MolNFT v1 · #95308 · protein
Structure of strictosidine synthase in complex with 2-(1-methyl-1H- indol-3-YL)ETHANAMINE
4IMB: “Structure of strictosidine synthase in complex with 2-(1-methyl-1H- indol-3-YL)ETHANAMINE”. X-ray diffraction, 1 ligand (1ES), 7 pockets (best druggability 0.71). MolNFT v1 #95308 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4IMB
- Type
- protein
- Length
- 602 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
- 1ES
- Pockets
- 7 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Strictosidine synthase (EC 4.3.3.2) | protein | 301 | 6% helix, 49% strand | P68175 |
| B | Strictosidine synthase (EC 4.3.3.2) | protein | 301 | 6% helix, 48% strand | P68175 |
Ligands and binding sites
- 1ES · 2-(1-methyl-1H-indol-3-yl)ethanamine · 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 | 288 | 0.71 | 0.85 | 32 | 1ES |
| 2 | 295 | 0.70 | 0.84 | 31 | empty |
| 3 | 184 | 0.58 | 0.81 | 23 | empty |
| 4 | 170 | 0.55 | 0.81 | 23 | empty |
| 5 | 185 | 0.46 | 0.75 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 577 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4IMB · Structure of strictosidine synthase in complex with 2-(1-methyl-1H-indol-3-yl)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 4IMB · PDBe 4IMB · UniProt P68175
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