MolNFT v1 · #122072 · protein
Murine endoplasmic reticulum alpha-glucosidase II with 1- deoxynojirimycin
5IEE · Neutral alpha-glucosidase ab: “Murine endoplasmic reticulum alpha-glucosidase II with 1- deoxynojirimycin”. X-ray diffraction, 3 ligands (NOJ, NAG, CA), 8 pockets (best druggability 0.59). MolNFT v1 #122072 on GenesisL1: 3D…
- PDB
- 5IEE
- 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
- NOJ, NAG, CA
- Pockets
- 8 · best druggability 0.59
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
- NOJ · 1-deoxynojirimycin · 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 · 10 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B
- P6G · Hexaethylene glycol · additive · 4 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 418 | 0.59 | 0.75 | 49 | FMT, P6G |
| 2 | 119 | 0.56 | 0.83 | 27 | NOJ |
| 3 | 149 | 0.50 | 0.79 | 22 | empty |
| 4 | 117 | 0.44 | 0.78 | 20 | empty |
| 5 | 85 | 0.42 | 0.79 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 746 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 5IEE · Murine endoplasmic reticulum alpha-glucosidase II with 1-deoxynojirimycin · 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 5IEE · PDBe 5IEE · UniProt Q8BHN3 · UniProt O08795
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