Research workbench
Crystal structure of an alpha-L-fucosidase GH29 from bacteroides thetaiotaomicron in complex with deoxyfuconojirimycin
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
- 2XIB
- Type
- protein
- Length
- 1,748 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-L-fucosidase
- UniProt
- Q8A3I4
- Ligands
- DFU, SO4
- Pockets
- 8 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Alpha-L-fucosidase | protein | 437 | 32% helix, 22% strand | Q8A3I4 |
Ligands and binding sites
- DFU · (2S,3R,4S,5R)-2-methylpiperidine-3,4,5-triol · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 5 copies · chains A, B, C, D
- GOL · Glycerol · additive · 5 copies · chains A, B, C, D
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1038 | 0.73 | 0.76 | 83 | empty |
| 2 | 725 | 0.71 | 0.78 | 71 | empty |
| 3 | 621 | 0.69 | 0.78 | 69 | empty |
| 4 | 59 | 0.43 | 0.82 | 17 | DFU |
| 5 | 54 | 0.41 | 0.82 | 18 | DFU |
Interfaces
3 interfaces between chains.
- C–D · 350 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 345 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 187 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2XIB · 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 2XIB · PDBe 2XIB · UniProt Q8A3I4
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