+Open data
-Basic information
Entry | Database: PDB / ID: 4ez3 | ||||||
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Title | CDK2 in complex with NSC 134199 | ||||||
Components | Cyclin-dependent kinase 2 | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / protein kinase / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
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 maintenance in response to DNA damage / G0 and Early G1 / Telomere Extension By Telomerase / cellular response to nitric oxide / Activation of the pre-replicative complex / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / 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-dependent protein kinase holoenzyme complex / mitotic G1 DNA damage checkpoint signaling / Cyclin A:Cdk2-associated events at S phase entry / condensed chromosome / regulation of mitotic cell cycle / regulation of G2/M transition of mitotic cell cycle / post-translational protein modification / cyclin binding / positive regulation of DNA replication / male germ cell nucleus / meiotic cell cycle / 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 / Orc1 removal from chromatin / Transcriptional regulation of granulopoiesis / G1/S transition of mitotic cell cycle / G2/M transition of mitotic cell cycle / Cyclin D associated events in G1 / 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) / peptidyl-serine phosphorylation / regulation of gene expression / Regulation of TP53 Activity through Phosphorylation / transcription regulator complex / Ras protein signal transduction / DNA replication / chromosome, telomeric region / endosome / chromatin remodeling / protein phosphorylation / protein domain specific binding / cell division / 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 / negative regulation of transcription by RNA polymerase II / magnesium ion binding / signal transduction / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Alam, R. / Martin, M. / Zhu, J.-Y. / Schonbrunn, E. | ||||||
Citation | Journal: Chembiochem / Year: 2012 Title: A Novel Approach to the Discovery of Small-Molecule Ligands of CDK2. Authors: Martin, M.P. / Alam, R. / Betzi, S. / Ingles, D.J. / Zhu, J.Y. / Schonbrunn, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ez3.cif.gz | 134 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ez3.ent.gz | 103.4 KB | Display | PDB format |
PDBx/mmJSON format | 4ez3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ez3_validation.pdf.gz | 692.4 KB | Display | wwPDB validaton report |
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Full document | 4ez3_full_validation.pdf.gz | 699.6 KB | Display | |
Data in XML | 4ez3_validation.xml.gz | 14.6 KB | Display | |
Data in CIF | 4ez3_validation.cif.gz | 19.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ez/4ez3 ftp://data.pdbj.org/pub/pdb/validation_reports/ez/4ez3 | HTTPS FTP |
-Related structure data
Related structure data | 3ti1C 3tiyC 3tizC 4erwC 4ez7C 3pxzS 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: 34761.348 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CDK2, CDKN2 / Plasmid: pGEX6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): TUNER(DE3) / References: UniProt: P24941, cyclin-dependent kinase |
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#2: Chemical | ChemComp-0S0 / |
#3: Chemical | ChemComp-EDO / |
#4: 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: 1.93 Å3/Da / Density % sol: 36.35 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 5 mg/mL CDK2 protein, 5% v/v PEG3350, 50 mM HEPES/NaOH, pH 7.5, 50 mM sodium/potassium phosphate, pH 7.5, 10 mM NSC134199 soak, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Apr 29, 2012 |
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. obs: 18753 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7 % / Rmerge(I) obs: 0.07 / Rsym value: 0.065 / Net I/σ(I): 21 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 7 % / Rmerge(I) obs: 0.359 / Mean I/σ(I) obs: 6.4 / Rsym value: 0.33 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3PXZ Resolution: 2→18.505 Å / SU ML: 0.2 / σ(F): 1.99 / Phase error: 21.78 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2→18.505 Å
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Refine LS restraints |
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LS refinement shell |
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