Research workbench
Crystal structure of a bacterial fucosidase with PHENYL((1R,2R,3R,4R, 5R,6R)-2,3,4-trihydroxy-5-methyl-7-AZABICYCLO[4.1.0]HEPTAN-7-yl) methanone
Analyse Crystal structure of a bacterial fucosidase with PHENYL((1R,2R,3R,4R… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WSK
- Type
- protein
- Length
- 1,782 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-L-fucosidase
- UniProt
- Q8A3I4
- Ligands
- 3U2, SO4
- Pockets
- 11 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Alpha-L-fucosidase | protein | 445 | 32% helix, 22% strand | Q8A3I4 |
| B | Alpha-L-fucosidase | protein | 446 | 31% helix, 22% strand | Q8A3I4 |
| C | Alpha-L-fucosidase | protein | 446 | 31% helix, 23% strand | Q8A3I4 |
Ligands and binding sites
- 3U2 · N-[(1S,2R,3R,4S,5R)-3,4,5-trihydroxy-2-methylcyclohexyl]benzamide · ligand · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 6 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
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 876 | 0.70 | 0.75 | 70 | empty |
| 2 | 584 | 0.68 | 0.77 | 57 | empty |
| 3 | 515 | 0.67 | 0.78 | 66 | empty |
| 4 | 108 | 0.44 | 0.78 | 20 | 3U2 |
| 5 | 75 | 0.41 | 0.79 | 16 | 3U2 |
Interfaces
3 interfaces between chains.
- A–B · 347 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 333 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 122 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 4WSK · Crystal structure of a bacterial fucosidase with… · 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 4WSK · PDBe 4WSK · UniProt Q8A3I4
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