MolNFT v1 · #81760 · protein
Scaffold tailoring by a newly detected pictet-spenglerase ac-tivity of strictosidine synthase (STR1): from the common tryp-toline skeleton to the rare piperazino-indole framework
3V1S: “Scaffold tailoring by a newly detected pictet-spenglerase ac-tivity of strictosidine synthase (STR1): from…”. X-ray diffraction, 1 ligand (0LH), 7 pockets (best druggability 0.71). MolNFT v1 #81760 on GenesisL1: 3D structure…
- PDB
- 3V1S
- Type
- protein
- Length
- 604 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
- 0LH
- Pockets
- 7 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 7% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Strictosidine synthase (EC 4.3.3.2) | protein | 302 | 7% helix, 48% strand | P68175 |
Ligands and binding sites
- 0LH · 2-(1H-indol-1-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 | 297 | 0.71 | 0.84 | 29 | 0LH |
| 2 | 305 | 0.70 | 0.84 | 30 | 0LH |
| 3 | 172 | 0.59 | 0.82 | 22 | empty |
| 4 | 198 | 0.58 | 0.81 | 28 | empty |
| 5 | 183 | 0.47 | 0.75 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 624 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3V1S · Scaffold tailoring by a newly detected Pictet-Spenglerase ac-tivity of strictosidine… · 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 3V1S · PDBe 3V1S · UniProt P68175
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