Research workbench
Alpha-L-fucosidase complexed with inhibitor, F10
Analyse Alpha-L-fucosidase complexed with inhibitor, F10 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ZX5
- Type
- protein
- Length
- 882 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-L-fucosidase, putative
- EC
- 3.2.1.51
- UniProt
- Q9WYE2
- Ligands
- ZX5
- Pockets
- 6 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Alpha-L-fucosidase, putative (EC 3.2.1.51) | protein | 441 | 31% helix, 19% strand | Q9WYE2 |
Ligands and binding sites
- ZX5 · 3-(1H-indol-3-yl)-N-{[(2R,3R,4R,5R,6S)-3,4,5-trihydroxy-6-methylpiperidin-2-yl]methyl}propanamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 862 | 0.70 | 0.75 | 58 | empty |
| 2 | 262 | 0.60 | 0.79 | 33 | ZX5 |
| 3 | 282 | 0.57 | 0.77 | 43 | ZX5 |
| 4 | 98 | 0.35 | 0.74 | 13 | empty |
| 5 | 92 | 0.34 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 835 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 2ZX5 · alpha-L-fucosidase complexed with inhibitor, F10 · 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 Q9WYE2
- Elsewhere: RCSB PDB 2ZX5 · PDBe 2ZX5 · UniProt Q9WYE2
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