Research workbench
Crystal structure of thermotoga maritima alpha-fucosidase in complex with fucose
Analyse Crystal structure of thermotoga maritima alpha-fucosidase in complex with fucose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ODU
- Type
- protein
- Length
- 846 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative alpha-L-fucosidase
- EC
- 3.2.1.51
- UniProt
- Q9WYE2
- Ligands
- FUL
- Pockets
- 7 · best druggability 0.50
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative alpha-L-fucosidase (EC 3.2.1.51) | protein | 422 | 32% helix, 20% strand | Q9WYE2 |
| B | Putative alpha-L-fucosidase (EC 3.2.1.51) | protein | 424 | 33% helix, 20% strand | Q9WYE2 |
Ligands and binding sites
- FUL · beta-L-fucopyranose · sugar · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 108 | 0.50 | 0.80 | 20 | FUL |
| 2 | 97 | 0.47 | 0.80 | 19 | FUL |
| 3 | 61 | 0.33 | 0.77 | 17 | empty |
| 4 | 64 | 0.31 | 0.75 | 12 | empty |
| 5 | 75 | 0.31 | 0.74 | 21 | empty |
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 1ODU · Crystal structure of thermotoga maritima alpha-fucosidase in complex with fucose · 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 Q9WYE2
- Elsewhere: RCSB PDB 1ODU · PDBe 1ODU · UniProt Q9WYE2
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