MolNFT v1 · #171720 · protein
Strictosidine synthase from catharanthus roseus in complex with racemic 1-methyl-2,3,4,9-tetrahydro-1H-beta-carboline
6ZEA: “Strictosidine synthase from catharanthus roseus in complex with racemic…”. X-ray diffraction, 2 ligands (QGH, QGK), 2 pockets (best druggability 0.67). MolNFT v1 #171720 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6ZEA
- Type
- protein
- Length
- 308 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Strictosidine synthase
- EC
- 4.3.3.2
- UniProt
- P18417
- Ligands
- QGH, QGK
- Pockets
- 2 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 8% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Strictosidine synthase (EC 4.3.3.2) | protein | 308 | 8% helix, 46% strand | P18417 |
Ligands and binding sites
- QGH · (1~{R})-1-methyl-2,3,4,9-tetrahydro-1~{H}-pyrido[3,4-b]indole · ligand · chains A
- QGK · (1~{S})-1-methyl-2,3,4,9-tetrahydro-1~{H}-pyrido[3,4-b]indole · ligand · chains A
- EDO · 1,2-ethanediol · additive · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 324 | 0.67 | 0.81 | 30 | QGH, QGK |
| 2 | 165 | 0.55 | 0.81 | 26 | EDO |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6ZEA · Strictosidine Synthase from Catharanthus roseus in complex with racemic… · the same entry in another collection · chain A against A, TM-score 1.00
- P18417 · AlphaFold monomer V2.0 prediction for strictosidine synthase (P18417) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P18417
- Elsewhere: RCSB PDB 6ZEA · PDBe 6ZEA · UniProt P18417
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