Research workbench
Crystal of raucaffricine glucosidase in complex with inhibitor
Analyse Crystal of raucaffricine glucosidase in complex with inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZJ6
- Type
- protein
- Length
- 938 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Raucaffricine-O-beta-D-glucosidase
- EC
- 3.2.1.125
- UniProt
- Q9SPP9
- Ligands
- VM2, SO4
- Pockets
- 3 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Raucaffricine-O-beta-D-glucosidase (EC 3.2.1.125) | protein | 469 | 46% helix, 18% strand | Q9SPP9 |
Ligands and binding sites
- VM2 · (1R,2S,3S,4R,5R)-4-(cyclohexylmethylamino)-5-(hydroxymethyl)cyclopentane-1,2,3-triol · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1060 | 0.78 | 0.80 | 90 | empty |
| 2 | 396 | 0.70 | 0.81 | 45 | VM2 |
| 3 | 394 | 0.68 | 0.80 | 47 | VM2 |
Interfaces
1 interface between chains.
- A–B · 768 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3ZJ6 · Crystal of Raucaffricine Glucosidase in complex with inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
- Q9SPP9 · AlphaFold monomer V2.0 prediction for raucaffricine-O-beta-D- glucosidase (Q9SPP9) · a predicted model of the same protein · 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 Q9SPP9
- Elsewhere: RCSB PDB 3ZJ6 · PDBe 3ZJ6 · UniProt Q9SPP9
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