Research workbench
Structure of alpha-galactosidase from lactobacillus acidophilus ncfm with galactose
Analyse Structure of alpha-galactosidase from lactobacillus acidophilus ncfm with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XN2
- Type
- protein
- Length
- 729 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-galactosidase
- EC
- 3.2.1.22
- UniProt
- Q7WWP9
- Ligands
- GLA
- Pockets
- 7 · best druggability 0.59
Structure
x-ray diffraction · 1 distinct chain · 22% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-galactosidase (EC 3.2.1.22) | protein | 729 | 22% helix, 32% strand | Q7WWP9 |
Ligands and binding sites
- GLA · alpha-D-galactopyranose · sugar · chains A
- GOL · Glycerol · additive · 25 copies · chains A
- IMD · Imidazole · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 127 | 0.59 | 0.85 | 24 | GOL |
| 2 | 112 | 0.48 | 0.80 | 30 | GLA, IMD |
| 3 | 129 | 0.45 | 0.77 | 20 | empty |
| 4 | 122 | 0.42 | 0.77 | 24 | empty |
| 5 | 111 | 0.41 | 0.76 | 18 | GOL |
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 2XN2 · Structure of alpha-galactosidase from Lactobacillus acidophilus NCFM with galactose · 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
- Every structure of UniProt Q7WWP9
- Elsewhere: RCSB PDB 2XN2 · PDBe 2XN2 · UniProt Q7WWP9
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