Research workbench
Murine endoplasmic reticulum alpha-glucosidase II with castanospermine
Analyse Murine endoplasmic reticulum alpha-glucosidase II with castanospermine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IED
- Type
- protein
- Length
- 945 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neutral alpha-glucosidase ab; Glucosidase 2 subunit beta
- EC
- 3.2.1.84
- UniProt
- Q8BHN3, O08795
- Ligands
- CTS, NAG, CA
- Pockets
- 9 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 20% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Neutral alpha-glucosidase ab (EC 3.2.1.84) | protein | 857 | 21% helix, 31% strand | Q8BHN3 |
| B | Glucosidase 2 subunit beta | protein | 88 | 7% helix, 14% strand | O08795 |
Ligands and binding sites
- CTS · Castanospermine · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- CA · Calcium ion · metal · 2 copies · chains A, B
- FMT · Formic acid · additive · 12 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · 4 copies · chains A, B
- P6G · Hexaethylene glycol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 429 | 0.61 | 0.76 | 48 | FMT, PG4 |
| 2 | 123 | 0.58 | 0.84 | 27 | EDO, CTS |
| 3 | 165 | 0.52 | 0.78 | 23 | empty |
| 4 | 122 | 0.44 | 0.78 | 20 | empty |
| 5 | 53 | 0.44 | 0.83 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 747 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 5IED · Murine endoplasmic reticulum alpha-glucosidase II with castanospermine · the same entry in another collection · chain A against A, TM-score 1.00
- Q8BHN3 · AlphaFold monomer V2.0 prediction for neutral alpha-glucosidase ab (Q8BHN3) · a predicted model of the same protein · chain A against A, TM-score 1.00
- O08795 · AlphaFold monomer V2.0 prediction for glucosidase 2 subunit beta (O08795) · a predicted model of the same protein · chain B against A, TM-score 0.91
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 5IED · PDBe 5IED · UniProt Q8BHN3 · UniProt O08795
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