Research workbench
Crystal structure of an alpha-L-fucosidase GH29 from bacteroides thetaiotaomicron in complex with a novel iminosugar fucosidase inhibitor
Analyse Crystal structure of an alpha-L-fucosidase GH29 from bacteroides… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2WVT
- Type
- protein
- Length
- 877 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-L-fucosidase
- UniProt
- Q8A3I4
- Ligands
- FHN
- Pockets
- 4 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-L-fucosidase | protein | 438 | 32% helix, 23% strand | Q8A3I4 |
| B | Alpha-L-fucosidase | protein | 439 | 32% helix, 23% strand | Q8A3I4 |
Ligands and binding sites
- FHN · (2S,3R,5R,6S)-3,4,5-trihydroxy-2,6-bis(hydroxymethyl)piperidinium · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 5 copies · chains A, B
- IMD · Imidazole · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1075 | 0.81 | 0.82 | 93 | GOL |
| 2 | 74 | 0.44 | 0.81 | 18 | FHN |
| 3 | 67 | 0.43 | 0.81 | 18 | FHN, GOL |
| 4 | 70 | 0.30 | 0.74 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1131 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 2WVT · Crystal structure of an alpha-L-fucosidase GH29 from Bacteroides thetaiotaomicron in… · 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 Q8A3I4
- Elsewhere: RCSB PDB 2WVT · PDBe 2WVT · UniProt Q8A3I4
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