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The crystal structure of an alpha-(1-3,4)-fucosidase from bifidobacterium longum subsp. infantis atcc 15697
Analyse The crystal structure of an alpha-(1-3,4)-fucosidase from bifidobacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MO4
- Type
- protein
- Length
- 914 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-1,3/4-fucosidase
- UniProt
- B7GNN8
- Ligands
- TYR
- Pockets
- 12 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-1,3/4-fucosidase | protein | 455 | 30% helix, 26% strand | B7GNN8 |
| B | Alpha-1,3/4-fucosidase | protein | 459 | 30% helix, 26% strand | B7GNN8 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 521 | 0.73 | 0.82 | 41 | empty |
| 2 | 177 | 0.55 | 0.80 | 36 | empty |
| 3 | 106 | 0.52 | 0.83 | 25 | empty |
| 4 | 176 | 0.50 | 0.77 | 27 | TYR |
| 5 | 176 | 0.48 | 0.76 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1380 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 modified (engineered).
Compared structures
- 3MO4 · The crystal structure of an alpha-(1-3,4)-fucosidase from Bifidobacterium longum subsp.… · 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 B7GNN8
- Elsewhere: RCSB PDB 3MO4 · PDBe 3MO4 · UniProt B7GNN8
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