Research workbench
Pharmacological chaperoning in human alpha-galactosidase
Analyse Pharmacological chaperoning in human alpha-galactosidase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3S5Y
- Type
- protein
- Length
- 781 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-galactosidase a
- EC
- 3.2.1.22
- UniProt
- P06280
- Ligands
- DGJ, NAG, BMA, FUC, XYP, MAN
- Pockets
- 3 · best druggability 0.55
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-galactosidase a (EC 3.2.1.22) | protein | 390 | 32% helix, 25% strand | P06280 |
| B | Alpha-galactosidase a (EC 3.2.1.22) | protein | 391 | 31% helix, 25% strand | P06280 |
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 · 11 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 4 copies
- FUC · alpha-L-fucopyranose · sugar · 4 copies · chains A
- XYP · beta-D-xylopyranose · sugar · 3 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 3 copies · chains B
- 2PE · Nonaethylene glycol · additive · 5 copies · chains A, B
- ACY · Acetic acid · additive · 2 copies · chains B
- EDO · 1,2-ethanediol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 309 | 0.55 | 0.76 | 37 | empty |
| 2 | 100 | 0.39 | 0.77 | 17 | empty |
| 3 | 106 | 0.38 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1078 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
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 P06280
- Elsewhere: RCSB PDB 3S5Y · PDBe 3S5Y · UniProt P06280
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