MolNFT v1 · #116415 · protein
Iridoid synthase G150A mutant from catharanthus roseus - binary complex with NADP+
5DCY: “Iridoid synthase G150A mutant from catharanthus roseus - binary complex with NADP+”. X-ray diffraction, 1 ligand (NAP), 4 pockets (best druggability 0.87). MolNFT v1 #116415 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5DCY
- Type
- protein
- Length
- 723 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
- Pockets
- 4 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Iridoid synthase (EC 1.3.1.99) | protein | 366 | 39% helix, 15% strand | K7WDL7 |
| B | Iridoid synthase (EC 1.3.1.99) | protein | 357 | 40% helix, 14% strand | K7WDL7 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B
- PGE · Triethylene glycol · additive · 2 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1105 | 0.87 | 0.88 | 112 | NAP, PGE, EDO |
| 2 | 619 | 0.83 | 0.88 | 66 | NAP, PGE |
| 3 | 109 | 0.43 | 0.78 | 16 | empty |
| 4 | 71 | 0.36 | 0.77 | 21 | EDO |
Interfaces
1 interface between chains.
- A–B · 948 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 5DCY · Iridoid synthase G150A mutant from Catharanthus roseus - binary complex with NADP+ · 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 B against A, TM-score 1.00
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 5DCY · PDBe 5DCY · UniProt K7WDL7
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