+Open data
-Basic information
Entry | Database: PDB / ID: 6yl6 | |||||||||
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Title | Cdk2(F80C) | |||||||||
Components | Cyclin-dependent kinase 2 | |||||||||
Keywords | TRANSFERASE / Covalent inhibitor / Cysteine modification / Kinase / Allosteric inhibitor | |||||||||
Function / homology | Function and homology information 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 ...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 / 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 / cyclin-dependent protein kinase holoenzyme complex / cellular response to nitric oxide / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / Cajal body / 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 / 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 / cyclin binding / post-translational protein modification / meiotic cell cycle / positive regulation of DNA replication / response to organic substance / male germ cell nucleus / G1/S transition of mitotic cell cycle / potassium ion transport / DNA Damage/Telomere Stress Induced Senescence / CDK-mediated phosphorylation and removal of Cdc6 / SCF(Skp2)-mediated degradation of p27/p21 / Meiotic recombination / Orc1 removal from chromatin / Transcriptional regulation of granulopoiesis / Cyclin D associated events in G1 / G2/M transition of mitotic cell cycle / cellular senescence / Regulation of TP53 Degradation / nuclear envelope / 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 / Ras protein signal transduction / Regulation of TP53 Activity through Phosphorylation / transcription regulator complex / DNA replication / chromosome, telomeric region / endosome / chromatin remodeling / protein domain specific binding / cell division / protein phosphorylation / protein serine kinase activity / DNA repair / protein serine/threonine kinase activity / centrosome / DNA-templated transcription / positive regulation of cell population proliferation / positive regulation of DNA-templated transcription / magnesium ion binding / negative regulation of transcription by RNA polymerase II / signal transduction / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | |||||||||
Authors | Craven, G. / Morgan, R.M.L. / Mann, D.J. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: Chembiochem / Year: 2020 Title: Multiparameter Kinetic Analysis for Covalent Fragment Optimization by Using Quantitative Irreversible Tethering (qIT). Authors: Craven, G.B. / Affron, D.P. / Kosel, T. / Wong, T.L.M. / Jukes, Z.H. / Liu, C.T. / Morgan, R.M.L. / Armstrong, A. / Mann, D.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6yl6.cif.gz | 80 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6yl6.ent.gz | 56.7 KB | Display | PDB format |
PDBx/mmJSON format | 6yl6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yl/6yl6 ftp://data.pdbj.org/pub/pdb/validation_reports/yl/6yl6 | HTTPS FTP |
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-Related structure data
Related structure data | 6yl1C 6ylkC 4ek3S 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: 34311.848 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CDK2, CDKN2 / Production host: Escherichia coli (E. coli) / References: UniProt: P24941, cyclin-dependent kinase |
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#2: 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: 1.96 Å3/Da / Density % sol: 37.21 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: Protein solution: 8 mg/mL, 100 mM phosphate buffer (pH6.2) Reservoir solution: 8-12% PEG3350, HEPES (0.1 M pH 7.5 - 8.5) PH range: 7.5 |
-Data collection
Diffraction | Mean temperature: 298 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 16, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→42.41 Å / Num. obs: 29979 / % possible obs: 98.88 % / Redundancy: 2 % / Biso Wilson estimate: 24.24 Å2 / CC1/2: 1 / Net I/σ(I): 16.92 |
Reflection shell | Resolution: 1.7→1.761 Å / Num. unique obs: 2672 / CC1/2: 0.782 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4EK3 Resolution: 1.7→42.41 Å / Cross valid method: FREE R-VALUE
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Displacement parameters | Biso mean: 29.7 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→42.41 Å
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Refine LS restraints |
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