MolNFT v1 · #116411 · protein
Iridoid synthase from catharanthus roseus - ternary complex with NADP+ and triethylene glycol carboxylic acid
5DCU: “Iridoid synthase from catharanthus roseus - ternary complex with NADP+ and triethylene glycol carboxylic acid”. X-ray diffraction, 2 ligands (NAP, TEG), 4 pockets (best druggability 0.88). MolNFT v1 #116411 on GenesisL1: 3D…
- PDB
- 5DCU
- Type
- protein
- Length
- 728 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Iridoid synthase
- EC
- 1.3.1.99
- UniProt
- K7WDL7
- Ligands
- NAP, TEG
- Pockets
- 4 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Iridoid synthase (EC 1.3.1.99) | protein | 364 | 40% helix, 14% strand | K7WDL7 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- TEG · [2-(2-hydroxyethoxy)ethoxy]acetic acid · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1187 | 0.88 | 0.89 | 118 | NAP, TEG |
| 2 | 503 | 0.85 | 0.91 | 53 | NAP, TEG |
| 3 | 284 | 0.52 | 0.74 | 31 | empty |
| 4 | 58 | 0.33 | 0.77 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 966 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5DCU · Iridoid synthase from Catharanthus roseus - ternary complex with NADP+ and triethylene… · 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 0.99
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 5DCU · PDBe 5DCU · UniProt K7WDL7
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