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Yorodumi- PDB-1xo2: Crystal structure of a human cyclin-dependent kinase 6 complex wi... -
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-Basic information
Entry | Database: PDB / ID: 1xo2 | ||||||
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Title | Crystal structure of a human cyclin-dependent kinase 6 complex with a flavonol inhibitor, fisetin | ||||||
Components |
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Keywords | CELL CYCLE/TRANSFERASE / human cyclin-dependent kinase 6 / fisetin / CELL CYCLE-TRANSFERASE COMPLEX | ||||||
Function / homology | Function and homology information cyclin D2-CDK6 complex / cyclin D3-CDK6 complex / cyclin D1-CDK6 complex / cell dedifferentiation / Drug-mediated inhibition of CDK4/CDK6 activity / Evasion of Oncogene Induced Senescence Due to Defective p16INK4A binding to CDK4 and CDK6 / Evasion of Oxidative Stress Induced Senescence Due to Defective p16INK4A binding to CDK4 and CDK6 / FBXO family protein binding / lateral ventricle development / negative regulation of myeloid cell differentiation ...cyclin D2-CDK6 complex / cyclin D3-CDK6 complex / cyclin D1-CDK6 complex / cell dedifferentiation / Drug-mediated inhibition of CDK4/CDK6 activity / Evasion of Oncogene Induced Senescence Due to Defective p16INK4A binding to CDK4 and CDK6 / Evasion of Oxidative Stress Induced Senescence Due to Defective p16INK4A binding to CDK4 and CDK6 / FBXO family protein binding / lateral ventricle development / negative regulation of myeloid cell differentiation / type B pancreatic cell development / negative regulation of monocyte differentiation / astrocyte development / dentate gyrus development / regulation of hematopoietic stem cell differentiation / gliogenesis / regulation of cell motility / Regulation of RUNX1 Expression and Activity / cyclin-dependent protein serine/threonine kinase regulator activity / positive regulation of cell-matrix adhesion / generation of neurons / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / negative regulation of cellular senescence / negative regulation of cell differentiation / negative regulation of cell cycle / hematopoietic stem cell differentiation / negative regulation of osteoblast differentiation / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / cyclin-dependent protein kinase holoenzyme complex / ruffle / Notch signaling pathway / regulation of G2/M transition of mitotic cell cycle / cyclin binding / response to virus / regulation of erythrocyte differentiation / Oncogene Induced Senescence / G1/S transition of mitotic cell cycle / negative regulation of epithelial cell proliferation / Cyclin D associated events in G1 / positive regulation of fibroblast proliferation / T cell differentiation in thymus / Senescence-Associated Secretory Phenotype (SASP) / regulation of gene expression / Oxidative Stress Induced Senescence / regulation of cell cycle / protein phosphorylation / negative regulation of cell population proliferation / cell division / protein serine kinase activity / centrosome / positive regulation of gene expression / negative regulation of transcription by RNA polymerase II / signal transduction / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Saimiriine herpesvirus 2 (Herpesvirus saimiri) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Lu, H.S. / Chang, D.J. / Baratte, B. / Meijer, L. / Schulze-Gahmen, U. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2005 Title: Crystal Structure of a Human Cyclin-Dependent Kinase 6 Complex with a Flavonol Inhibitor, Fisetin. Authors: Lu, H.S. / Chang, D.J. / Baratte, B. / Meijer, L. / Schulze-Gahmen, U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1xo2.cif.gz | 117.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xo2.ent.gz | 90.4 KB | Display | PDB format |
PDBx/mmJSON format | 1xo2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1xo2_validation.pdf.gz | 725.3 KB | Display | wwPDB validaton report |
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Full document | 1xo2_full_validation.pdf.gz | 751.4 KB | Display | |
Data in XML | 1xo2_validation.xml.gz | 23.6 KB | Display | |
Data in CIF | 1xo2_validation.cif.gz | 31.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xo/1xo2 ftp://data.pdbj.org/pub/pdb/validation_reports/xo/1xo2 | HTTPS FTP |
-Related structure data
Related structure data | 1jowS 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: 28665.416 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saimiriine herpesvirus 2 (Herpesvirus saimiri) Genus: Rhadinovirus / Gene: 72, ECLF2 / Plasmid: pFASTBacHTa / Cell line (production host): sf-9 / Production host: Escherichia coli (E. coli) / References: UniProt: Q01043 |
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#2: Protein | Mass: 35066.332 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CDK6 / Plasmid: pFASTBac1 / Cell line (production host): sf-9 / Production host: Escherichia coli (E. coli) / References: UniProt: Q00534, EC: 2.7.1.37 |
#3: Chemical | ChemComp-FSE / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 51 % |
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å |
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Detector | Detector: CCD / Date: Feb 23, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 14353 / % possible obs: 91.5 % / Redundancy: 8.16 % / Biso Wilson estimate: 50 Å2 / Rmerge(I) obs: 0.122 / Net I/σ(I): 18.3 |
Reflection shell | Resolution: 2.8→2.88 Å / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 3.1 / Num. unique all: 1154 / % possible all: 90.9 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1JOW Resolution: 2.9→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.9→20 Å
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Refine LS restraints |
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