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- PDB-7nxk: Crystal structure of human Cdk12/Cyclin K in complex with the inh... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7nxk | |||||||||
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Title | Crystal structure of human Cdk12/Cyclin K in complex with the inhibitor BSJ-01-175 | |||||||||
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![]() | TRANSCRIPTION / CDK12 / Cyclin K / CCNK / BSJ-01-175 / kinase | |||||||||
Function / homology | ![]() 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 | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Anand, K. / Dust, S. / Kaltheuner, I.H. / Geyer, M. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure-activity relationship study of THZ531 derivatives enables the discovery of BSJ-01-175 as a dual CDK12/13 covalent inhibitor with efficacy in Ewing sarcoma. Authors: Jiang, B. / Jiang, J. / Kaltheuner, I.H. / Iniguez, A.B. / Anand, K. / Ferguson, F.M. / Ficarro, S.B. / Seong, B.K.A. / Greifenberg, A.K. / Dust, S. / Kwiatkowski, N.P. / Marto, J.A. / ...Authors: Jiang, B. / Jiang, J. / Kaltheuner, I.H. / Iniguez, A.B. / Anand, K. / Ferguson, F.M. / Ficarro, S.B. / Seong, B.K.A. / Greifenberg, A.K. / Dust, S. / Kwiatkowski, N.P. / Marto, J.A. / Stegmaier, K. / Zhang, T. / Geyer, M. / Gray, N.S. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 241.5 KB | Display | ![]() |
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PDB format | ![]() | 187.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 947.2 KB | Display | ![]() |
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Full document | ![]() | 969.6 KB | Display | |
Data in XML | ![]() | 43.8 KB | Display | |
Data in CIF | ![]() | 57.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7nxjC ![]() 4nstS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 40764.992 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9NYV4, cyclin-dependent kinase, [RNA-polymerase]-subunit kinase #2: Protein | Mass: 31429.172 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.42 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.1 M MES, pH 6.0, 30% PEGmixture (medium weight pegs), 0.3 M NDSB, 0.2 M MgCl2. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 16, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3→49 Å / Num. obs: 25438 / % possible obs: 97 % / Redundancy: 3.35 % / Rrim(I) all: 0.19 / Net I/σ(I): 5.4 |
Reflection shell | Resolution: 3→3.14 Å / Num. unique obs: 3186 / Rrim(I) all: 0.99 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4NST Resolution: 3→49 Å / SU ML: 0.56 / Cross valid method: FREE R-VALUE / σ(F): 1.95 / Phase error: 34.82 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→49 Å
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Refine LS restraints |
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LS refinement shell |
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