[English] 日本語
Yorodumi- PDB-1fvv: THE STRUCTURE OF CDK2/CYCLIN A IN COMPLEX WITH AN OXINDOLE INHIBITOR -
+Open data
-Basic information
Entry | Database: PDB / ID: 1fvv | ||||||
---|---|---|---|---|---|---|---|
Title | THE STRUCTURE OF CDK2/CYCLIN A IN COMPLEX WITH AN OXINDOLE INHIBITOR | ||||||
Components |
| ||||||
Keywords | TRANSFERASE / CELL CYCLE / cyclin-dependent kinase / cyclin A | ||||||
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 / cellular response to cocaine ...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 / cellular response to cocaine / response to glucagon / 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 / cyclin-dependent kinase / animal organ regeneration / 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 / 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 / G2/M transition of mitotic cell cycle / positive regulation of fibroblast proliferation / 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 / negative regulation of transcription by RNA polymerase II / magnesium ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å | ||||||
Authors | Davis, S.T. / Benson, B.G. / Bramson, H.N. / Chapman, D.E. / Dickerson, S.H. / Dold, K.M. / Eberwein, D.J. / Edelstein, M. / Frye, S.V. / Gampe Jr., R.T. ...Davis, S.T. / Benson, B.G. / Bramson, H.N. / Chapman, D.E. / Dickerson, S.H. / Dold, K.M. / Eberwein, D.J. / Edelstein, M. / Frye, S.V. / Gampe Jr., R.T. / Griffin, R.J. / Harris, P.A. / Hassell, A.M. / Holmes, W.D. / Hunter, R.N. / Knick, V.B. / Lackey, K. / Lovejoy, B. / Luzzio, M.J. / Murray, D. / Parker, P. / Rocque, W.J. / Shewchuk, L. / Veal, J.M. / Walker, D.H. / Kuyper, L.K. | ||||||
Citation | Journal: Science / Year: 2001 Title: Prevention of chemotherapy-induced alopecia in rats by CDK inhibitors. Authors: Davis, S.T. / Benson, B.G. / Bramson, H.N. / Chapman, D.E. / Dickerson, S.H. / Dold, K.M. / Eberwein, D.J. / Edelstein, M. / Frye, S.V. / Gampe Jr, R.T. / Griffin, R.J. / Harris, P.A. / ...Authors: Davis, S.T. / Benson, B.G. / Bramson, H.N. / Chapman, D.E. / Dickerson, S.H. / Dold, K.M. / Eberwein, D.J. / Edelstein, M. / Frye, S.V. / Gampe Jr, R.T. / Griffin, R.J. / Harris, P.A. / Hassell, A.M. / Holmes, W.D. / Hunter, R.N. / Knick, V.B. / Lackey, K. / Lovejoy, B. / Luzzio, M.J. / Murray, D. / Parker, P. / Rocque, W.J. / Shewchuk, L. / Veal, J.M. / Walker, D.H. / Kuyper, L.F. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1fvv.cif.gz | 231.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1fvv.ent.gz | 188 KB | Display | PDB format |
PDBx/mmJSON format | 1fvv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fv/1fvv ftp://data.pdbj.org/pub/pdb/validation_reports/fv/1fvv | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
2 |
| ||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 33976.488 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PFASTBAC1 OR PACHLT-A / Production host: Escherichia coli (E. coli) / References: UniProt: P24941, EC: 2.7.1.37 #2: Protein | Mass: 29867.512 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P20248 #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.11 Å3/Da / Density % sol: 70.09 % | |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.7 Details: 1.5 M sodium acetate, 100 mM sodium cacodylate, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 277K | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 7.5 / Details: Shewchuk L., (2000) J. Med. Chem., 43, 133. | |||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jan 3, 2000 |
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→20 Å / Num. all: 50936 / Num. obs: 50936 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10 % / Biso Wilson estimate: 91.3 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 36 |
Reflection shell | Resolution: 2.8→2.98 Å / Redundancy: 9 % / Rmerge(I) obs: 0.29 / Num. unique all: 7029 / % possible all: 90.2 |
Reflection | *PLUS Num. measured all: 541713 / Rmerge(I) obs: 0.07 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.8→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→20 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor Rfree: 0.26 / Rfactor Rwork: 0.26 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
|