Research workbench
Crystal structure of alpha-L-fucosidase from vibrio sp. strain EJY3
Analyse Crystal structure of alpha-L-fucosidase from vibrio sp. strain EJY3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DB5
- Type
- protein
- Length
- 586 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-L-fucosidase
- Ligands
- PO4
- Pockets
- 3 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-L-fucosidase | protein | 586 | 26% helix, 29% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 362 | 0.79 | 0.89 | 67 | empty |
| 2 | 423 | 0.63 | 0.77 | 55 | GOL, PO4 |
| 3 | 101 | 0.41 | 0.77 | 20 | empty |
Modifications
Observed in the structure: 11 modified (engineered).
Compared structures
- 7DB5 · Crystal structure of alpha-L-fucosidase from Vibrio sp. strain EJY3 · 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
- Elsewhere: RCSB PDB 7DB5 · PDBe 7DB5
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