+Open data
-Basic information
Entry | Database: PDB / ID: 2c4g | ||||||
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Title | STRUCTURE OF CDK2-CYCLIN A WITH PHA-533514 | ||||||
Components |
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Keywords | TRANSFERASE / PROTEIN KINASE / SERINE/THREONINE-PROTEIN KINASE / PHOSPHORYLATION / CELL DIVISION / CYCLIN / ATP-BINDING / CELL CYCLE / MITOSIS / NUCLEOTIDE-BINDING / POLYMORPHISM | ||||||
Function / homology | Function and homology information Phosphorylation of proteins involved in the G2/M transition by Cyclin A:Cdc2 complexes / cyclin A2-CDK1 complex / cell cycle G1/S phase transition / cellular response to luteinizing hormone stimulus / mitotic cell cycle phase transition / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / cellular response to leptin stimulus / male pronucleus / female pronucleus / response to glucagon ...Phosphorylation of proteins involved in the G2/M transition by Cyclin A:Cdc2 complexes / cyclin A2-CDK1 complex / cell cycle G1/S phase transition / cellular response to luteinizing hormone stimulus / mitotic cell cycle phase transition / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / cellular response to leptin stimulus / male pronucleus / female pronucleus / response to glucagon / cellular response to cocaine / cyclin-dependent protein serine/threonine kinase regulator activity / cellular response to insulin-like growth factor stimulus / positive regulation of DNA biosynthetic process / cochlea development / cyclin A1-CDK2 complex / cyclin E2-CDK2 complex / cyclin E1-CDK2 complex / cellular response to platelet-derived growth factor stimulus / 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 / regulation of DNA replication / 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 / animal organ regeneration / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / Activation of ATR in response to replication stress / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / 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 / cellular response to estradiol stimulus / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / 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 / positive regulation of fibroblast proliferation / 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 / cellular response to hypoxia / 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 / Ub-specific processing proteases / 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 / protein kinase binding / positive regulation of DNA-templated transcription / magnesium ion binding / negative regulation of transcription by RNA polymerase II Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Cameron, A. / Fogliatto, G. / Pevarello, P. / Fancelli, D. / Vulpetti, A. / Amici, R. / Villa, M. / Pittala, V. / Ciomei, M. / Mercurio, C. ...Cameron, A. / Fogliatto, G. / Pevarello, P. / Fancelli, D. / Vulpetti, A. / Amici, R. / Villa, M. / Pittala, V. / Ciomei, M. / Mercurio, C. / Bischoff, J.R. / Roletto, F. / Varasi, M. / Brasca, M.G. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2006 Title: 3-Amino-1,4,5,6-Tetrahydropyrrolo[3,4-C]Pyrazoles: A New Class of Cdk2 Inhibitors. Authors: Pevarello, P. / Fancelli, D. / Vulpetti, A. / Amici, R. / Villa, M. / Pittala, V. / Vianello, P. / Cameron, A. / Ciomei, M. / Mercurio, C. / Bischoff, J.R. / Roletto, F. / Varasi, M. / Brasca, M.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2c4g.cif.gz | 218.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2c4g.ent.gz | 178.6 KB | Display | PDB format |
PDBx/mmJSON format | 2c4g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c4/2c4g ftp://data.pdbj.org/pub/pdb/validation_reports/c4/2c4g | HTTPS FTP |
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-Related structure data
Related structure data | 1finS 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.37982, -0.82165, 0.425), Vector: |
-Components
#1: Protein | Mass: 35251.883 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: P24941, EC: 2.7.1.37 #2: Protein | Mass: 30278.967 Da / Num. of mol.: 2 / Fragment: RESIDUES 173-432 (C-TERMINAL PORTION) Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX6P / Production host: ESCHERICHIA COLI BL21 (bacteria) / References: UniProt: P20248 #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | 5 AMINO ACIDS EXTRA AT THE N-TERMINUS DUE TO CLONING PROTOCOL | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4 Å3/Da / Density % sol: 0.64 % |
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Crystal grow | pH: 7 / Details: 20% AMMONIUM SULPHATE, 1M KCL, 40MM HEPES PH 7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.934 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 20, 2003 / Details: TOROIDAL MIRROR |
Radiation | Monochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→30 Å / Num. obs: 61565 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 61.9 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 17 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 2.4 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1FIN Resolution: 2.7→29.93 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: BFACTOR_MODEL / Cross valid method: THROUGHOUT / σ(F): 0 Details: BULK SOLVENT MODEL USED. UNIDENTIFIED DENSITY SEEN NEAR TO RESIDUE GLU 28 HAS BEEN MODELLED WITH WATER MOLECULES.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 55.3764 Å2 / ksol: 0.340186 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 70.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→29.93 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINTS / Rms dev position: 0.2 Å / Weight position: 150 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6 /
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Xplor file | Serial no: 1 / Param file: PROTEIN_TPO.PARAM / Topol file: 514.TOP |