Research workbench
Galactosidase domain of alpha-galactosidase-sucrose kinase, agask, in complex with galactose
Analyse Galactosidase domain of alpha-galactosidase-sucrose kinase, agask, in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YFO
- Type
- protein
- Length
- 719 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-galactosidase-sucrose kinase agask
- EC
- 3.2.1.22
- Ligands
- GLA, GAL, NA, PO4
- Pockets
- 6 · best druggability 0.49
Structure
x-ray diffraction · 1 distinct chain · 22% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-galactosidase-sucrose kinase agask (EC 3.2.1.22) | protein | 719 | 22% helix, 33% strand | — |
Ligands and binding sites
- GLA · alpha-D-galactopyranose · sugar · chains A
- GAL · beta-D-galactopyranose · sugar · chains A
- NA · Sodium ion · metal · 27 copies · chains A
- PO4 · Phosphate ion · ion · chains A
- PGE · Triethylene glycol · additive · 4 copies · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 97 | 0.49 | 0.81 | 18 | empty |
| 2 | 129 | 0.48 | 0.79 | 31 | NA, GLA, GAL |
| 3 | 129 | 0.43 | 0.77 | 27 | empty |
| 4 | 90 | 0.40 | 0.77 | 19 | empty |
| 5 | 60 | 0.40 | 0.81 | 15 | empty |
Compared structures
- 2YFO · GALACTOSIDASE DOMAIN OF ALPHA-GALACTOSIDASE-SUCROSE KINASE, AGASK, in complex with… · the same entry in another collection · 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
- Elsewhere: RCSB PDB 2YFO · PDBe 2YFO
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