Research workbench

Iridoid synthase from catharanthus roseus - ligand free structure

Analyse Iridoid synthase from catharanthus roseus - ligand free structure in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

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.

Pocket	Volume (Å³)	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

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.