MolNFT v1 · #80719 · protein
Structures of alkaloid biosynthetic glucosidases decode substrate specificity
3U57 · Raucaffricine-O-beta-D-glucosidase: “Structures of alkaloid biosynthetic glucosidases decode substrate specificity”. X-ray diffraction, 2 ligands (DH8, CL), 4 pockets (best druggability 0.78). MolNFT v1 #80719 on GenesisL1: 3D…
- PDB
- 3U57
- Type
- protein
- Length
- 942 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
- DH8, CL
- Pockets
- 4 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Raucaffricine-O-beta-D-glucosidase (EC 3.2.1.125) | protein | 471 | 47% helix, 17% strand | Q9SPP9 |
Ligands and binding sites
- DH8 · (2beta,7beta,16S,17R,19E,21beta)-21-(beta-D-glucopyranosyloxy)-2,7-dihydro-7,17-cyclosarpagan-17-yl acetate · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1079 | 0.78 | 0.80 | 95 | empty |
| 2 | 460 | 0.71 | 0.81 | 45 | DH8 |
| 3 | 458 | 0.70 | 0.80 | 45 | DH8 |
| 4 | 50 | 0.28 | 0.75 | 10 | empty |
Interfaces
1 interface between chains.
- A–B · 735 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3U57 · Structures of Alkaloid Biosynthetic Glucosidases Decode Substrate Specificity · 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 3U57 · PDBe 3U57 · UniProt Q9SPP9
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