Research workbench
High speed X-ray analysis of plant enzymes at room temperature
Analyse High speed X-ray analysis of plant enzymes at room temperature in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4EK7
- Type
- protein
- Length
- 940 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
- BGC, CL
- Pockets
- 3 · 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 | 470 | 47% helix, 17% strand | Q9SPP9 |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains 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 | 1104 | 0.78 | 0.80 | 94 | empty |
| 2 | 452 | 0.71 | 0.81 | 44 | BGC |
| 3 | 399 | 0.69 | 0.81 | 43 | BGC |
Interfaces
1 interface between chains.
- A–B · 743 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4EK7 · High speed X-ray analysis of plant enzymes at room temperature · 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 4EK7 · PDBe 4EK7 · UniProt Q9SPP9
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