MolNFT v1 · #128328 · protein
Crystal structure of human lysosomal acid-alpha-glucosidase, gaa
5NN3 · Lysosomal alpha-glucosidase: “Crystal structure of human lysosomal acid-alpha-glucosidase, gaa”. X-ray diffraction, 6 ligands (NAG, FUC, BMA), 11 pockets (best druggability 0.59). MolNFT v1 #128328 on GenesisL1: 3D structure…
- PDB
- 5NN3
- Type
- protein
- Length
- 845 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
- NAG, FUC, BMA, MAN, CL, SO4
- Pockets
- 11 · best druggability 0.59
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 | 845 | 22% helix, 30% strand | P10253 |
Ligands and binding sites
- 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 · 8 copies · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · 11 copies · chains A
- PGE · Triethylene glycol · additive · chains A
- PEG · Di(hydroxyethyl)ether · additive · 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 | 111 | 0.59 | 0.86 | 19 | empty |
| 2 | 92 | 0.58 | 0.86 | 21 | empty |
| 3 | 147 | 0.55 | 0.80 | 25 | empty |
| 4 | 90 | 0.52 | 0.84 | 24 | empty |
| 5 | 175 | 0.51 | 0.78 | 21 | SO4 |
Modifications
Observed in the structure: 5 disulfide, 5 glycan, 1 modified (disulfide, N-glycosylation, oxidation).
Compared structures
- 5NN3 · Crystal structure of human lysosomal acid-alpha-glucosidase, GAA · 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 5NN3 · PDBe 5NN3 · UniProt P10253
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