Research workbench
Murine endoplasmic reticulum alpha-glucosidase I with N-9'- methoxynonyl-1-deoxynojirimycin
Analyse Murine endoplasmic reticulum alpha-glucosidase I with N-9'… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MHF
- Type
- protein
- Length
- 3,032 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mannosyl-oligosaccharide glucosidase
- EC
- 3.2.1.106
- UniProt
- Q80UM7
- Ligands
- 7PG, 6A9, NAG, BMA, SO4
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 4 distinct chains · 32% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mannosyl-oligosaccharide glucosidase (EC 3.2.1.106) | protein | 751 | 32% helix, 24% strand | Q80UM7 |
| B | Mannosyl-oligosaccharide glucosidase (EC 3.2.1.106) | protein | 752 | 32% helix, 24% strand | Q80UM7 |
| C | Mannosyl-oligosaccharide glucosidase (EC 3.2.1.106) | protein | 762 | 32% helix, 24% strand | Q80UM7 |
| D | Mannosyl-oligosaccharide glucosidase (EC 3.2.1.106) | protein | 767 | 33% helix, 24% strand | Q80UM7 |
Ligands and binding sites
- 7PG · 2,5,8,11,14,17,20,23-octaoxapentacosan-25-ol · ligand · 6 copies · chains A, D, B, C
- 6A9 · N-9'-methoxynonyl-1-deoxynojirimycin · ligand · 4 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B, C, D
- BMA · beta-D-mannopyranose · sugar · 2 copies
- SO4 · Sulfate ion · ion · 12 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1184 | 0.88 | 0.89 | 133 | empty |
| 2 | 1160 | 0.88 | 0.89 | 133 | empty |
| 3 | 709 | 0.73 | 0.79 | 70 | 6A9 |
| 4 | 395 | 0.69 | 0.81 | 53 | SO4 |
| 5 | 354 | 0.69 | 0.82 | 50 | 6A9 |
Interfaces
5 interfaces between chains.
- B–C · 1549 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 1498 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 384 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 370 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 149 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 60 modified, 4 glycan (methylation, nonstandard, N-glycosylation).
Compared structures
- 5MHF · Murine endoplasmic reticulum alpha-glucosidase I with… · the same entry in another collection · chain D against D, TM-score 1.00
- Q80UM7 · AlphaFold monomer V2.0 prediction for mannosyl-oligosaccharide glucosidase (Q80UM7) · a predicted model of the same protein · chain D against A, TM-score 0.99
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 Q80UM7
- Elsewhere: RCSB PDB 5MHF · PDBe 5MHF · UniProt Q80UM7
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