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- PDB-1ckp: HUMAN CYCLIN DEPENDENT KINASE 2 COMPLEXED WITH THE INHIBITOR PURV... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ckp | ||||||
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Title | HUMAN CYCLIN DEPENDENT KINASE 2 COMPLEXED WITH THE INHIBITOR PURVALANOL B | ||||||
![]() | PROTEIN (CYCLIN-DEPENDENT PROTEIN KINASE 2) | ||||||
![]() | HORMONE/GROWTH FACTOR / PROTEIN KINASE / CELL CYCLE / PHOSPHORYLATION / CELL DIVISION / MITOSIS / INHIBITION / HORMONE-GROWTH FACTOR COMPLEX | ||||||
Function / homology | ![]() 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 / cellular response to nitric oxide / cyclin-dependent protein kinase holoenzyme complex / 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 / 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 / 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 / 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 / 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 / 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 | ![]() | ||||||
Method | ![]() | ||||||
![]() | Gray, N.S. / Thunnissen, A.M.W.H. / Schultz, P.G. / Kim, S.H. | ||||||
![]() | ![]() Title: Exploiting chemical libraries, structure, and genomics in the search for kinase inhibitors. Authors: Gray, N.S. / Wodicka, L. / Thunnissen, A.M. / 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. #1: ![]() 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. #2: ![]() 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. #3: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 72.6 KB | Display | ![]() |
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PDB format | ![]() | 53 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 491.5 KB | Display | ![]() |
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Full document | ![]() | 493.2 KB | Display | |
Data in XML | ![]() | 7.7 KB | Display | |
Data in CIF | ![]() | 11.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1hckS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-PVB / |
#3: Chemical | ChemComp-EDO / |
#4: Water | ChemComp-HOH / |
Nonpolymer details | 3-CHLORO-4-CARBOXYANI |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 36 % |
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Crystal grow | pH: 7.4 / Details: pH 7.4 |
Crystal grow | *PLUS Method: unknown |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Feb 15, 1996 / Details: MIRROR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→32 Å / Num. obs: 17655 / % possible obs: 98.7 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 2.05→2.11 Å / Rmerge(I) obs: 0.185 / % possible all: 91.6 |
Reflection shell | *PLUS % possible obs: 91.6 % |
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Processing
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Refinement | Method to determine structure: OTHER Starting model: PDB ENTRY 1HCK Resolution: 2.05→32 Å / Isotropic thermal model: RESTRAINED / Cross valid method: FREE-R / σ(F): 2 Details: REFINEMENT BEGUN WITH X-PLOR PC AND RIGID BODY REFINEMENT. ETHYLENE GLYCOL MOLECULE HAS BEEN REFINED WITH OCCUPANCY OF 0.7
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Displacement parameters | Biso mean: 30.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.05→32 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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