Research workbench
Crystal structure of 1,2-a-L-fucosidase from bifidobacterium bifidum in complex with deoxyfuconojirimycin
Analyse Crystal structure of 1,2-a-L-fucosidase from bifidobacterium bifidum in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2EAC
- Type
- protein
- Length
- 1,766 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-fucosidase
- EC
- 3.2.1.63
- UniProt
- Q6JV24
- Ligands
- DFU, CA
- Pockets
- 20 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-fucosidase (EC 3.2.1.63) | protein | 881 | 31% helix, 25% strand | Q6JV24 |
| B | Alpha-fucosidase (EC 3.2.1.63) | protein | 885 | 31% helix, 25% strand | Q6JV24 |
Ligands and binding sites
- DFU · (2S,3R,4S,5R)-2-methylpiperidine-3,4,5-triol · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1070 | 0.71 | 0.75 | 91 | empty |
| 2 | 196 | 0.57 | 0.80 | 26 | empty |
| 3 | 196 | 0.57 | 0.80 | 28 | empty |
| 4 | 210 | 0.53 | 0.78 | 33 | empty |
| 5 | 71 | 0.48 | 0.83 | 17 | DFU |
Interfaces
1 interface between chains.
- A–B · 376 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 2EAC · Crystal structure of 1,2-a-L-fucosidase from Bifidobacterium bifidum in complex 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 Q6JV24
- Elsewhere: RCSB PDB 2EAC · PDBe 2EAC · UniProt Q6JV24
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