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Yorodumi- PDB-1p5e: The structure of phospho-CDK2/cyclin A in complex with the inhibi... -
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-Basic information
Entry | Database: PDB / ID: 1p5e | ||||||
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Title | The structure of phospho-CDK2/cyclin A in complex with the inhibitor 4,5,6,7-tetrabromobenzotriazole (TBS) | ||||||
Components |
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Keywords | CELL CYCLE / Kinase inhibitor / CDK2 / TBS | ||||||
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 / cellular response to leptin stimulus / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / 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 / cellular response to leptin stimulus / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / male pronucleus / female pronucleus / cellular response to cocaine / response to glucagon / cyclin-dependent protein serine/threonine kinase regulator activity / positive regulation of DNA biosynthetic process / cellular response to insulin-like growth factor stimulus / cyclin A1-CDK2 complex / cyclin E2-CDK2 complex / cyclin E1-CDK2 complex / cochlea development / 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 / cellular response to platelet-derived growth factor stimulus / 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 / telomere maintenance in response to DNA damage / centrosome duplication / G0 and Early G1 / Telomere Extension By Telomerase / cellular response to nitric oxide / Activation of the pre-replicative complex / animal organ regeneration / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / Activation of ATR in response to replication stress / Cyclin E associated events during G1/S transition / Cajal body / Cyclin A/B1/B2 associated events during G2/M transition / cyclin-dependent protein kinase holoenzyme complex / mitotic G1 DNA damage checkpoint signaling / Cyclin A:Cdk2-associated events at S phase entry / condensed chromosome / regulation of G2/M transition of mitotic cell cycle / regulation of mitotic cell cycle / post-translational protein modification / cyclin binding / positive regulation of DNA replication / male germ cell nucleus / meiotic cell cycle / cellular response to estradiol stimulus / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / 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 / Transcriptional regulation of granulopoiesis / G1/S transition of mitotic cell cycle / Cyclin D associated events in G1 / G2/M transition of mitotic cell cycle / cellular senescence / positive regulation of fibroblast proliferation / 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) / peptidyl-serine phosphorylation / regulation of gene expression / Regulation of TP53 Activity through Phosphorylation / transcription regulator complex / Ras protein signal transduction / DNA replication / chromosome, telomeric region / Ub-specific processing proteases / endosome / chromatin remodeling / protein phosphorylation / protein domain specific binding / cell division / protein serine kinase activity / DNA repair / protein serine/threonine kinase activity / centrosome / DNA-templated transcription / positive regulation of cell population proliferation / protein kinase binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 Å | ||||||
Authors | De Moliner, E. / Brown, N.R. / Johnson, L.N. | ||||||
Citation | Journal: Eur.J.Biochem. / Year: 2003 Title: Alternative binding modes of an inhibitor to two different kinases Authors: De Moliner, E. / Brown, N.R. / Johnson, L.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1p5e.cif.gz | 228.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1p5e.ent.gz | 190.1 KB | Display | PDB format |
PDBx/mmJSON format | 1p5e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1p5e_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 1p5e_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 1p5e_validation.xml.gz | 42.6 KB | Display | |
Data in CIF | 1p5e_validation.cif.gz | 59.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p5/1p5e ftp://data.pdbj.org/pub/pdb/validation_reports/p5/1p5e | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 34143.547 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CDK2 / Plasmid: PGex 3c / Production host: Escherichia coli (E. coli) / Strain (production host): B834 (DE3) pLysS References: UniProt: P24941, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor #2: Protein | Mass: 29624.297 Da / Num. of mol.: 2 / Fragment: residues 175-432 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CCNA2 OR CCNA OR CCN1 / Plasmid: pET21d / Production host: Escherichia coli (E. coli) / Strain (production host): B834 (DE3) pLysS / References: UniProt: P20248 #3: Chemical | #4: Water | ChemComp-HOH / | |
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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: 2.86 Å3/Da / Density % sol: 57.06 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 10 mg/ml pCDK2/cyclin A, 0.5 mM TBS, 1.25 M Ammonium Sulphate, 0.85 M KCl, HEPES 100mM, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 277 K / pH: 7.4 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 29, 2001 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.22→46.97 Å / Num. all: 73111 / Num. obs: 72014 / % possible obs: 98.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.8 % / Biso Wilson estimate: 30.8 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.054 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 2.22→2.3 Å / Redundancy: 2.22 % / Rmerge(I) obs: 0.334 / Mean I/σ(I) obs: 3.2 / Num. unique all: 6238 / Rsym value: 0.232 / % possible all: 98.6 |
Reflection | *PLUS Rmerge(I) obs: 0.05 |
Reflection shell | *PLUS % possible obs: 98.5 % / Redundancy: 2.2 % / Num. unique obs: 6225 / Rmerge(I) obs: 0.232 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.22→46.97 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 34.7439 Å2 / ksol: 0.386293 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.22→46.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.22→2.36 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
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Xplor file |
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Refine LS restraints | *PLUS
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