MolNFT v1 · #57000 · protein
Alpha-L-fucosidase complexed with inhibitor, B4
2ZX9 · Alpha-L-fucosidase, putative: “Alpha-L-fucosidase complexed with inhibitor, B4”. X-ray diffraction, 1 ligand (ZX9), 5 pockets (best druggability 0.70). MolNFT v1 #57000 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2ZX9
- Type
- protein
- Length
- 884 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
- ZX9
- Pockets
- 5 · 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 | 442 | 31% helix, 19% strand | Q9WYE2 |
Ligands and binding sites
- ZX9 · (2S)-2-cyclopentyl-2-phenyl-N-{[(2R,3R,4R,5R,6S)-3,4,5-trihydroxy-6-methylpiperidin-2-yl]methyl}ethanamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 908 | 0.70 | 0.76 | 57 | empty |
| 2 | 376 | 0.61 | 0.77 | 59 | ZX9 |
| 3 | 254 | 0.59 | 0.78 | 31 | ZX9 |
| 4 | 88 | 0.33 | 0.74 | 13 | empty |
| 5 | 87 | 0.33 | 0.74 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 847 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 2ZX9 · alpha-L-fucosidase complexed with inhibitor, B4 · 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 2ZX9 · PDBe 2ZX9 · UniProt Q9WYE2
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