Research workbench
Structure of strictosidine synthase, the biosynthetic entry to the monoterpenoid indole alkaloid family
Analyse Structure of strictosidine synthase, the biosynthetic entry to the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2FPB
- Type
- protein
- Length
- 610 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Strictosidine synthase
- EC
- 4.3.3.2
- UniProt
- P68175
- Ligands
- TSS
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 7% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Strictosidine synthase (EC 4.3.3.2) | protein | 305 | 7% helix, 50% strand | P68175 |
Ligands and binding sites
- TSS · 2-(1H-indol-3-yl)ethanamine · 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 | 227 | 0.73 | 0.88 | 30 | TSS |
| 2 | 240 | 0.66 | 0.83 | 31 | TSS |
| 3 | 194 | 0.58 | 0.81 | 26 | empty |
| 4 | 181 | 0.57 | 0.81 | 22 | empty |
| 5 | 168 | 0.48 | 0.76 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 842 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified, 2 disulfide (engineered, disulfide).
Compared structures
- 2FPB · Structure of Strictosidine Synthase, the Biosynthetic Entry to the Monoterpenoid Indole… · the same entry in another collection · chain B against B, 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 2FPB · PDBe 2FPB · UniProt P68175
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