Research workbench
Crystal structure of apo-alpha glucosidase
Analyse Crystal structure of apo-alpha glucosidase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7L9E
- Type
- protein
- Length
- 1,878 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neutral alpha-glucosidase ab trypsin-cleaved fragment #1; Neutral alpha-glucosidase ab…
- EC
- 3.2.1.207
- UniProt
- Q8BHN3, O08795
- Ligands
- CA, SO4
- Pockets
- 20 · best druggability 0.69
Structure
x-ray diffraction · 7 distinct chains · 15% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | Neutral alpha-glucosidase ab trypsin-cleaved fragment #1 (EC 3.2.1.207) | protein | 150 | 5% helix, 45% strand | Q8BHN3 |
| F | Neutral alpha-glucosidase ab trypsin-cleaved fragment #2 (EC 3.2.1.207) | protein | 105 | 0% helix, 38% strand | Q8BHN3 |
| A, C | Neutral alpha-glucosidase ab trypsin-cleaved fragment #3 (EC 3.2.1.207) | protein | 597 | 28% helix, 27% strand | Q8BHN3 |
| B | Glucosidase 2 subunit beta | protein | 85 | 7% helix, 14% strand | O08795 |
| G | Neutral alpha-glucosidase ab trypsin-cleaved fragment #1 (EC 3.2.1.207) | protein | 153 | 7% helix, 44% strand | Q8BHN3 |
| H | Neutral alpha-glucosidase ab trypsin-cleaved fragment #2 (EC 3.2.1.207) | protein | 107 | 0% helix, 37% strand | Q8BHN3 |
| D | Glucosidase 2 subunit beta | protein | 84 | 7% helix, 14% strand | O08795 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 3 copies · chains A, C
- EDO · 1,2-ethanediol · additive · 23 copies · chains E, A, F, B, G, H, C, D
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · chains A
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 | 296 | 0.69 | 0.84 | 34 | SO4 |
| 2 | 62 | 0.60 | 0.91 | 15 | empty |
| 3 | 407 | 0.59 | 0.75 | 49 | empty |
| 4 | 255 | 0.58 | 0.78 | 40 | EDO |
| 5 | 277 | 0.58 | 0.77 | 37 | EDO |
Interfaces
9 interfaces between chains.
- F–A · 3899 Ų buried · 70 hydrogen bonds · protein-protein
- H–C · 3836 Ų buried · 68 hydrogen bonds · protein-protein
- G–H · 2081 Ų buried · 31 hydrogen bonds · protein-protein
- E–F · 1840 Ų buried · 31 hydrogen bonds · protein-protein
- G–C · 1788 Ų buried · 19 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 Q8BHN3
- Every structure of UniProt O08795
- Elsewhere: RCSB PDB 7L9E · PDBe 7L9E · UniProt Q8BHN3 · UniProt O08795
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