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Yorodumi- PDB-1oiy: Structure of human Thr160-phospho CDK2/cyclin A complexed with a ... -
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-Basic information
Entry | Database: PDB / ID: 1oiy | ||||||
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Title | Structure of human Thr160-phospho CDK2/cyclin A complexed with a 6-cyclohexylmethyloxy-2-anilino-purine inhibitor | ||||||
Components |
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Keywords | KINASE / TRANSFERASE / SERINE/THREONINE-PROTEIN KINASE / ATP-BINDING / CELL CYCLE / CELL DIVISION / MITOSIS / PHOSPHORYLATION | ||||||
Function / homology | Function and homology information G2 Phase / Phosphorylation of proteins involved in the G2/M transition by Cyclin A:Cdc2 complexes / cyclin A2-CDK1 complex / cyclin A2-CDK2 complex / cell cycle G1/S phase transition / cellular response to luteinizing hormone stimulus / p53-Dependent G1 DNA Damage Response / mitotic cell cycle phase transition / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / Regulation of APC/C activators between G1/S and early anaphase ...G2 Phase / Phosphorylation of proteins involved in the G2/M transition by Cyclin A:Cdc2 complexes / cyclin A2-CDK1 complex / cyclin A2-CDK2 complex / cell cycle G1/S phase transition / cellular response to luteinizing hormone stimulus / p53-Dependent G1 DNA Damage Response / mitotic cell cycle phase transition / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / Regulation of APC/C activators between G1/S and early anaphase / cellular response to leptin stimulus / male pronucleus / Telomere Extension By Telomerase / G0 and Early G1 / female pronucleus / response to glucagon / cellular response to cocaine / cellular response to nitric oxide / cyclin-dependent protein serine/threonine kinase regulator activity / cellular response to insulin-like growth factor stimulus / positive regulation of DNA biosynthetic process / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / cochlea development / cellular response to platelet-derived growth factor stimulus / Cyclin A/B1/B2 associated events during G2/M transition / Cyclin A:Cdk2-associated events at S phase entry / cyclin-dependent protein kinase holoenzyme complex / regulation of DNA replication / animal organ regeneration / post-translational protein modification / cellular response to estradiol stimulus / DNA Damage/Telomere Stress Induced Senescence / CDK-mediated phosphorylation and removal of Cdc6 / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / SCF(Skp2)-mediated degradation of p27/p21 / Orc1 removal from chromatin / G1/S transition of mitotic cell cycle / G2/M transition of mitotic cell cycle / positive regulation of fibroblast proliferation / Regulation of TP53 Degradation / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / cellular response to hypoxia / Regulation of TP53 Activity through Phosphorylation / Ras protein signal transduction / Ub-specific processing proteases / protein domain specific binding / cell division / centrosome / DNA-templated transcription / positive regulation of DNA-templated transcription / protein kinase binding / nucleoplasm / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Pratt, D.J. / Endicott, J.A. / Noble, M.E.M. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2004 Title: N2-Substituted O6-Cyclohexylmethylguanine Derivatives: Potent Inhibitors of Cyclin-Dependent Kinases 1 and 2 Authors: Hardcastle, I.R. / Arris, C.E. / Bentley, J. / Boyle, F.T. / Chen, Y. / Curtin, N.J. / Endicott, J.A. / Gibson, A.E. / Golding, B.T. / Griffin, R.J. / Jewsbury, P. / Menyerol, J. / ...Authors: Hardcastle, I.R. / Arris, C.E. / Bentley, J. / Boyle, F.T. / Chen, Y. / Curtin, N.J. / Endicott, J.A. / Gibson, A.E. / Golding, B.T. / Griffin, R.J. / Jewsbury, P. / Menyerol, J. / Mesguiche, V. / Newell, D.R. / Noble, M.E.M. / Pratt, D.J. / Wang, L.-Z. / Whitfield, H.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1oiy.cif.gz | 238 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1oiy.ent.gz | 191.4 KB | Display | PDB format |
PDBx/mmJSON format | 1oiy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1oiy_validation.pdf.gz | 847.7 KB | Display | wwPDB validaton report |
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Full document | 1oiy_full_validation.pdf.gz | 894.4 KB | Display | |
Data in XML | 1oiy_validation.xml.gz | 38.1 KB | Display | |
Data in CIF | 1oiy_validation.cif.gz | 57.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oi/1oiy ftp://data.pdbj.org/pub/pdb/validation_reports/oi/1oiy | HTTPS FTP |
-Related structure data
Related structure data | 1oi9C 1oiuC 1h1sS 1h0u S: Starting model for refinement C: citing same article (ref.) |
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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:
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-Components
-Protein , 2 types, 4 molecules ACBD
#1: Protein | Mass: 34354.770 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: PHOSPHORYLATED ON THR160 / Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P24941, EC: 2.7.1.37 #2: Protein | Mass: 29884.605 Da / Num. of mol.: 2 / Fragment: RESIDUES 174-432 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P20248 |
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-Non-polymers , 4 types, 283 molecules
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-MG / | #6: Water | ChemComp-HOH / | |
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-Details
Compound details | CYCLIN CONTROLS THE CELL CYCLE AT THE G1/S (START) AND THE G2/M (MITOSIS) TRANSITIONS. KINASE ...CYCLIN CONTROLS THE CELL CYCLE AT THE G1/S (START) AND THE G2/M (MITOSIS) TRANSITION |
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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: 2.8 Å3/Da / Density % sol: 55.6 % / Description: USED DATA TO 3.5 A FOR MR |
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Crystal grow | pH: 7 Details: 0.7-0.85 M POTASSIUM CHLORIDE, 1.1-1.25 M AMMONIUM SULFATE, 40 MM HEPES, PH 7.0, 5 MM DITHIOTHREITOL, 10 MG/ML PROTEIN, 8M SODIUM FORMATE CRYO-PROTECTANT |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9393 |
Detector | Type: ADSC CCD / Detector: CCD / Date: May 10, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9393 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→47.14 Å / Num. obs: 53738 / % possible obs: 92.3 % / Observed criterion σ(I): 1 / Redundancy: 2.27 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 5.0142 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 1.83 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 2.56 / % possible all: 80.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1H1S Resolution: 2.4→100 Å / Cor.coef. Fo:Fc: 0.893 / Cor.coef. Fo:Fc free: 0.822 / SU B: 10.77 / SU ML: 0.252 / Cross valid method: THROUGHOUT / ESU R: 0.501 / ESU R Free: 0.332 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.11 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→100 Å
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Refine LS restraints |
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