MolNFT v1 · #96307 · protein
Crystal structure of a bacterial fucosidase with iminosugar inhibitor (2S,3S,4R,5S)-2-[N-(PROPYLFERROCENE)]AMINOETHYL-5-methylpyrrolidine- 3,4-diol
4JFW · Alpha-L-fucosidase: “Crystal structure of a bacterial fucosidase with iminosugar inhibitor…”. X-ray diffraction, 2 ligands (H58, SO4), 8 pockets (best druggability 0.68). MolNFT v1 #96307 on GenesisL1: 3D structure, binding sites…
- PDB
- 4JFW
- Type
- protein
- Length
- 1,755 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-L-fucosidase
- UniProt
- Q8A3I4
- Ligands
- H58, SO4
- Pockets
- 8 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Alpha-L-fucosidase | protein | 439 | 32% helix, 22% strand | Q8A3I4 |
| D | Alpha-L-fucosidase | protein | 438 | 32% helix, 22% strand | Q8A3I4 |
Ligands and binding sites
- H58 · (3alpha)-[3-({2-[(2S,3S,4R,5S)-3,4-dihydroxy-5-methylpyrrolidin-2-yl]ethyl}amino)propyl]ferrocene · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 7 copies · chains A, B, C, D
- IMD · Imidazole · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 836 | 0.68 | 0.74 | 72 | empty |
| 2 | 431 | 0.63 | 0.77 | 56 | empty |
| 3 | 405 | 0.61 | 0.77 | 48 | empty |
| 4 | 90 | 0.41 | 0.78 | 25 | empty |
| 5 | 61 | 0.40 | 0.80 | 17 | H58, SO4 |
Interfaces
3 interfaces between chains.
- A–C · 310 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 268 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 92 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4JFW · 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 4JFW · PDBe 4JFW · UniProt Q8A3I4
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