Research workbench
Crystal structure of alpha-1,3/4-fucosidase from bifidobacterium longum subsp. infantis complexed with deoxyfuconojirimycin
Analyse Crystal structure of alpha-1,3/4-fucosidase from bifidobacterium longum subsp.… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3UES
- Type
- protein
- Length
- 915 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-1,3/4-fucosidase
- EC
- 3.2.1.111
- UniProt
- B7GNN8
- Ligands
- DFU, NA
- Pockets
- 9 · best druggability 0.74
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 (EC 3.2.1.111) | protein | 457 | 29% helix, 26% strand | B7GNN8 |
| B | Alpha-1,3/4-fucosidase (EC 3.2.1.111) | protein | 458 | 30% helix, 26% strand | B7GNN8 |
Ligands and binding sites
- DFU · (2S,3R,4S,5R)-2-methylpiperidine-3,4,5-triol · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 519 | 0.74 | 0.82 | 44 | empty |
| 2 | 95 | 0.53 | 0.84 | 25 | empty |
| 3 | 197 | 0.49 | 0.76 | 40 | empty |
| 4 | 100 | 0.49 | 0.81 | 24 | empty |
| 5 | 143 | 0.48 | 0.78 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 1205 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 3UES · Crystal structure of alpha-1,3/4-fucosidase from Bifidobacterium longum subsp. infantis… · 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 3UES · PDBe 3UES · UniProt B7GNN8
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