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Yorodumi- PDB-5l2w: The X-ray co-crystal structure of human CDK2/CyclinE and Dinaciclib. -
+Open data
-Basic information
Entry | Database: PDB / ID: 5l2w | ||||||
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Title | The X-ray co-crystal structure of human CDK2/CyclinE and Dinaciclib. | ||||||
Components |
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Keywords | Transferase/Cell Cycle/Inhibitor / cyclin-dependent kinase / kinase inhibitor / kinase selectivity / Transferase-Cell Cycle-Inhibitor complex | ||||||
Function / homology | Function and homology information positive regulation of mesenchymal stem cell proliferation / homologous chromosome pairing at meiosis / RHOBTB3 ATPase cycle / cyclin-dependent protein serine/threonine kinase regulator activity / G1/S-Specific Transcription / cyclin A1-CDK2 complex / cyclin E2-CDK2 complex / cyclin E1-CDK2 complex / cyclin A2-CDK2 complex / positive regulation of DNA-templated DNA replication initiation ...positive regulation of mesenchymal stem cell proliferation / homologous chromosome pairing at meiosis / RHOBTB3 ATPase cycle / cyclin-dependent protein serine/threonine kinase regulator activity / G1/S-Specific Transcription / cyclin A1-CDK2 complex / cyclin E2-CDK2 complex / cyclin E1-CDK2 complex / cyclin A2-CDK2 complex / positive regulation of DNA-templated DNA replication initiation / G2 Phase / cyclin-dependent protein kinase activity / Y chromosome / Phosphorylation of proteins involved in G1/S transition by active Cyclin E:Cdk2 complexes / positive regulation of heterochromatin formation / p53-Dependent G1 DNA Damage Response / X chromosome / PTK6 Regulates Cell Cycle / regulation of anaphase-promoting complex-dependent catabolic process / Association of TriC/CCT with target proteins during biosynthesis / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / centriole replication / Regulation of APC/C activators between G1/S and early anaphase / centrosome duplication / Telomere Extension By Telomerase / G0 and Early G1 / Activation of the pre-replicative complex / DNA replication initiation / cellular response to nitric oxide / cyclin-dependent protein kinase holoenzyme complex / positive regulation of G1/S transition of mitotic cell cycle / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / Activation of ATR in response to replication stress / Cyclin E associated events during G1/S transition / Cyclin A/B1/B2 associated events during G2/M transition / Cajal body / Cyclin A:Cdk2-associated events at S phase entry / condensed chromosome / mitotic G1 DNA damage checkpoint signaling / regulation of mitotic cell cycle / regulation of G2/M transition of mitotic cell cycle / telomere maintenance / cyclin binding / post-translational protein modification / : / meiotic cell cycle / positive regulation of DNA replication / male germ cell nucleus / potassium ion transport / DNA Damage/Telomere Stress Induced Senescence / CDK-mediated phosphorylation and removal of Cdc6 / Meiotic recombination / SCF(Skp2)-mediated degradation of p27/p21 / Wnt signaling pathway / Orc1 removal from chromatin / G1/S transition of mitotic cell cycle / Transcriptional regulation of granulopoiesis / G2/M transition of mitotic cell cycle / Cyclin D associated events in G1 / regulation of protein localization / cellular senescence / Regulation of TP53 Degradation / nuclear envelope / kinase activity / Factors involved in megakaryocyte development and platelet production / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / regulation of gene expression / peptidyl-serine phosphorylation / DNA replication / Regulation of TP53 Activity through Phosphorylation / transcription regulator complex / Ras protein signal transduction / chromosome, telomeric region / endosome / chromatin remodeling / protein domain specific binding / cell division / protein phosphorylation / DNA repair / protein serine kinase activity / protein serine/threonine kinase activity / DNA-templated transcription / centrosome / positive regulation of cell population proliferation / protein kinase binding / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / magnesium ion binding / signal transduction / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.8 Å | ||||||
Authors | Chen, P. / Ferre, R.A. / Deihl, W. / Yu, X. / He, Y.-A. | ||||||
Citation | Journal: Mol.Cancer Ther. / Year: 2016 Title: Spectrum and Degree of CDK Drug Interactions Predicts Clinical Performance. Authors: Chen, P. / Lee, N.V. / Hu, W. / Xu, M. / Ferre, R.A. / Lam, H. / Bergqvist, S. / Solowiej, J. / Diehl, W. / He, Y.A. / Yu, X. / Nagata, A. / VanArsdale, T. / Murray, B.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5l2w.cif.gz | 134.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5l2w.ent.gz | 101.4 KB | Display | PDB format |
PDBx/mmJSON format | 5l2w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5l2w_validation.pdf.gz | 824.4 KB | Display | wwPDB validaton report |
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Full document | 5l2w_full_validation.pdf.gz | 831.3 KB | Display | |
Data in XML | 5l2w_validation.xml.gz | 22.7 KB | Display | |
Data in CIF | 5l2w_validation.cif.gz | 31.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l2/5l2w ftp://data.pdbj.org/pub/pdb/validation_reports/l2/5l2w | HTTPS FTP |
-Related structure data
Related structure data | 5l2iC 5l2sC 5l2tC 1w98S C: citing same article (ref.) 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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Unit cell |
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-Components
#1: Protein | Mass: 34143.547 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CDK2, CDKN2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P24941, cyclin-dependent kinase |
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#2: Protein | Mass: 35690.262 Da / Num. of mol.: 1 / Fragment: UNP residues 81-363 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CCNE1, CCNE / Production host: Escherichia coli (E. coli) / References: UniProt: P24864 |
#3: Chemical | ChemComp-1QK / |
#4: Chemical | ChemComp-GOL / |
#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: 2.73 Å3/Da / Density % sol: 55.03 % |
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Crystal grow | Temperature: 286.15 K / Method: vapor diffusion, sitting drop / Details: PEG20K, 180mM Mg(HCO2)2, 0.1M MES pH 6.0 |
-Data collection
Diffraction | Mean temperature: 98.15 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 9, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→45 Å / Num. obs: 19770 / % possible obs: 99.9 % / Redundancy: 12.76 % / Biso Wilson estimate: 100.25 Å2 / Net I/σ(I): 22.9 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1W98 Resolution: 2.8→45 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.9244 / SU R Cruickshank DPI: 1.334 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 2.166 / SU Rfree Blow DPI: 0.335 / SU Rfree Cruickshank DPI: 0.337
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Displacement parameters | Biso mean: 84.34 Å2
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Refine analyze | Luzzati coordinate error obs: 0.378 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.8→45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.95 Å / Total num. of bins used: 10
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