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Crystal structure of a bacterial fucosidase with a multivalent iminocyclitol inhibitor
Analyse Crystal structure of a bacterial fucosidase with a multivalent iminocyclitol… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JL1
- Type
- protein
- Length
- 878 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-L-fucosidase
- UniProt
- Q8A3I4
- Ligands
- LM5, SO4
- Pockets
- 5 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Alpha-L-fucosidase | protein | 439 | 32% helix, 23% strand | Q8A3I4 |
Ligands and binding sites
- LM5 · (3S,4R,5S)-N-benzyl-3,4-dihydroxy-5-methyl-D-prolinamide · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
- IMD · Imidazole · additive · 6 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 702 | 0.68 | 0.76 | 73 | GOL |
| 2 | 71 | 0.40 | 0.79 | 17 | LM5, SO4 |
| 3 | 53 | 0.40 | 0.81 | 16 | empty |
| 4 | 63 | 0.38 | 0.79 | 17 | LM5 |
| 5 | 51 | 0.27 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 282 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4JL1 · Crystal structure of a bacterial fucosidase with a multivalent iminocyclitol inhibitor · 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 4JL1 · PDBe 4JL1 · UniProt Q8A3I4
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