Research workbench
Crystal structure of beta-L-arabinopyranosidase complexed with D- galactose
Analyse Crystal structure of beta-L-arabinopyranosidase complexed with D- galactose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3A23
- Type
- protein
- Length
- 1,226 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative secreted alpha-galactosidase
- UniProt
- Q82L26
- Ligands
- 1PG, GAL, SO4
- Pockets
- 10 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 23% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative secreted alpha-galactosidase | protein | 614 | 22% helix, 32% strand | Q82L26 |
| B | Putative secreted alpha-galactosidase | protein | 612 | 23% helix, 32% strand | Q82L26 |
Ligands and binding sites
- 1PG · 2-(2-{2-[2-(2-methoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethanol · ligand · 2 copies · chains A, B
- GAL · beta-D-galactopyranose · sugar · 3 copies · chains A, B
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
- GOL · Glycerol · additive · 19 copies · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 590 | 0.83 | 0.88 | 98 | GOL |
| 2 | 287 | 0.81 | 0.92 | 56 | GOL |
| 3 | 337 | 0.73 | 0.85 | 55 | GOL |
| 4 | 234 | 0.70 | 0.86 | 37 | GAL, GOL |
| 5 | 228 | 0.69 | 0.85 | 43 | GAL |
Interfaces
1 interface between chains.
- A–B · 946 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 1 glycan (disulfide, glycosylation).
Compared structures
- 3A23 · Crystal Structure of beta-L-Arabinopyranosidase complexed with D-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 Q82L26
- Elsewhere: RCSB PDB 3A23 · PDBe 3A23 · UniProt Q82L26
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