Research workbench
Crystal Structure of Strictosidine in complex with 1H-indole-4-ethanamine
Analyse Crystal Structure of Strictosidine in complex with 1H-indole-4-ethanamine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6N5V
- Type
- protein
- Length
- 610 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.549
- Source
- Rauvolfia serpentina
- Molecule
- Strictosidine synthase
- EC
- 4.3.3.2
- UniProt
- P68175
- Ligands
- KDY
- Pockets
- 7 · best druggability 0.69
Structure
x-ray diffraction · resolution 2.549 · 1 distinct chain · 8% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Strictosidine synthase (EC 4.3.3.2) | protein | 305 | 8% helix, 48% strand | P68175 |
Ligands and binding sites
- KDY · 2-(1H-indol-4-yl)ethan-1-amine · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 242 | 0.69 | 0.85 | 27 | KDY |
| 2 | 219 | 0.68 | 0.85 | 27 | KDY |
| 3 | 197 | 0.58 | 0.81 | 24 | empty |
| 4 | 211 | 0.58 | 0.80 | 23 | empty |
| 5 | 174 | 0.47 | 0.75 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 818 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6N5V · Crystal structure of strictosidine in complex with 1H-indole-4- ethanamine · the same entry in another collection · chain A against A, TM-score 1.00
- P68175 · AlphaFold monomer V2.0 prediction for strictosidine synthase (P68175) · 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 P68175
- Elsewhere: RCSB PDB 6N5V · PDBe 6N5V · UniProt P68175
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