MolNFT v1 · #121051 · protein
Murine endoplasmic reticulum alpha-glucosidase II with bound substrate analogue
5HJO · Neutral alpha-glucosidase ab: “Murine endoplasmic reticulum alpha-glucosidase II with bound substrate analogue”. X-ray diffraction, 6 ligands (DGO, Z61, NAG), 20 pockets (best druggability 0.68). MolNFT v1 #121051 on GenesisL1: 3D…
- PDB
- 5HJO
- Type
- protein
- Length
- 1,874 residues
- Chains
- 4
- 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
- DGO, Z61, NAG, BMA, MAN, CA
- Pockets
- 20 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 20% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Neutral alpha-glucosidase ab (EC 3.2.1.84) | protein | 854 | 21% helix, 31% strand | Q8BHN3 |
| B, D | Glucosidase 2 subunit beta | protein | 83 | 7% helix, 14% strand | O08795 |
Ligands and binding sites
- DGO · D-glucal · ligand · 4 copies · chains A, C, B, D
- Z61 · 2-deoxy-alpha-D-arabino-hexopyranose · ligand · 2 copies · chains A, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, C
- BMA · beta-D-mannopyranose · sugar · 2 copies
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A, C
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- FMT · Formic acid · additive · 20 copies · chains A, B, C, D
- ACT · Acetate ion · additive · 2 copies · chains A, C
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 298 | 0.68 | 0.83 | 36 | empty |
| 2 | 430 | 0.61 | 0.76 | 46 | FMT |
| 3 | 412 | 0.61 | 0.76 | 44 | FMT |
| 4 | 280 | 0.59 | 0.78 | 41 | DGO, Z61 |
| 5 | 275 | 0.59 | 0.78 | 37 | DGO, Z61 |
Interfaces
3 interfaces between chains.
- A–C · 902 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 753 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 748 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 5HJO · Murine endoplasmic reticulum alpha-glucosidase II with bound substrate analogue · 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 0.96
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 5HJO · PDBe 5HJO · UniProt Q8BHN3 · UniProt O08795
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