Research workbench
Crystal structure of rice DWARF14 in complex with synthetic strigolactone GR24
Analyse Crystal structure of rice DWARF14 in complex with synthetic strigolactone GR24 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DJ5
- Type
- protein
- Length
- 533 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable strigolactone esterase D14
- EC
- 3.1.-.-
- UniProt
- Q10QA5
- Ligands
- GR2
- Pockets
- 5 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable strigolactone esterase D14 (EC 3.1.-.-) | protein | 266 | 47% helix, 16% strand | Q10QA5 |
| B | Probable strigolactone esterase D14 (EC 3.1.-.-) | protein | 267 | 48% helix, 16% strand | Q10QA5 |
Ligands and binding sites
- GR2 · (3E,3aR,8bS)-3-({[(2R)-4-methyl-5-oxo-2,5-dihydrofuran-2-yl]oxy}methylidene)-3,3a,4,8b-tetrahydro-2H-indeno[1,2-b]furan-2-one · ligand · chains A
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 | 160 | 0.68 | 0.87 | 22 | GR2 |
| 2 | 136 | 0.68 | 0.88 | 20 | empty |
| 3 | 207 | 0.54 | 0.79 | 32 | empty |
| 4 | 129 | 0.42 | 0.76 | 28 | empty |
| 5 | 102 | 0.41 | 0.77 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 638 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5DJ5 · Crystal structure of rice DWARF14 in complex with synthetic strigolactone GR24 · the same entry in another collection · chain A against A, TM-score 1.00
- Q10QA5 · AlphaFold monomer V2.0 prediction for strigolactone esterase D14 (Q10QA5) · 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 Q10QA5
- Elsewhere: RCSB PDB 5DJ5 · PDBe 5DJ5 · UniProt Q10QA5
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