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Yorodumi- PDB-1dm2: HUMAN CYCLIN-DEPENDENT KINASE 2 COMPLEXED WITH THE INHIBITOR HYME... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dm2 | ||||||
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Title | HUMAN CYCLIN-DEPENDENT KINASE 2 COMPLEXED WITH THE INHIBITOR HYMENIALDISINE | ||||||
Components | CYCLIN-DEPENDENT KINASE 2 | ||||||
Keywords | CELL CYCLE / PROTEIN KINASE / PHOSPHORYLATION / CELL DIVISION / MITOSIS / INHIBITION | ||||||
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 / Cajal body / 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 / Cyclin A:Cdk2-associated events at S phase entry / condensed chromosome / mitotic G1 DNA damage checkpoint signaling / regulation of G2/M transition of mitotic cell cycle / cyclin binding / post-translational protein modification / meiotic cell cycle / male germ cell nucleus / response to organic substance / 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 / cell division / protein domain specific binding / protein phosphorylation / DNA repair / protein serine kinase activity / centrosome / protein serine/threonine kinase activity / 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 / Resolution: 2.1 Å | ||||||
Authors | Thunnissen, A.M. / Kim, S.-H. | ||||||
Citation | Journal: Chem.Biol. / Year: 2000 Title: Inhibition of cyclin-dependent kinases, GSK-3beta and CK1 by hymenialdisine, a marine sponge constituent. Authors: Meijer, L. / Thunnissen, A.M. / White, A.W. / Garnier, M. / Nikolic, M. / Tsai, L.H. / Walter, J. / Cleverley, K.E. / Salinas, P.C. / Wu, Y.Z. / Biernat, J. / Mandelkow, E.M. / Kim, S.H. / Pettit, G.R. #1: Journal: Science / Year: 1998 Title: Exploiting Chemical Libraries, Structure, and Genomics in the Search for Kinase Inhibitors Authors: Gray, N.S. / Wodicka, L. / Thunnissen, A.M.W.H. / Norman, T.C. / Kwon, S. / Espinoza, F.H. / Morgan, D.O. / Barnes, G. / Leclerc, S. / Meijer, L. / Kim, S.-H. / Lockhart, D.J. / Schultz, P.G. #2: Journal: Eur.J.Biochem. / Year: 1997 Title: Inhibition of Cyclin-Dependent Kinases by Purine Analogues-Crystal Structure of Human Cdk2 Complexed with Roscovitine Authors: De Azevedo, W.F. / Leclerc, S. / Meijer, L. / Havlicek, L. / Strnad, M. / Kim, S.-H. #3: Journal: Proteins / Year: 1995 Title: Multiple Modes of Ligand Recognition: Crystal Structures of Cyclin-Dependent Protein Kinase 2 in Complex with ATP and Two Inhibitors, Olomoucine and Isopentenyladenine Authors: Schultze-Gahmen, U. / Brandsen, J. / Jones, H.D. / Morgan, D.O. / Meijer, L. / Vesely, J. / Kim, S.-H. #4: Journal: Nature / Year: 1993 Title: Crystal Structure of Cyclin-Dependent Kinase 2 Authors: De Bondt, H.L. / Rosenblatt, J. / Jancarik, J. / Jones, H.D. / Morgan, D.O. / Kim, S.-H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dm2.cif.gz | 70.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dm2.ent.gz | 52.4 KB | Display | PDB format |
PDBx/mmJSON format | 1dm2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dm/1dm2 ftp://data.pdbj.org/pub/pdb/validation_reports/dm/1dm2 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 33976.488 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line: SF9 CELLS / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: P24941, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor | ||
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#2: Chemical | ChemComp-HMD / | ||
#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: 2 Å3/Da / Density % sol: 45 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: HEPES, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 278K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion / Details: Rosenblatt, J., (1993) J. Mol. Biol., 230, 1317. | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Feb 5, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→30 Å / Num. all: 51723 / Num. obs: 16264 / % possible obs: 98.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.2 % / Biso Wilson estimate: 13.3 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 21.2 |
Reflection shell | Resolution: 2.1→2.16 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.223 / % possible all: 86.6 |
-Processing
Software |
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Refinement | Resolution: 2.1→30 Å / σ(F): 1 / σ(I): 1 / Stereochemistry target values: ENGH & HUBER
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Displacement parameters | Biso mean: 34.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati sigma a obs: 0.33 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→30 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 30 Å / σ(F): 1 / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 34.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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