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Yorodumi- PDB-6b3e: Crystal structure of human CDK12/CyclinK in complex with an inhibitor -
+Open data
-Basic information
Entry | Database: PDB / ID: 6b3e | ||||||
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Title | Crystal structure of human CDK12/CyclinK in complex with an inhibitor | ||||||
Components |
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Keywords | TRANSFERASE/INHIBITOR / Inhibitor / complex / kinase / TRANSFERASE / TRANSFERASE-INHIBITOR complex | ||||||
Function / homology | Function and homology information cyclin K-CDK12 complex / cyclin K-CDK13 complex / nuclear cyclin-dependent protein kinase holoenzyme complex / regulation of MAP kinase activity / cyclin/CDK positive transcription elongation factor complex / negative regulation by host of viral genome replication / negative regulation of stem cell differentiation / cyclin-dependent protein serine/threonine kinase activator activity / positive regulation of DNA-templated transcription, elongation / [RNA-polymerase]-subunit kinase ...cyclin K-CDK12 complex / cyclin K-CDK13 complex / nuclear cyclin-dependent protein kinase holoenzyme complex / regulation of MAP kinase activity / cyclin/CDK positive transcription elongation factor complex / negative regulation by host of viral genome replication / negative regulation of stem cell differentiation / cyclin-dependent protein serine/threonine kinase activator activity / positive regulation of DNA-templated transcription, elongation / [RNA-polymerase]-subunit kinase / regulation of cyclin-dependent protein serine/threonine kinase activity / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / RNA polymerase II transcribes snRNA genes / regulation of signal transduction / cyclin-dependent kinase / Formation of HIV elongation complex in the absence of HIV Tat / cyclin-dependent protein serine/threonine kinase activity / 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 / RNA splicing / TP53 Regulates Transcription of DNA Repair Genes / positive regulation of transcription elongation by RNA polymerase II / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / mRNA processing / transcription by RNA polymerase II / protein autophosphorylation / protein kinase activity / nuclear speck / cell cycle / cell division / protein serine kinase activity / DNA damage response / regulation of transcription by RNA polymerase II / protein kinase binding / positive regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.06 Å | ||||||
Authors | Ferguson, A.D. | ||||||
Citation | Journal: ChemMedChem / Year: 2018 Title: Structure-Based Design of Selective Noncovalent CDK12 Inhibitors. Authors: Johannes, J.W. / Denz, C.R. / Su, N. / Wu, A. / Impastato, A.C. / Mlynarski, S. / Varnes, J.G. / Prince, D.B. / Cidado, J. / Gao, N. / Haddrick, M. / Jones, N.H. / Li, S. / Li, X. / Liu, Y. ...Authors: Johannes, J.W. / Denz, C.R. / Su, N. / Wu, A. / Impastato, A.C. / Mlynarski, S. / Varnes, J.G. / Prince, D.B. / Cidado, J. / Gao, N. / Haddrick, M. / Jones, N.H. / Li, S. / Li, X. / Liu, Y. / Nguyen, T.B. / O'Connell, N. / Rivers, E. / Robbins, D.W. / Tomlinson, R. / Yao, T. / Zhu, X. / Ferguson, A.D. / Lamb, M.L. / Manchester, J.I. / Guichard, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6b3e.cif.gz | 462.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6b3e.ent.gz | 380.3 KB | Display | PDB format |
PDBx/mmJSON format | 6b3e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6b3e_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6b3e_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6b3e_validation.xml.gz | 40.2 KB | Display | |
Data in CIF | 6b3e_validation.cif.gz | 54.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b3/6b3e ftp://data.pdbj.org/pub/pdb/validation_reports/b3/6b3e | HTTPS FTP |
-Related structure data
Related structure data | 4nstS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 2 types, 4 molecules ACBD
#1: Protein | Mass: 37127.969 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CDK12, CRK7, CRKRS, KIAA0904 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q9NYV4, cyclin-dependent kinase, [RNA-polymerase]-subunit kinase #2: Protein | Mass: 31372.125 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CCNK, CPR4 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O75909 |
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-Non-polymers , 4 types, 16 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.56 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M Bis-Tris, pH 6.5, 20.5% PEG 3350, 0.4 M MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 5, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.06→88.08 Å / Num. obs: 22962 / % possible obs: 93.5 % / Redundancy: 3.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.055 / Rrim(I) all: 0.028 / Net I/av σ(I): 16.6 / Net I/σ(I): 16.6 |
Reflection shell | Resolution: 3.05→3.06 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.528 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 260 / CC1/2: 0.897 / Rpim(I) all: 0.445 / Rrim(I) all: 0.63 / % possible all: 95.2 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4NST Resolution: 3.06→88.08 Å / Rfactor Rfree error: 0.01 / Cross valid method: FREE R-VALUE
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Displacement parameters | Biso max: 235.89 Å2 / Biso mean: 88.7713 Å2 / Biso min: 30.01 Å2 | |||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.06→88.08 Å
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