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- PDB-6w9e: Crystal Structure of Human CDK9/cyclinT1 in complex with MC180295 -
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Open data
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Basic information
Entry | Database: PDB / ID: 6w9e | |||||||||
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Title | Crystal Structure of Human CDK9/cyclinT1 in complex with MC180295 | |||||||||
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![]() | TRANSCRIPTION / CDK9 / CYCLIN T1 / MC180295 / complex / transcriptional regulator | |||||||||
Function / homology | ![]() P-TEFb complex / Interactions of Tat with host cellular proteins / 7SK snRNA binding / cyclin/CDK positive transcription elongation factor complex / regulation of muscle cell differentiation / regulation of mRNA 3'-end processing / positive regulation of protein localization to chromatin / nucleus localization / cyclin-dependent protein serine/threonine kinase activator activity / positive regulation by host of viral transcription ...P-TEFb complex / Interactions of Tat with host cellular proteins / 7SK snRNA binding / cyclin/CDK positive transcription elongation factor complex / regulation of muscle cell differentiation / regulation of mRNA 3'-end processing / positive regulation of protein localization to chromatin / nucleus localization / cyclin-dependent protein serine/threonine kinase activator activity / positive regulation by host of viral transcription / positive regulation of DNA-templated transcription, elongation / RNA polymerase binding / [RNA-polymerase]-subunit kinase / negative regulation of protein localization to chromatin / transcription elongation-coupled chromatin remodeling / regulation of cyclin-dependent protein serine/threonine kinase activity / replication fork processing / cellular response to cytokine stimulus / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / RNA polymerase II transcribes snRNA genes / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / cyclin-dependent kinase / Formation of HIV elongation complex in the absence of HIV Tat / cyclin-dependent protein serine/threonine kinase activity / regulation of DNA repair / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / RNA polymerase II CTD heptapeptide repeat kinase activity / cyclin binding / transcription elongation factor complex / molecular condensate scaffold activity / transcription elongation by RNA polymerase II / TP53 Regulates Transcription of DNA Repair Genes / transcription initiation at RNA polymerase II promoter / positive regulation of transcription elongation by RNA polymerase II / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / PML body / transcription coactivator binding / cytoplasmic ribonucleoprotein granule / kinase activity / DNA-binding transcription factor binding / Estrogen-dependent gene expression / cell population proliferation / transcription by RNA polymerase II / transcription cis-regulatory region binding / regulation of cell cycle / protein kinase activity / response to xenobiotic stimulus / cell cycle / RNA polymerase II cis-regulatory region sequence-specific DNA binding / cell division / protein phosphorylation / DNA repair / protein serine kinase activity / protein serine/threonine kinase activity / chromatin binding / regulation of transcription by RNA polymerase II / protein kinase binding / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / ATP binding / membrane / nucleus / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Zhang, P. / Wu, J. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Comparative Modeling of CDK9 Inhibitors to Explore Selectivity and Structure-Activity Relationships Authors: Kirubakaran, P. / Morton, G. / Zhang, P. / Zhang, H. / Abou-Gharbia, M. / Issa, J. / Wu, J. / Childers, W. / Karanicolas, J. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 133.1 KB | Display | ![]() |
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PDB format | ![]() | 101.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 22.4 KB | Display | |
Data in CIF | ![]() | 30.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3blqS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 38111.090 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() References: UniProt: P50750, cyclin-dependent kinase, [RNA-polymerase]-subunit kinase |
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#2: Protein | Mass: 30096.453 Da / Num. of mol.: 1 / Mutation: Q77R, E96G, F241L Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() References: UniProt: O60563 |
-Non-polymers , 4 types, 33 molecules ![](data/chem/img/TO7.gif)
![](data/chem/img/TOJ.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/TOJ.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-PO4 / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.13 Å3/Da / Density % sol: 70.2 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 0.1M Na/K phosphate pH6.2, 200mM NaCl, 4mM TCEP and 1~6% PEG1000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 21, 2018 |
Radiation | Monochromator: Double crystal Si (111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97935 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→86.67 Å / Num. obs: 19797 / % possible obs: 99.6 % / Redundancy: 4.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.061 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 3.1→3.18 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.885 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1424 / CC1/2: 0.566 / % possible all: 96.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3blq Resolution: 3.1→86.67 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.937 / SU B: 18.092 / SU ML: 0.298 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 7.028 / ESU R Free: 0.348 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
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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: 107.3 Å2
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Refinement step | Cycle: LAST / Resolution: 3.1→86.67 Å
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