MolNFT v1 · #109106 · protein
Crystal structure of a bacterial fucodiase in complex with 1-((1R,2R, 3R,4R,5R,6R)-2,3,4-trihydroxy-5-methyl-7-AZABICYCLO[4.1.0]HEPTAN-7- YL)ETHAN-1-one
4WSJ · Alpha-L-fucosidase: “Crystal structure of a bacterial fucodiase in complex with 1-((1R,2R…”. X-ray diffraction, 2 ligands (3U3, SO4), 8 pockets (best druggability 0.69). MolNFT v1 #109106 on GenesisL1: 3D structure, binding sites…
- PDB
- 4WSJ
- Type
- protein
- Length
- 1,761 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-L-fucosidase
- UniProt
- Q8A3I4
- Ligands
- 3U3, SO4
- Pockets
- 8 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 32% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-L-fucosidase | protein | 439 | 32% helix, 23% strand | Q8A3I4 |
| B | Alpha-L-fucosidase | protein | 445 | 31% helix, 22% strand | Q8A3I4 |
| C | Alpha-L-fucosidase | protein | 437 | 32% helix, 22% strand | Q8A3I4 |
| D | Alpha-L-fucosidase | protein | 440 | 32% helix, 23% strand | Q8A3I4 |
Ligands and binding sites
- 3U3 · N-[(1S,2R,3R,4S,5R)-3,4,5-trihydroxy-2-methylcyclohexyl]acetamide · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 5 copies · chains A, B, C
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 | 858 | 0.69 | 0.75 | 73 | empty |
| 2 | 536 | 0.67 | 0.78 | 59 | empty |
| 3 | 598 | 0.67 | 0.77 | 63 | empty |
| 4 | 127 | 0.46 | 0.77 | 29 | 3U3 |
| 5 | 101 | 0.43 | 0.78 | 18 | 3U3 |
Interfaces
3 interfaces between chains.
- C–D · 328 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 325 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 114 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 4WSJ · Crystal structure of a bacterial fucodiase in complex with… · 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 4WSJ · PDBe 4WSJ · UniProt Q8A3I4
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