[English] 日本語
![](img/lk-miru.gif)
- PDB-6hov: Crystal Structure of BRD4 first bromodomain in complex with ferul... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6hov | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of BRD4 first bromodomain in complex with ferulic acid | ||||||
![]() | Bromodomain-containing protein 4 | ||||||
![]() | TRANSCRIPTION / four helical bundle | ||||||
Function / homology | ![]() RNA polymerase II C-terminal domain binding / negative regulation of DNA damage checkpoint / P-TEFb complex binding / negative regulation by host of viral transcription / positive regulation of T-helper 17 cell lineage commitment / positive regulation of G2/M transition of mitotic cell cycle / histone reader activity / RNA polymerase II CTD heptapeptide repeat kinase activity / condensed nuclear chromosome / positive regulation of transcription elongation by RNA polymerase II ...RNA polymerase II C-terminal domain binding / negative regulation of DNA damage checkpoint / P-TEFb complex binding / negative regulation by host of viral transcription / positive regulation of T-helper 17 cell lineage commitment / positive regulation of G2/M transition of mitotic cell cycle / histone reader activity / RNA polymerase II CTD heptapeptide repeat kinase activity / condensed nuclear chromosome / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / lysine-acetylated histone binding / p53 binding / chromosome / regulation of inflammatory response / positive regulation of canonical NF-kappaB signal transduction / Potential therapeutics for SARS / transcription coactivator activity / transcription cis-regulatory region binding / chromatin remodeling / DNA damage response / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / enzyme binding / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Dalle Vedove, A. / Lolli, G. | ||||||
![]() | ![]() Title: Biochemical and cellular mechanism of protein kinase CK2 inhibition by deceptive curcumin. Authors: Cozza, G. / Zonta, F. / Dalle Vedove, A. / Venerando, A. / Dall'Acqua, S. / Battistutta, R. / Ruzzene, M. / Lolli, G. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 45.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 29.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 433.2 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 433.8 KB | Display | |
Data in XML | ![]() | 9.3 KB | Display | |
Data in CIF | ![]() | 12.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6hopC ![]() 6hoqC ![]() 6horC ![]() 6hotC ![]() 6houC ![]() 4iooS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 15099.380 Da / Num. of mol.: 1 / Fragment: bromodomain (residues 44-168) Mutation: First two residues SM derive from the expression tag Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
---|---|---|---|---|---|
#2: Chemical | #3: Chemical | ChemComp-FER / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 40 % / Mosaicity: 0.36 ° |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 16% PEG 3350, 20% ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 16, 2017 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.85→43.8 Å / Num. obs: 11081 / % possible obs: 99.7 % / Redundancy: 6.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.052 / Rrim(I) all: 0.139 / Net I/σ(I): 10 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Phasing
Phasing | Method: ![]() |
---|
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 4IOO Resolution: 1.85→28.917 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.03
| |||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 63.71 Å2 / Biso mean: 22.1224 Å2 / Biso min: 9.71 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.85→28.917 Å
| |||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4
|