Research workbench
Crystal structure of a GH29 alpha-L-fucosidase GH29 from bacteroides thetaiotaomicron in complex with a 5-membered iminocyclitol inhibitor
Analyse Crystal structure of a GH29 alpha-L-fucosidase GH29 from bacteroides… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4J28
- Type
- protein
- Length
- 876 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-L-fucosidase
- UniProt
- Q8A3I4
- Ligands
- EAT, SO4
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Alpha-L-fucosidase | protein | 438 | 32% helix, 22% strand | Q8A3I4 |
Ligands and binding sites
- EAT · (2S,3S,4R,5S)-2-(1H-benzimidazol-2-yl)-5-methylpyrrolidine-3,4-diol · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- IMD · Imidazole · additive · 6 copies · chains A, B
- GOL · Glycerol · additive · 2 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 | 699 | 0.69 | 0.77 | 81 | SO4, GOL |
| 2 | 101 | 0.45 | 0.79 | 24 | EAT |
| 3 | 55 | 0.35 | 0.78 | 16 | EAT, IMD |
Interfaces
1 interface between chains.
- A–B · 278 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4J28 · Crystal structure of a gh29 alpha-l-fucosidase gh29 from bacteroides thetaiotaomicron in… · 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 Q8A3I4
- Elsewhere: RCSB PDB 4J28 · PDBe 4J28 · UniProt Q8A3I4
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