Research workbench
Crystal structure of GH36 alpha-galactosidase agaa A355E from geobacillus stearothermophilus in complex with 1- deoxygalactonojirimycin
Analyse Crystal structure of GH36 alpha-galactosidase agaa A355E from geobacillus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4FNS
- Type
- protein
- Length
- 2,872 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-galactosidase agaa
- EC
- 3.2.1.22
- UniProt
- Q9ALJ4
- Ligands
- DGJ, SO4
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 22% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Alpha-galactosidase agaa (EC 3.2.1.22) | protein | 718 | 22% helix, 32% strand | Q9ALJ4 |
Ligands and binding sites
- DGJ · (2R,3S,4R,5S)-2-(hydroxymethyl)piperidine-3,4,5-triol · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 8 copies · chains A, C, B, D
- EDO · 1,2-ethanediol · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1041 | 0.83 | 0.84 | 115 | empty |
| 2 | 1198 | 0.83 | 0.84 | 124 | SO4 |
| 3 | 1140 | 0.83 | 0.84 | 123 | SO4 |
| 4 | 679 | 0.83 | 0.87 | 65 | EDO |
| 5 | 575 | 0.83 | 0.88 | 67 | empty |
Interfaces
6 interfaces between chains.
- B–C · 3347 Ų buried · 73 hydrogen bonds · protein-protein
- A–D · 3313 Ų buried · 70 hydrogen bonds · protein-protein
- C–D · 1961 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 1930 Ų buried · 35 hydrogen bonds · protein-protein
- B–D · 843 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 4FNS · Crystal structure of GH36 alpha-galactosidase AgaA A355E from Geobacillus… · the same entry in another collection · chain D against D, TM-score 1.00
- Q9ALJ4 · AlphaFold monomer V2.0 prediction for alpha-galactosidase agaa (Q9ALJ4) · a predicted model of the same protein · chain D 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 Q9ALJ4
- Elsewhere: RCSB PDB 4FNS · PDBe 4FNS · UniProt Q9ALJ4
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