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Yorodumi- PDB-1e9h: Thr 160 phosphorylated CDK2 - Human cyclin A3 complex with the in... -
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-Basic information
Entry | Database: PDB / ID: 1e9h | ||||||
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Title | Thr 160 phosphorylated CDK2 - Human cyclin A3 complex with the inhibitor indirubin-5-sulphonate bound | ||||||
Components |
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Keywords | CELL CYCLE / COMPLEX (PROTEIN KINASE-CYCLIN) / KINASES / INHIBITOR / CYCLIN / COMPLEX / PHOSPHORYLATION | ||||||
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 DNA replication / regulation of anaphase-promoting complex-dependent catabolic process / 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 / cellular response to nitric oxide / cyclin-dependent protein kinase holoenzyme complex / 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 / Cajal body / Cyclin A:Cdk2-associated events at S phase entry / condensed chromosome / mitotic G1 DNA damage checkpoint signaling / regulation of mitotic cell cycle / regulation of G2/M transition of mitotic cell cycle / cyclin binding / post-translational protein modification / : / meiotic cell cycle / positive regulation of DNA replication / male germ cell nucleus / 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 / SCF(Skp2)-mediated degradation of p27/p21 / Meiotic recombination / Orc1 removal from chromatin / G1/S transition of mitotic cell cycle / Transcriptional regulation of granulopoiesis / G2/M transition of mitotic cell cycle / Cyclin D associated events in G1 / 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) / regulation of gene expression / peptidyl-serine phosphorylation / DNA replication / Regulation of TP53 Activity through Phosphorylation / transcription regulator complex / Ras protein signal transduction / chromosome, telomeric region / Ub-specific processing proteases / endosome / chromatin remodeling / protein domain specific binding / cell division / protein phosphorylation / DNA repair / protein serine kinase activity / protein serine/threonine kinase activity / DNA-templated transcription / centrosome / positive regulation of cell population proliferation / protein kinase binding / positive regulation of DNA-templated transcription Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Davies, T.G. / Tunnah, P. / Noble, M.E.M. / Endicott, J.A. | ||||||
Citation | Journal: Structure / Year: 2001 Title: Inhibitor Binding to Active and Inactive Cdk2: The Crystal Structure of Cdk2-Cyclin A/Indirubin-5-Sulphonate Authors: Davies, T.G. / Tunnah, P. / Meijer, L. / Marko, D. / Eisenbrand, G. / Endicott, J.A. / Noble, M.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1e9h.cif.gz | 238.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1e9h.ent.gz | 192.1 KB | Display | PDB format |
PDBx/mmJSON format | 1e9h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1e9h_validation.pdf.gz | 555.4 KB | Display | wwPDB validaton report |
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Full document | 1e9h_full_validation.pdf.gz | 607.6 KB | Display | |
Data in XML | 1e9h_validation.xml.gz | 30.2 KB | Display | |
Data in CIF | 1e9h_validation.cif.gz | 45.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e9/1e9h ftp://data.pdbj.org/pub/pdb/validation_reports/e9/1e9h | HTTPS FTP |
-Related structure data
Related structure data | |
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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: (-0.999932, -0.011239, 0.003138), Vector: |
-Components
#1: Protein | Mass: 33873.195 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: PHOSPHORYLATED ON THR 160 CHAINS A AND C ARE ASYMETRIC UNIT COPIES Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P24941, EC: 2.7.1.37 #2: Protein | Mass: 29964.713 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: TRUNCATED FRAGMENT OF CYCLIN A. IN COMPLEX WITH CDK2 CHAINS B AND D ARE ASYMETRIC UNIT COPIES Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P20248 #3: Chemical | #4: Water | ChemComp-HOH / | Compound details | THE CDK2 SHOWS MAXIMAL ACTIVITY DURING S PHASE AND G2 AND INTERACTS WITH CYCLINS A, D, OR E. IT IS ...THE CDK2 SHOWS MAXIMAL ACTIVITY DURING S PHASE AND G2 AND INTERACTS WITH CYCLINS A, D, OR E. IT IS PROBABLY INVOLVED IN THE CONTROL OF THE CELL CYCLE. CYCLIN IS ESSENTIAL FOR THE CONTROL OF 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: 2.91 Å3/Da / Density % sol: 57.71 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7 / Details: pH 7.00 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging 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: ID14-2 / Wavelength: 0.933 |
Detector | Date: Apr 15, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. obs: 47127 / % possible obs: 90.1 % / Redundancy: 3 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 4.1 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 1.9 / % possible all: 90.1 |
Reflection | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 20 Å / Num. measured all: 143005 / Rmerge(I) obs: 0.103 |
Reflection shell | *PLUS % possible obs: 63.8 % / Rmerge(I) obs: 0.388 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: UNPUBLISHED STRUCTURE Resolution: 2.5→100 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2.5→100 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 100 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |