MolNFT v1 · #89401 · protein
Pharmacological chaperones for human alpha-N-acetylgalactosaminidase
4DO6: “Pharmacological chaperones for human alpha-N-acetylgalactosaminidase”. X-ray diffraction, 6 ligands (NAG, MAN, BMA), 7 pockets (best druggability 0.56). MolNFT v1 #89401 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4DO6
- Type
- protein
- Length
- 788 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
- NAG, MAN, BMA, GLC, FUC, BGC
- Pockets
- 7 · best druggability 0.56
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-N-acetylgalactosaminidase (EC 3.2.1.49) | protein | 388 | 32% helix, 24% strand | P17050 |
| B | Alpha-N-acetylgalactosaminidase (EC 3.2.1.49) | protein | 400 | 34% helix, 23% strand | P17050 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 4 copies
- BMA · beta-D-mannopyranose · sugar · 3 copies
- GLC · alpha-D-glucopyranose · sugar · 3 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar
- BGC · beta-D-glucopyranose · sugar · chains A, B
- 2PE · Nonaethylene glycol · additive · 2 copies · chains B
- CIT · Citric acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 295 | 0.56 | 0.77 | 38 | empty |
| 2 | 216 | 0.52 | 0.77 | 43 | empty |
| 3 | 58 | 0.43 | 0.83 | 19 | empty |
| 4 | 69 | 0.42 | 0.81 | 22 | empty |
| 5 | 87 | 0.36 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1026 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 4DO6 · 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 4DO6 · PDBe 4DO6 · UniProt P17050
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