MolNFT v1 · #115590 · protein
Crystal structure of iridoid synthase at 2.2-ångström resolution
5COA: “Crystal structure of iridoid synthase at 2.2-ångström resolution”. X-ray diffraction, 1 ligand (SO4), 11 pockets (best druggability 0.78). MolNFT v1 #115590 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5COA
- Type
- protein
- Length
- 712 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
- SO4
- Pockets
- 11 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Iridoid synthase (EC 1.3.1.99) | protein | 361 | 40% helix, 14% strand | K7WDL7 |
| B | Iridoid synthase (EC 1.3.1.99) | protein | 351 | 41% helix, 15% strand | K7WDL7 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 781 | 0.78 | 0.82 | 63 | P6G, SO4 |
| 2 | 796 | 0.77 | 0.81 | 63 | SO4 |
| 3 | 77 | 0.71 | 0.96 | 24 | empty |
| 4 | 362 | 0.59 | 0.76 | 35 | SO4 |
| 5 | 258 | 0.57 | 0.78 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 1241 Ų buried · 34 hydrogen bonds · protein-protein
Compared structures
- 5COA · Crystal structure of iridoid synthase at 2.2-angstrom resolution · 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 0.97
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 5COA · PDBe 5COA · UniProt K7WDL7
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