Research workbench
Crystal structure of an alpha-L-fucosidase GH29 trapped covalent intermediate from bacteroides thetaiotaomicron in complex with 2- fluoro-fucosyl fluoride using an E288Q mutant
Analyse Crystal structure of an alpha-L-fucosidase GH29 trapped covalent intermediate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2WVS
- Type
- protein
- Length
- 1,752 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-L-fucosidase
- UniProt
- Q8A3I4
- Ligands
- FUF, SO4
- Pockets
- 8 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-L-fucosidase | protein | 439 | 32% helix, 22% strand | Q8A3I4 |
| B | Alpha-L-fucosidase | protein | 437 | 32% helix, 21% strand | Q8A3I4 |
| C, D | Alpha-L-fucosidase | protein | 438 | 32% helix, 22% strand | Q8A3I4 |
Ligands and binding sites
- FUF · 2-deoxy-2-fluoro-beta-L-fucopyranose · ligand · 5 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
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 | 1090 | 0.74 | 0.77 | 87 | empty |
| 2 | 705 | 0.69 | 0.76 | 62 | empty |
| 3 | 621 | 0.69 | 0.77 | 61 | empty |
| 4 | 74 | 0.42 | 0.80 | 19 | FUF, SO4 |
| 5 | 59 | 0.42 | 0.81 | 17 | FUF |
Interfaces
3 interfaces between chains.
- C–D · 362 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 329 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 212 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 2WVS · Crystal structure of an alpha-L-fucosidase GH29 trapped covalent intermediate from… · 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 2WVS · PDBe 2WVS · UniProt Q8A3I4
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