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Yorodumi- PDB-5bnj: CDK8/CYCC IN COMPLEX WITH 8-{3-Chloro-5-[4-(1-methyl-1H-pyrazol-4... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5bnj | ||||||
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Title | CDK8/CYCC IN COMPLEX WITH 8-{3-Chloro-5-[4-(1-methyl-1H-pyrazol-4-yl)-phenyl]-pyridin- 4-yl}-2,8-diaza-spiro[4.5]decan-1-one | ||||||
Components |
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Keywords | TRANSFERASE / CDK8 KINASE / CYCLIN C | ||||||
Function / homology | Function and homology information CKM complex / negative regulation of triglyceride metabolic process / G0 to G1 transition / mediator complex / Generic Transcription Pathway / [RNA-polymerase]-subunit kinase / cyclin-dependent protein serine/threonine kinase regulator activity / negative regulation of Notch signaling pathway / cyclin-dependent protein kinase holoenzyme complex / cyclin-dependent kinase ...CKM complex / negative regulation of triglyceride metabolic process / G0 to G1 transition / mediator complex / Generic Transcription Pathway / [RNA-polymerase]-subunit kinase / cyclin-dependent protein serine/threonine kinase regulator activity / negative regulation of Notch signaling pathway / cyclin-dependent protein kinase holoenzyme complex / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / ubiquitin ligase complex / RNA polymerase II CTD heptapeptide repeat kinase activity / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / PPARA activates gene expression / NOTCH1 Intracellular Domain Regulates Transcription / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / Transcriptional regulation of white adipocyte differentiation / ubiquitin protein ligase activity / protein ubiquitination / protein kinase activity / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / nucleolus / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / ATP binding / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 Å | ||||||
Authors | Musil, D. / Blagg, J. / Wienke, D. | ||||||
Citation | Journal: Nat.Chem.Biol. / Year: 2015 Title: A selective chemical probe for exploring the role of CDK8 and CDK19 in human disease. Authors: Dale, T. / Clarke, P.A. / Esdar, C. / Waalboer, D. / Adeniji-Popoola, O. / Ortiz-Ruiz, M.J. / Mallinger, A. / Samant, R.S. / Czodrowski, P. / Musil, D. / Schwarz, D. / Schneider, K. / ...Authors: Dale, T. / Clarke, P.A. / Esdar, C. / Waalboer, D. / Adeniji-Popoola, O. / Ortiz-Ruiz, M.J. / Mallinger, A. / Samant, R.S. / Czodrowski, P. / Musil, D. / Schwarz, D. / Schneider, K. / Stubbs, M. / Ewan, K. / Fraser, E. / TePoele, R. / Court, W. / Box, G. / Valenti, M. / de Haven Brandon, A. / Gowan, S. / Rohdich, F. / Raynaud, F. / Schneider, R. / Poeschke, O. / Blaukat, A. / Workman, P. / Schiemann, K. / Eccles, S.A. / Wienke, D. / Blagg, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5bnj.cif.gz | 132.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5bnj.ent.gz | 105.8 KB | Display | PDB format |
PDBx/mmJSON format | 5bnj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bn/5bnj ftp://data.pdbj.org/pub/pdb/validation_reports/bn/5bnj | HTTPS FTP |
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-Related structure data
Related structure data | |
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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: 46990.801 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, residues 3-405 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CDK8 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: P49336, cyclin-dependent kinase, [RNA-polymerase]-subunit kinase | ||
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#2: Protein | Mass: 33479.953 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CCNC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P24863 | ||
#3: Chemical | ChemComp-4TV / | ||
#4: Chemical | #5: 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: 3.08 Å3/Da / Density % sol: 60.09 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 6.9 / Details: 20% PEG3350, 0.2 M sodium formate, pH 6.9, |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: May 22, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.64→86.27 Å / Num. obs: 25877 / % possible obs: 97.8 % / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 2.64→2.89 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.523 / Rejects: 0 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: NONE Resolution: 2.64→86.27 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.889 / SU B: 11.401 / SU ML: 0.234 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.588 / ESU R Free: 0.327 / 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 / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 87.88 Å2 / Biso mean: 46.604 Å2 / Biso min: 28.58 Å2
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Refinement step | Cycle: final / Resolution: 2.64→86.27 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.64→2.709 Å / Total num. of bins used: 20
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