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Yorodumi- PDB-4bci: Structure of CDK9 in complex with cyclin T and a 2-amino-4-hetero... -
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-Basic information
Entry | Database: PDB / ID: 4bci | ||||||
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Title | Structure of CDK9 in complex with cyclin T and a 2-amino-4-heteroaryl- pyrimidine inhibitor | ||||||
Components |
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Keywords | TRANSFERASE/CELL CYCLE / TRANSFERASE-CELL CYCLE COMPLEX / CDK-CYCLIN COMPLEX / TRANSCRIPTION-PROTEIN BINDING / STRUCTURE-BASED DRUG DESIGN | ||||||
Function / homology | Function and homology information 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 / RNA polymerase binding / positive regulation of DNA-templated transcription, elongation / negative regulation of protein localization to chromatin / [RNA-polymerase]-subunit kinase / transcription elongation-coupled chromatin remodeling / replication fork processing / regulation of cyclin-dependent protein serine/threonine kinase activity / 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 / transcription elongation factor complex / molecular condensate scaffold activity / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / TP53 Regulates Transcription of DNA Repair Genes / 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 / protein serine kinase activity / DNA repair / 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 | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 3.1 Å | ||||||
Authors | Hole, A.J. / Baumli, S. / Wang, S. / Endicott, J.A. / Noble, M.E.M. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2013 Title: Comparative Structural and Functional Studies of 4-(Thiazol- 5-Yl)-2-(Phenylamino)Pyrimidine-5-Carbonitrile Cdk9 Inhibitors Suggest the Basis for Isotype Selectivity. Authors: Hole, A.J. / Baumli, S. / Shao, H. / Shi, S. / Pepper, C. / Fischer, P.M. / Wang, S. / Endicott, J.A. / Noble, M.E.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4bci.cif.gz | 241 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bci.ent.gz | 205.2 KB | Display | PDB format |
PDBx/mmJSON format | 4bci.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bc/4bci ftp://data.pdbj.org/pub/pdb/validation_reports/bc/4bci | HTTPS FTP |
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-Related structure data
Related structure data | 4bcfC 4bchC 4bcjC 4bckC 4bcmC 4bcnC 4bcoC 4bcqC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 38054.082 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-330 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PVL1392 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / Strain (production host): SF9 References: UniProt: P50750, cyclin-dependent kinase, [RNA-polymerase]-subunit kinase |
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#2: Protein | Mass: 30119.426 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-259 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PVL1392 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / Strain (production host): SF9 / References: UniProt: O60563 |
#3: Chemical | ChemComp-T3E / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 47 % / Description: NONE |
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Crystal grow | Temperature: 277 K / pH: 6.2 Details: CRYSTALS WERE GROWN AT 4C USING 10-16% PEG 1000, 100MM NAK-PHOSPHATE PH 6.2, 500MM NACL, 4MM TCEP AS THE PRECIPITANT SOLUTION. THEY WERE SUBSEQUENTLY SOAKED IN THE PRESENCE OF COMPOUND. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.979 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.97→60.04 Å / Num. obs: 20202 / % possible obs: 99.3 % / Redundancy: 3.63 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 8.61 |
Reflection shell | Resolution: 3.1→3.27 Å / Redundancy: 3.68 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 1.29 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER / Resolution: 3.1→37.428 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.943 / SU B: 38.216 / SU ML: 0.295 / Cross valid method: THROUGHOUT / ESU R: 1.356 / ESU R Free: 0.343 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 110.632 Å2
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Refinement step | Cycle: LAST / Resolution: 3.1→37.428 Å
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