Research workbench
Structure of human alpha-galactosidase
Analyse Structure of 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
- 1R46
- 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
- NAG, MAN, FUC
- Pockets
- 3 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-galactosidase a (EC 3.2.1.22) | protein | 390 | 29% helix, 23% strand | P06280 |
| B | Alpha-galactosidase a (EC 3.2.1.22) | protein | 391 | 28% helix, 22% strand | P06280 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 8 copies · chains A
- FUC · alpha-L-fucopyranose · sugar
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, 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 | 426 | 0.59 | 0.75 | 67 | empty |
| 2 | 57 | 0.49 | 0.86 | 20 | empty |
| 3 | 72 | 0.32 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1168 Ų buried · 20 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 1R46 · PDBe 1R46 · UniProt P06280
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