+Open data
-Basic information
Entry | Database: PDB / ID: 5nev | |||||||||
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Title | CDK2/Cyclin A in complex with compound 73 | |||||||||
Components |
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Keywords | TRANSFERASE / CDK2 CYCLIN A / CDK2 SELECTIVE TRANSFERASE | |||||||||
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 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 / Meiotic recombination / SCF(Skp2)-mediated degradation of p27/p21 / 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: 2.97 Å | |||||||||
Authors | Coxon, C.R. / Anscombe, E. / Harnor, S.J. / Martin, M.P. / Carbain, B. / Hardcastle, I.R. / Harlow, L.K. / Korolchuk, S. / Matheson, C.J. / Noble, M.E.M. ...Coxon, C.R. / Anscombe, E. / Harnor, S.J. / Martin, M.P. / Carbain, B. / Hardcastle, I.R. / Harlow, L.K. / Korolchuk, S. / Matheson, C.J. / Noble, M.E.M. / Newell, D.R. / Turner, D. / Sivaprakasam, M. / Wang, L.Z. / Wong, C. / Golding, B.T. / Griffin, R.J. / Cano, G. | |||||||||
Citation | Journal: J. Med. Chem. / Year: 2017 Title: Cyclin-Dependent Kinase (CDK) Inhibitors: Structure-Activity Relationships and Insights into the CDK-2 Selectivity of 6-Substituted 2-Arylaminopurines. Authors: Coxon, C.R. / Anscombe, E. / Harnor, S.J. / Martin, M.P. / Carbain, B. / Golding, B.T. / Hardcastle, I.R. / Harlow, L.K. / Korolchuk, S. / Matheson, C.J. / Newell, D.R. / Noble, M.E. / ...Authors: Coxon, C.R. / Anscombe, E. / Harnor, S.J. / Martin, M.P. / Carbain, B. / Golding, B.T. / Hardcastle, I.R. / Harlow, L.K. / Korolchuk, S. / Matheson, C.J. / Newell, D.R. / Noble, M.E. / Sivaprakasam, M. / Tudhope, S.J. / Turner, D.M. / Wang, L.Z. / Wedge, S.R. / Wong, C. / Griffin, R.J. / Endicott, J.A. / Cano, C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5nev.cif.gz | 459.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5nev.ent.gz | 381.1 KB | Display | PDB format |
PDBx/mmJSON format | 5nev.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5nev_validation.pdf.gz | 1003.6 KB | Display | wwPDB validaton report |
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Full document | 5nev_full_validation.pdf.gz | 1021.2 KB | Display | |
Data in XML | 5nev_validation.xml.gz | 40.4 KB | Display | |
Data in CIF | 5nev_validation.cif.gz | 55.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ne/5nev ftp://data.pdbj.org/pub/pdb/validation_reports/ne/5nev | HTTPS FTP |
-Related structure data
Related structure data | 5lqfC 1h1sS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
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-Components
#1: Protein | Mass: 34467.926 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CDK2, CDKN2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P24941, cyclin-dependent kinase #2: Protein | Mass: 29884.605 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CCNA2, CCN1, CCNA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / 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: 2.81 Å3/Da / Density % sol: 56.29 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 Details: PROTEIN AT 5MG PER ML. 0.6 TO 0.8M KCL, 0.9 TO 1.2M (NH402SO4, AND 100MM HEPES (PH 7.0) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.969 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 12, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.969 Å / Relative weight: 1 |
Reflection | Resolution: 2.97→66.03 Å / Num. obs: 30773 / % possible obs: 100 % / Redundancy: 704 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 6.7 |
Reflection shell | Resolution: 2.97→3.13 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 1.6 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1H1S Resolution: 2.97→66.03 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.908 / SU B: 52.79 / SU ML: 0.423 / Cross valid method: THROUGHOUT / ESU R Free: 0.438 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 80.244 Å2
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Refinement step | Cycle: 1 / Resolution: 2.97→66.03 Å
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Refine LS restraints |
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