MolNFT v1 · #115591 · protein
Crystal structure of iridoid synthase in complex with NADP+ and 8- oxogeranial at 2.65-ångström resolution
5COB: “Crystal structure of iridoid synthase in complex with NADP+ and 8- oxogeranial at 2.65-ångström resolution”. X-ray diffraction, 2 ligands (NAP, XOG), 17 pockets (best druggability 0.87). MolNFT v1 #115591 on GenesisL1: 3D structure…
- PDB
- 5COB
- Type
- protein
- Length
- 1,460 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Iridoid synthase
- EC
- 1.3.1.99
- UniProt
- K7WDL7
- Ligands
- NAP, XOG
- Pockets
- 17 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Iridoid synthase (EC 1.3.1.99) | protein | 365 | 39% helix, 14% strand | K7WDL7 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- XOG · (2E,6E)-2,6-dimethylocta-2,6-dienedial · ligand · 4 copies · chains A, B, C, D
- PG4 · Tetraethylene glycol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1027 | 0.87 | 0.88 | 92 | NAP, XOG, PG4 |
| 2 | 586 | 0.83 | 0.88 | 61 | NAP, XOG, PG4 |
| 3 | 606 | 0.81 | 0.86 | 61 | NAP, XOG, PG4 |
| 4 | 682 | 0.81 | 0.85 | 69 | NAP, XOG, PG4 |
| 5 | 77 | 0.73 | 0.97 | 24 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1054 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 1046 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 889 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5COB · Crystal structure of iridoid synthase in complex with NADP+ and 8-oxogeranial at… · 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 0.98
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 5COB · PDBe 5COB · UniProt K7WDL7
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