Research workbench
Crystal structure of strictosidine glucosidase in complex with inhibitor-1
Analyse Crystal structure of strictosidine glucosidase in complex with inhibitor-1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZJ7
- Type
- protein
- Length
- 934 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Strictosidine-O-beta-D-glucosidase
- EC
- 3.2.1.105
- UniProt
- Q8GU20
- Ligands
- C1K
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Strictosidine-O-beta-D-glucosidase (EC 3.2.1.105) | protein | 467 | 45% helix, 17% strand | Q8GU20 |
Ligands and binding sites
- C1K · (1R,2S,3S,4R,5R)-4-(cyclohexylamino)-5-(hydroxymethyl)cyclopentane-1,2,3-triol · ligand · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 236 | 0.81 | 0.94 | 41 | empty |
| 2 | 493 | 0.74 | 0.83 | 47 | C1K |
| 3 | 481 | 0.73 | 0.82 | 45 | C1K |
| 4 | 167 | 0.45 | 0.75 | 17 | empty |
| 5 | 146 | 0.44 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 663 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 3ZJ7 · Crystal structure of strictosidine glucosidase in complex with inhibitor-1 · the same entry in another collection · chain A against A, TM-score 1.00
- Q8GU20 · AlphaFold monomer V2.0 prediction for strictosidine-O-beta-D- glucosidase (Q8GU20) · 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 Q8GU20
- Elsewhere: RCSB PDB 3ZJ7 · PDBe 3ZJ7 · UniProt Q8GU20
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