MolNFT v1 · #116678 · protein
Crystal structure of glucosidase II alpha subunit (dnj-bound from)
5DKY · Alpha glucosidase-like protein: “Crystal structure of glucosidase II alpha subunit (dnj-bound from)”. X-ray diffraction, 1 ligand (NOJ), 12 pockets (best druggability 0.74). MolNFT v1 #116678 on GenesisL1: 3D structure, binding…
- PDB
- 5DKY
- Type
- protein
- Length
- 928 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha glucosidase-like protein
- UniProt
- G0SG42
- Ligands
- NOJ
- Pockets
- 12 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 22% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha glucosidase-like protein | protein | 928 | 22% helix, 29% strand | G0SG42 |
Ligands and binding sites
- NOJ · 1-deoxynojirimycin · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 80 | 0.74 | 0.96 | 21 | NOJ |
| 2 | 56 | 0.67 | 0.96 | 31 | empty |
| 3 | 81 | 0.60 | 0.89 | 18 | empty |
| 4 | 212 | 0.52 | 0.77 | 32 | empty |
| 5 | 177 | 0.48 | 0.76 | 30 | empty |
Compared structures
- 5DKY · Crystal structure of glucosidase II alpha subunit (DNJ-bound from) · the same entry in another collection · chain A against A, TM-score 1.00
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 G0SG42
- Elsewhere: RCSB PDB 5DKY · PDBe 5DKY · UniProt G0SG42
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