Research workbench
Co-crystal structure of alpha glucosidase with compound 4
Analyse Co-crystal structure of alpha glucosidase with compound 4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7K9Q
- Type
- protein
- Length
- 1,885 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
- W9S, CA, SO4
- Pockets
- 20 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 20% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha glucosidase 2 alpha neutral subunit | protein | 853 | 21% helix, 32% strand | A1A4T2 |
| B | Glucosidase 2 subunit beta | protein | 87 | 7% helix, 14% strand | O08795 |
| C | Alpha glucosidase 2 alpha neutral subunit | protein | 857 | 21% helix, 31% strand | A1A4T2 |
| D | Glucosidase 2 subunit beta | protein | 88 | 7% helix, 14% strand | O08795 |
Ligands and binding sites
- W9S · (1S,2S,3R,4S,5S)-5-amino-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 · 6 copies · chains A, C, B
- EDO · 1,2-ethanediol · additive · 33 copies · chains A, C, B, D
- PEG · Di(hydroxyethyl)ether · additive · 10 copies · chains A, C, D
- PGE · Triethylene glycol · additive · 4 copies · chains A, B, C
- PG4 · Tetraethylene glycol · additive · chains 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 | 67 | 0.71 | 0.96 | 29 | empty |
| 2 | 262 | 0.67 | 0.84 | 38 | SO4 |
| 3 | 93 | 0.63 | 0.89 | 32 | empty |
| 4 | 254 | 0.59 | 0.79 | 37 | W9S, PEG, EDO |
| 5 | 264 | 0.59 | 0.78 | 40 | W9S, EDO |
Interfaces
3 interfaces between chains.
- A–C · 900 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 738 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 734 Ų buried · 19 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 7K9Q · PDBe 7K9Q · UniProt A1A4T2 · UniProt O08795
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