MolNFT v1 · #95713 · protein
Structure of strictosidine synthase in complex with 2-(1H-indol-3-yl)- N-methylethanamine
4IYG: “Structure of strictosidine synthase in complex with 2-(1H-indol-3-yl)- N-methylethanamine”. X-ray diffraction, 1 ligand (1HU), 7 pockets (best druggability 0.72). MolNFT v1 #95713 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4IYG
- 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
- 1HU
- Pockets
- 7 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 6% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Strictosidine synthase (EC 4.3.3.2) | protein | 302 | 6% helix, 48% strand | P68175 |
Ligands and binding sites
- 1HU · 2-(1H-indol-3-yl)-N-methylethanamine · ligand · chains A
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 | 322 | 0.72 | 0.84 | 31 | empty |
| 2 | 300 | 0.70 | 0.84 | 31 | 1HU |
| 3 | 179 | 0.59 | 0.82 | 22 | empty |
| 4 | 157 | 0.56 | 0.82 | 21 | empty |
| 5 | 163 | 0.46 | 0.75 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 586 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4IYG · Structure of strictosidine synthase in complex with 2-(1H-INDOL-3-YL)-N-METHYLETHANAMINE · 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 4IYG · PDBe 4IYG · UniProt P68175
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