MolNFT v1 · #116484 · protein
Iridoid synthase from catharanthus roseus - ternary complex with NADP+ and geranic acid
5DF1: “Iridoid synthase from catharanthus roseus - ternary complex with NADP+ and geranic acid”. X-ray diffraction, 2 ligands (NAP, 58X), 4 pockets (best druggability 0.88). MolNFT v1 #116484 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5DF1
- Type
- protein
- Length
- 732 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, 58X
- 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 | 366 | 40% helix, 14% strand | K7WDL7 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- 58X · (2E)-3,7-dimethylocta-2,6-dienoic acid · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B
- IMD · Imidazole · additive · chains A
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 | 949 | 0.88 | 0.90 | 88 | NAP, 58X |
| 2 | 582 | 0.82 | 0.87 | 63 | NAP, 58X |
| 3 | 209 | 0.68 | 0.86 | 36 | EDO |
| 4 | 66 | 0.36 | 0.77 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1016 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5DF1 · Iridoid synthase from Catharanthus roseus - ternary complex with NADP+ and geranic acid · 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 5DF1 · PDBe 5DF1 · UniProt K7WDL7
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