Research workbench
Murine endoplasmic reticulum alpha-glucosidase II with bound covalent intermediate
Analyse Murine endoplasmic reticulum alpha-glucosidase II with bound covalent… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HJR
- Type
- protein
- Length
- 1,875 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
- OXM, 5GF, NAG, MAN, BMA, CA
- Pockets
- 18 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Neutral alpha-glucosidase ab (EC 3.2.1.84) | protein | 855 | 21% helix, 31% strand | Q8BHN3 |
| B, D | Glucosidase 2 subunit beta | protein | 83 | 7% helix, 14% strand | O08795 |
| C | Neutral alpha-glucosidase ab (EC 3.2.1.84) | protein | 854 | 21% helix, 31% strand | Q8BHN3 |
Ligands and binding sites
- OXM · Oxamic acid · ligand · 3 copies · chains A, C
- 5GF · 5-fluoro-beta-D-glucopyranose · ligand · 2 copies · chains A, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, C
- MAN · alpha-D-mannopyranose · sugar · 3 copies · chains A, C
- BMA · beta-D-mannopyranose · sugar · 2 copies
- CA · Calcium ion · metal · 4 copies · chains B, C, D
- FMT · Formic acid · additive · 32 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, C
- P6G · Hexaethylene glycol · additive · 4 copies · chains A, C
- TAR · D(-)-tartaric acid · additive · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 318 | 0.68 | 0.83 | 32 | TAR, OXM |
| 2 | 386 | 0.60 | 0.76 | 42 | FMT |
| 3 | 293 | 0.59 | 0.77 | 39 | 5GF |
| 4 | 350 | 0.58 | 0.76 | 44 | FMT |
| 5 | 243 | 0.57 | 0.78 | 36 | 5GF |
Interfaces
3 interfaces between chains.
- A–C · 878 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 741 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 733 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 2 covalent, 2 glycan (disulfide, covalent ligand, N-glycosylation).
Compared structures
- 5HJR · Murine endoplasmic reticulum alpha-glucosidase II with bound covalent intermediate · 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 5HJR · PDBe 5HJR · UniProt Q8BHN3 · UniProt O08795
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