Research workbench
Crystal structure of alpha-galactosidase a at pH 4.5 complexed with 1- deoxygalactonijirimycin
Analyse Crystal structure of alpha-galactosidase a at pH 4.5 complexed with 1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GXT
- 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
- NOJ, NAG, MAN, SO4
- Pockets
- 3 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-galactosidase a (EC 3.2.1.22) | protein | 390 | 32% helix, 23% strand | P06280 |
| B | Alpha-galactosidase a (EC 3.2.1.22) | protein | 391 | 32% helix, 24% strand | P06280 |
Ligands and binding sites
- NOJ · 1-deoxynojirimycin · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 5 copies · chains B
- SO4 · Sulfate ion · ion · 5 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 | 704 | 0.66 | 0.75 | 90 | empty |
| 2 | 63 | 0.40 | 0.81 | 18 | SO4 |
| 3 | 50 | 0.37 | 0.80 | 15 | NOJ |
Interfaces
1 interface between chains.
- A–B · 1022 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 3GXT · Crystal structure of alpha-galactosidase A at pH 4.5 complexed with… · the same entry in another collection · chain A against A, TM-score 1.00
- P06280 · AlphaFold monomer V2.0 prediction for alpha-galactosidase a (P06280) · 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 P06280
- Elsewhere: RCSB PDB 3GXT · PDBe 3GXT · UniProt P06280
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