MolNFT v1 · #96304 · protein
Crystal structure of a bacterial fucosidase with iminosugar inhibitor N-desmethyl-4-epi-(+)-codonopsinine
4JFT · Alpha-L-fucosidase: “Crystal structure of a bacterial fucosidase with iminosugar inhibitor N-desmethyl-4-epi-(+)-codonopsinine”. X-ray diffraction, 2 ligands (1KN, SO4), 4 pockets (best druggability 0.67). MolNFT v1 #96304 on…
- PDB
- 4JFT
- 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
- 1KN, SO4
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Alpha-L-fucosidase | protein | 438 | 32% helix, 23% strand | Q8A3I4 |
Ligands and binding sites
- 1KN · (2S,3S,4R,5S)-2-(4-methoxyphenyl)-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 · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 626 | 0.67 | 0.76 | 69 | GOL |
| 2 | 147 | 0.46 | 0.76 | 28 | 1KN |
| 3 | 51 | 0.41 | 0.83 | 16 | empty |
| 4 | 68 | 0.38 | 0.78 | 16 | 1KN |
Interfaces
1 interface between chains.
- A–B · 278 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4JFT · Crystal structure of a bacterial fucosidase with iminosugar inhibitor… · 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 4JFT · PDBe 4JFT · UniProt Q8A3I4
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