MolNFT v1 · #84387 · protein
Crystal structure of strictosidine glucosidase in complex with inhibitor-2
3ZJ8 · Strictosidine-O-beta-D-glucosidase: “Crystal structure of strictosidine glucosidase in complex with inhibitor-2”. X-ray diffraction, 1 ligand (LR1), 7 pockets (best druggability 0.81). MolNFT v1 #84387 on GenesisL1: 3D structure…
- PDB
- 3ZJ8
- Type
- protein
- Length
- 935 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
- LR1
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Strictosidine-O-beta-D-glucosidase (EC 3.2.1.105) | protein | 468 | 46% helix, 18% strand | Q8GU20 |
| B | Strictosidine-O-beta-D-glucosidase (EC 3.2.1.105) | protein | 467 | 46% helix, 18% strand | Q8GU20 |
Ligands and binding sites
- LR1 · (1R,2S,3S,4R,5R)-4-[(4-bromophenyl)methylamino]-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 | 269 | 0.81 | 0.93 | 40 | empty |
| 2 | 498 | 0.73 | 0.82 | 46 | LR1 |
| 3 | 477 | 0.72 | 0.81 | 45 | LR1 |
| 4 | 134 | 0.43 | 0.76 | 18 | empty |
| 5 | 140 | 0.41 | 0.75 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 648 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 3ZJ8 · Crystal structure of strictosidine glucosidase in complex with inhibitor-2 · 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 B 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 3ZJ8 · PDBe 3ZJ8 · UniProt Q8GU20
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