[English] 日本語
![](img/lk-miru.gif)
- PDB-3c6p: Small molecule agonists and antagonists of F-box protein-substrat... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3c6p | ||||||
---|---|---|---|---|---|---|---|
Title | Small molecule agonists and antagonists of F-box protein-substrate interactions in auxin perception and signaling | ||||||
![]() |
| ||||||
![]() | SIGNALING PROTEIN / auxin / ubiquitin ligase / F-box / small molecule / chemical biology / plant physiology / Auxin signaling pathway / Chromosome partition / Cytoplasm / Cytoskeleton / Developmental protein / Ethylene signaling pathway / Nucleus / Ubl conjugation pathway / Cell cycle / Leucine-rich repeat / Plant defense | ||||||
Function / homology | ![]() auxin receptor activity / auxin binding / lateral root formation / pollen maturation / stamen development / phragmoplast / jasmonic acid mediated signaling pathway / ethylene-activated signaling pathway / response to jasmonic acid / response to auxin ...auxin receptor activity / auxin binding / lateral root formation / pollen maturation / stamen development / phragmoplast / jasmonic acid mediated signaling pathway / ethylene-activated signaling pathway / response to jasmonic acid / response to auxin / auxin-activated signaling pathway / inositol hexakisphosphate binding / negative regulation of DNA recombination / cellular response to phosphate starvation / SCF ubiquitin ligase complex / chromosome segregation / defense response / microtubule cytoskeleton organization / spindle / ubiquitin-protein transferase activity / ubiquitin-dependent protein catabolic process / protein ubiquitination / mitochondrion / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tan, X. | ||||||
![]() | ![]() Title: Small-molecule agonists and antagonists of F-box protein-substrate interactions in auxin perception and signaling. Authors: Hayashi, K. / Tan, X. / Zheng, N. / Hatate, T. / Kimura, Y. / Kepinski, S. / Nozaki, H. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 151.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 117.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 3c6nC ![]() 3c6oC ![]() 1p1mS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 17876.043 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|---|
#2: Protein | Mass: 66875.438 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Chemical | ChemComp-IHP / |
#4: Chemical | ChemComp-2S3 / ( |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.95 Å3/Da / Density % sol: 58.33 % |
---|---|
Crystal grow | Temperature: 277 K / Method: evaporation / pH: 6 Details: 12-14% PEG 40,000, 100mM BTP pH6.0, 200mM NaCl, EVAPORATION, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 21, 2007 |
Radiation | Monochromator: Liquid Nitrogen cooled Dual Crystal / Protocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: neutron |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. all: 49550 / Num. obs: 24753 / % possible obs: 75 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Highest resolution: 2.7 Å / % possible all: 95 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1P1M Resolution: 2.7→49.71 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.919 / SU B: 16.787 / SU ML: 0.177 / Cross valid method: THROUGHOUT / ESU R: 0.93 / ESU R Free: 0.434 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.101 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→49.71 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.7→2.77 Å / Total num. of bins used: 20
|