Research workbench
Co-crystal structure of alpha glucosidase with compound 9
Analyse Co-crystal structure of alpha glucosidase with compound 9 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KBJ
- Type
- protein
- Length
- 1,877 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
- WAV, CA, SO4
- Pockets
- 20 · best druggability 0.72
Structure
x-ray diffraction · 7 distinct chains · 16% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | Neutral alpha-glucosidase ab trypsin-cleaved fragment #1 (EC 3.2.1.207) | protein | 152 | 5% helix, 45% strand | Q8BHN3 |
| H | Neutral alpha-glucosidase ab trypsin-cleaved fragment #2 (EC 3.2.1.207) | protein | 105 | 0% helix, 37% strand | Q8BHN3 |
| A, C | Neutral alpha-glucosidase ab trypsin-cleaved fragment #3 (EC 3.2.1.207) | protein | 597 | 28% helix, 28% strand | Q8BHN3 |
| B | Glucosidase 2 subunit beta | protein | 82 | 7% helix, 15% strand | O08795 |
| I | Neutral alpha-glucosidase ab trypsin-cleaved fragment #1 (EC 3.2.1.207) | protein | 153 | 7% helix, 44% strand | Q8BHN3 |
| J | Neutral alpha-glucosidase ab trypsin-cleaved fragment #2 (EC 3.2.1.207) | protein | 107 | 0% helix, 36% strand | Q8BHN3 |
| D | Glucosidase 2 subunit beta | protein | 84 | 7% helix, 14% strand | O08795 |
Ligands and binding sites
- WAV · (1S,2S,3R,4S,5S)-1-(hydroxymethyl)-5-{[2-(2-{[2-nitro-4-(triazan-1-yl)phenyl]amino}ethoxy) ethyl]amino}cyclohexane-1,2,3,4-tetrol · ligand · 2 copies · chains H, A, C, J
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 8 copies · chains G, A, B, I, J, C
- EDO · 1,2-ethanediol · additive · 35 copies · chains G, H, A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 11 copies · chains A, B, I, J, C, D
- PGE · Triethylene glycol · additive · 5 copies · chains G, A, B
- PG4 · Tetraethylene glycol · additive · 2 copies · chains H, A, C, 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, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 138 | 0.72 | 0.91 | 44 | SO4 |
| 2 | 301 | 0.68 | 0.83 | 36 | SO4 |
| 3 | 267 | 0.61 | 0.79 | 37 | PG4, EDO, WAV |
| 4 | 211 | 0.59 | 0.80 | 36 | WAV |
| 5 | 369 | 0.58 | 0.75 | 45 | EDO, PEG |
Interfaces
9 interfaces between chains.
- J–C · 3882 Ų buried · 70 hydrogen bonds · protein-protein
- H–A · 3877 Ų buried · 67 hydrogen bonds · protein-protein
- I–J · 2045 Ų buried · 30 hydrogen bonds · protein-protein
- G–H · 1958 Ų buried · 32 hydrogen bonds · protein-protein
- I–C · 1778 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 4 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 7KBJ · PDBe 7KBJ · UniProt Q8BHN3 · UniProt O08795
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