Research workbench
Pharmacological chaperones for human alpha-N-acetylgalactosaminidase
Analyse Pharmacological chaperones for human alpha-N-acetylgalactosaminidase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DO5
- Type
- protein
- Length
- 787 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-N-acetylgalactosaminidase
- EC
- 3.2.1.49
- UniProt
- P17050
- Ligands
- DGJ, NAG, MAN, BMA
- Pockets
- 6 · best druggability 0.56
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-N-acetylgalactosaminidase (EC 3.2.1.49) | protein | 387 | 32% helix, 25% strand | P17050 |
| B | Alpha-N-acetylgalactosaminidase (EC 3.2.1.49) | protein | 400 | 33% helix, 23% strand | P17050 |
Ligands and binding sites
- DGJ · (2R,3S,4R,5S)-2-(hydroxymethyl)piperidine-3,4,5-triol · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains A
- BMA · beta-D-mannopyranose · sugar · 2 copies
- GOL · Glycerol · additive · 14 copies · chains A, B
- CIT · Citric acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 297 | 0.56 | 0.77 | 41 | empty |
| 2 | 299 | 0.56 | 0.76 | 49 | GOL |
| 3 | 52 | 0.41 | 0.82 | 19 | DGJ, GOL |
| 4 | 69 | 0.39 | 0.79 | 21 | DGJ, GOL |
| 5 | 80 | 0.38 | 0.77 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1022 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 4DO5 · Pharmacological chaperones for human alpha-N-acetylgalactosaminidase · the same entry in another collection · chain A against A, TM-score 1.00
- P17050 · AlphaFold monomer V2.0 prediction for alpha-N-acetylgalactosaminidase (P17050) · 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 P17050
- Elsewhere: RCSB PDB 4DO5 · PDBe 4DO5 · UniProt P17050
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