MolNFT v1 · #116413 · protein
Iridoid synthase from catharanthus roseus - ligand free structure
5DCW: “Iridoid synthase from catharanthus roseus - ligand free structure”. X-ray diffraction, 2 pockets (best druggability 0.80). MolNFT v1 #116413 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5DCW
- Type
- protein
- Length
- 358 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Iridoid synthase
- EC
- 1.3.1.99
- UniProt
- K7WDL7
- Pockets
- 2 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Iridoid synthase (EC 1.3.1.99) | protein | 358 | 41% helix, 14% strand | K7WDL7 |
Ligands and binding sites
- 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 | 439 | 0.80 | 0.88 | 59 | empty |
| 2 | 222 | 0.69 | 0.86 | 31 | empty |
Compared structures
- 5DCW · Iridoid synthase from Catharanthus roseus - ligand free structure · the same entry in another collection · chain A against A, TM-score 1.00
- K7WDL7 · AlphaFold monomer V2.0 prediction for (S)-8-oxocitronellyl enol synthase (K7WDL7) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 K7WDL7
- Elsewhere: RCSB PDB 5DCW · PDBe 5DCW · UniProt K7WDL7
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