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- PDB-5efq: Crystal structure of human Cdk13/Cyclin K in complex with ADP-alu... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5efq | ||||||
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Title | Crystal structure of human Cdk13/Cyclin K in complex with ADP-aluminum fluoride | ||||||
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![]() | TRANSFERASE / kinase / cyclin / ADP | ||||||
Function / homology | ![]() cyclin K-CDK12 complex / cyclin K-CDK13 complex / nuclear cyclin-dependent protein kinase holoenzyme complex / cyclin/CDK positive transcription elongation factor complex / negative regulation by host of viral genome replication / alternative mRNA splicing, via spliceosome / 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 / cyclin/CDK positive transcription elongation factor complex / negative regulation by host of viral genome replication / alternative mRNA splicing, via spliceosome / 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 / hemopoiesis / 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 / TP53 Regulates Transcription of DNA Repair Genes / positive regulation of transcription elongation by RNA polymerase II / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / ficolin-1-rich granule lumen / transcription by RNA polymerase II / protein kinase activity / nuclear speck / cell cycle / cell division / protein phosphorylation / protein serine kinase activity / DNA damage response / Neutrophil degranulation / regulation of transcription by RNA polymerase II / protein kinase binding / Golgi apparatus / positive regulation of transcription by RNA polymerase II / RNA binding / extracellular space / extracellular region / nucleoplasm / ATP binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hoenig, D. / Greifenberg, A.K. / Anand, K. / Geyer, M. | ||||||
![]() | ![]() Title: Structural and Functional Analysis of the Cdk13/Cyclin K Complex. Authors: Greifenberg, A.K. / Honig, D. / Pilarova, K. / Duster, R. / Bartholomeeusen, K. / Bosken, C.A. / Anand, K. / Blazek, D. / Geyer, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 486.1 KB | Display | ![]() |
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PDB format | ![]() | 392.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 43.7 KB | Display | |
Data in CIF | ![]() | 61 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4nstS 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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2 | ![]()
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Unit cell |
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Components
-Protein , 2 types, 4 molecules ACBD
#1: Protein | Mass: 40521.863 Da / Num. of mol.: 2 / Fragment: UNP residues 694-1039 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q14004, 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.) ![]() ![]() ![]() |
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-Non-polymers , 4 types, 297 molecules ![](data/chem/img/ADP.gif)
![](data/chem/img/AF3.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/AF3.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-MG / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.12 % |
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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, 25.5% PEG 3350, 0.35 M MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 22, 2013 |
Radiation | Monochromator: Diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9998 Å / Relative weight: 1 |
Reflection | Resolution: 2→49.4 Å / Num. obs: 90134 / % possible obs: 96 % / Redundancy: 1 % / Net I/σ(I): 13 |
Reflection shell | Mean I/σ(I) obs: 1.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4NST Resolution: 2→46.186 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.93 / Phase error: 36.19 / 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: 2→46.186 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 10.0073 Å / Origin y: -26.8098 Å / Origin z: 3.2096 Å
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Refinement TLS group | Selection details: all |