Research workbench
Crystal structure of acid-alpha-galactosidase a complexed with galactose at pH 4.5
Analyse Crystal structure of acid-alpha-galactosidase a complexed with galactose at pH… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GXP
- 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
- TAM, NAG, MAN, GLA, SO4
- Pockets
- 3 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-galactosidase a (EC 3.2.1.22) | protein | 390 | 31% helix, 25% strand | P06280 |
| B | Alpha-galactosidase a (EC 3.2.1.22) | protein | 391 | 31% helix, 24% strand | P06280 |
Ligands and binding sites
- TAM · Tris(hydroxyethyl)aminomethane · ligand · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 3 copies
- GLA · alpha-D-galactopyranose · sugar · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 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 | 514 | 0.63 | 0.76 | 64 | empty |
| 2 | 179 | 0.46 | 0.75 | 34 | empty |
| 3 | 73 | 0.41 | 0.80 | 17 | TAM |
Interfaces
1 interface between chains.
- A–B · 1071 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 8 glycan (disulfide, N-glycosylation, glycosylation).
Compared structures
- 3GXP · Crystal structure of acid-alpha-galactosidase A complexed with galactose at pH 4.5 · 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 3GXP · PDBe 3GXP · UniProt P06280
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