MolNFT v1 · #128330 · protein
Crystal structure of human lysosomal acid-alpha-glucosidase, gaa, in complex with 1-deoxynojirimycin
5NN5 · Lysosomal alpha-glucosidase: “Crystal structure of human lysosomal acid-alpha-glucosidase, gaa, in complex with 1-deoxynojirimycin”. X-ray diffraction, 7 ligands (NOJ, NAG, FUC), 11 pockets (best druggability 0.58). MolNFT v1…
- PDB
- 5NN5
- Type
- protein
- Length
- 846 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysosomal alpha-glucosidase
- EC
- 3.2.1.20
- UniProt
- P10253
- Ligands
- NOJ, NAG, FUC, BMA, MAN, CL, SO4
- Pockets
- 11 · best druggability 0.58
Structure
x-ray diffraction · 1 distinct chain · 22% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysosomal alpha-glucosidase (EC 3.2.1.20) | protein | 846 | 22% helix, 30% strand | P10253 |
Ligands and binding sites
- NOJ · 1-deoxynojirimycin · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A
- BMA · beta-D-mannopyranose · sugar · 2 copies
- MAN · alpha-D-mannopyranose · sugar
- CL · Chloride ion · ion · 6 copies · chains A
- SO4 · Sulfate ion · ion · 4 copies · chains A
- EDO · 1,2-ethanediol · additive · 7 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 104 | 0.58 | 0.86 | 20 | empty |
| 2 | 88 | 0.55 | 0.85 | 19 | empty |
| 3 | 95 | 0.55 | 0.85 | 26 | empty |
| 4 | 194 | 0.52 | 0.78 | 28 | SO4 |
| 5 | 82 | 0.51 | 0.84 | 24 | empty |
Modifications
Observed in the structure: 5 disulfide, 5 glycan, 1 modified (disulfide, N-glycosylation, oxidation).
Compared structures
- 5NN5 · Crystal structure of human lysosomal acid-alpha-glucosidase, GAA, in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- P10253 · AlphaFold monomer V2.0 prediction for lysosomal alpha-glucosidase (P10253) · a predicted model of the same protein · 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 P10253
- Elsewhere: RCSB PDB 5NN5 · PDBe 5NN5 · UniProt P10253
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