Research workbench
Co-crystal structure of alpha glucosidase with compound 2
Analyse Co-crystal structure of alpha glucosidase with compound 2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7K9N
- Type
- protein
- Length
- 1,883 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
- W9G, CA, SO4
- Pockets
- 20 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha glucosidase 2 alpha neutral subunit | protein | 853 | 21% helix, 32% strand | A1A4T2 |
| B, D | Glucosidase 2 subunit beta | protein | 87 | 7% helix, 14% strand | O08795 |
| C | Alpha glucosidase 2 alpha neutral subunit | protein | 856 | 21% helix, 32% strand | A1A4T2 |
Ligands and binding sites
- W9G · (1S,2S,3R,4S,5S)-1-(hydroxymethyl)-5-[(9-methoxynonyl) amino]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 · 8 copies · chains A, C
- EDO · 1,2-ethanediol · additive · 28 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 8 copies · chains A, B, C, D
- PGE · Triethylene glycol · additive · 4 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · 3 copies · chains A, C, D
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 | 281 | 0.68 | 0.84 | 36 | SO4 |
| 2 | 279 | 0.61 | 0.79 | 39 | W9G, EDO |
| 3 | 269 | 0.59 | 0.78 | 40 | W9G, EDO |
| 4 | 320 | 0.56 | 0.76 | 48 | empty |
| 5 | 60 | 0.56 | 0.89 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–C · 891 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 743 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 737 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 2 covalent (disulfide, additive adduct).
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 7K9N · PDBe 7K9N · UniProt A1A4T2 · UniProt O08795
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.