MolNFT v1 · #158817 · protein
Crystal structure of DAD2 bound to quinazolinone derivative
6O5J · Probable strigolactone esterase DAD2: “Crystal structure of DAD2 bound to quinazolinone derivative”. X-ray diffraction, 1 ligand (LM7), 5 pockets (best druggability 0.75). MolNFT v1 #158817 on GenesisL1: 3D structure, binding sites…
- PDB
- 6O5J
- Type
- protein
- Length
- 528 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable strigolactone esterase DAD2
- EC
- 3.1.-.-
- UniProt
- J9U5U9
- Ligands
- LM7
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Probable strigolactone esterase DAD2 (EC 3.1.-.-) | protein | 264 | 48% helix, 17% strand | J9U5U9 |
Ligands and binding sites
- LM7 · 1-(4-hydroxy-3-nitrophenyl)quinazoline-2,4(1H,3H)-dione · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
- ACT · Acetate ion · additive · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 161 | 0.75 | 0.92 | 34 | LM7 |
| 2 | 156 | 0.74 | 0.91 | 31 | LM7 |
| 3 | 231 | 0.57 | 0.79 | 27 | empty |
| 4 | 203 | 0.47 | 0.75 | 33 | empty |
| 5 | 64 | 0.31 | 0.75 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 466 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6O5J · Crystal Structure of DAD2 bound to quinazoli derivative · the same entry in another collection · chain A against A, TM-score 1.00
- J9U5U9 · AlphaFold monomer V2.0 prediction for probable strigolactone esterase DAD2 (J9U5U9) · 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 J9U5U9
- Elsewhere: RCSB PDB 6O5J · PDBe 6O5J · UniProt J9U5U9
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