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Crystal structure of a michaelis complex of alpha-L-fucosidase GH29 from bacteroides thetaiotaomicron with the synthetic substrate 4- nitrophenyl-alpha-L-fucose
Analyse Crystal structure of a michaelis complex of alpha-L-fucosidase GH29 from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2WVU
- 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
- JFZ, SO4
- Pockets
- 7 · 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
- JFZ · 4-nitrophenyl 6-deoxy-alpha-L-galactopyranoside · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 7 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1131 | 0.73 | 0.76 | 93 | empty |
| 2 | 658 | 0.70 | 0.78 | 65 | empty |
| 3 | 590 | 0.68 | 0.77 | 56 | empty |
| 4 | 122 | 0.47 | 0.79 | 19 | SO4, JFZ |
| 5 | 114 | 0.46 | 0.78 | 19 | SO4, JFZ |
Interfaces
4 interfaces between chains.
- A–B · 355 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 315 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 203 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 13 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2WVU · Crystal structure of a Michaelis complex of alpha-L-fucosidase GH29 from Bacteroides… · 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 2WVU · PDBe 2WVU · UniProt Q8A3I4
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