand | A1A4T2 |
| D | Glucosidase 2 subunit beta | protein | 85 | 7% helix, 14% strand | O08795 |
Ligands and binding sites
- VND · (1S,2S,3R,4S,5S)-5-(butylamino)-1-(hydroxymethyl) cyclohexane-1,2,3,4-tetrol · ligand · 2 copies · chains A, C
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 5 copies · chains A, C
- EDO · 1,2-ethanediol · additive · 11 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 329 | 0.68 | 0.82 | 36 | SO4 |
| 2 | 62 | 0.68 | 0.95 | 29 | SO4 |
| 3 | 291 | 0.60 | 0.78 | 47 | VND, EDO |
| 4 | 232 | 0.57 | 0.79 | 40 | VND, EDO |
| 5 | 328 | 0.57 | 0.76 | 47 | empty |
Interfaces
3 interfaces between chains.
- A–C · 866 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 750 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 740 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide (disulfide).
Compared structures
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 A1A4T2
- Every structure of UniProt O08795
- Elsewhere: RCSB PDB 7JTY · PDBe 7JTY · UniProt A1A4T2 · UniProt O08795
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