+Open data
-Basic information
Entry | Database: PDB / ID: 5lqf | ||||||
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Title | CDK1/CyclinB1/CKS2 in complex with NU6102 | ||||||
Components |
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Keywords | TRANSFERASE / CDK1 CYCLIN B CKS2 CELL CYCLE NU6102 | ||||||
Function / homology | Function and homology information regulation of Schwann cell differentiation / cyclin A1-CDK1 complex / cyclin-dependent protein kinase activity / regulation of attachment of mitotic spindle microtubules to kinetochore / pronuclear fusion / cyclin B1-CDK1 complex / positive regulation of mitochondrial ATP synthesis coupled electron transport / Mitotic Prophase / positive regulation of mitotic sister chromatid segregation / histone kinase activity ...regulation of Schwann cell differentiation / cyclin A1-CDK1 complex / cyclin-dependent protein kinase activity / regulation of attachment of mitotic spindle microtubules to kinetochore / pronuclear fusion / cyclin B1-CDK1 complex / positive regulation of mitochondrial ATP synthesis coupled electron transport / Mitotic Prophase / positive regulation of mitotic sister chromatid segregation / histone kinase activity / Golgi disassembly / microtubule cytoskeleton organization involved in mitosis / G2/M DNA replication checkpoint / E2F-enabled inhibition of pre-replication complex formation / ventricular cardiac muscle cell development / Depolymerization of the Nuclear Lamina / positive regulation of attachment of spindle microtubules to kinetochore / MASTL Facilitates Mitotic Progression / regulation of mitotic cell cycle spindle assembly checkpoint / Activation of NIMA Kinases NEK9, NEK6, NEK7 / mitotic nuclear membrane disassembly / Phosphorylation of proteins involved in the G2/M transition by Cyclin A:Cdc2 complexes / Phosphorylation of Emi1 / cyclin A2-CDK1 complex / patched binding / Nuclear Pore Complex (NPC) Disassembly / Transcriptional regulation by RUNX2 / outer kinetochore / Phosphorylation of the APC/C / mitotic cell cycle phase transition / meiosis I / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / Initiation of Nuclear Envelope (NE) Reformation / Regulation of APC/C activators between G1/S and early anaphase / protein localization to kinetochore / Polo-like kinase mediated events / Golgi Cisternae Pericentriolar Stack Reorganization / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / cyclin-dependent protein serine/threonine kinase activator activity / cyclin-dependent kinase / Condensation of Prometaphase Chromosomes / response to copper ion / cyclin-dependent protein serine/threonine kinase activity / chromosome condensation / centrosome cycle / [RNA-polymerase]-subunit kinase / cyclin-dependent protein serine/threonine kinase regulator activity / SCF ubiquitin ligase complex / mitotic metaphase chromosome alignment / positive regulation of G2/M transition of mitotic cell cycle / positive regulation of DNA replication / G1/S-Specific Transcription / Cyclin A/B1/B2 associated events during G2/M transition / MAPK3 (ERK1) activation / cyclin-dependent protein kinase holoenzyme complex / response to amine / ubiquitin-like protein ligase binding / regulation of mitotic cell cycle / RNA polymerase II CTD heptapeptide repeat kinase activity / mitotic G2 DNA damage checkpoint signaling / regulation of embryonic development / cellular response to organic cyclic compound / cyclin binding / epithelial cell differentiation / response to axon injury / animal organ regeneration / Nuclear events stimulated by ALK signaling in cancer / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / response to cadmium ion / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / positive regulation of cardiac muscle cell proliferation / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / Resolution of Sister Chromatid Cohesion / Hsp70 protein binding / APC/C:Cdc20 mediated degradation of Cyclin B / ERK1 and ERK2 cascade / AURKA Activation by TPX2 / positive regulation of mitotic cell cycle / Condensation of Prophase Chromosomes / mitotic spindle organization / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / response to activity / ubiquitin binding / spindle microtubule / regulation of circadian rhythm / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / peptidyl-threonine phosphorylation / MAPK6/MAPK4 signaling / PKR-mediated signaling / G1/S transition of mitotic cell cycle / response to toxic substance / mitotic spindle / G2/M transition of mitotic cell cycle / spindle pole / microtubule cytoskeleton organization / positive regulation of protein localization to nucleus / positive regulation of fibroblast proliferation Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å | ||||||
Authors | Coxon, C.R. / Anscombe, E. / Harnor, S.J. / Martin, M.P. / Carbain, B.J. / Hardcastle, I.R. / Harlow, L.K. / Korolchuk, S. / Matheson, C.J. / Noble, M.E. ...Coxon, C.R. / Anscombe, E. / Harnor, S.J. / Martin, M.P. / Carbain, B.J. / Hardcastle, I.R. / Harlow, L.K. / Korolchuk, S. / Matheson, C.J. / Noble, M.E. / Newell, D.R. / Turner, D.M. / Sivaprakasam, M. / Wang, L.Z. / Wong, C. / Golding, B.T. / Griffin, R.J. / Endicott, J.A. / Cano, C. | ||||||
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 | 5lqf.cif.gz | 528.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lqf.ent.gz | 436.6 KB | Display | PDB format |
PDBx/mmJSON format | 5lqf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5lqf_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 5lqf_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 5lqf_validation.xml.gz | 48.4 KB | Display | |
Data in CIF | 5lqf_validation.cif.gz | 68.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lq/5lqf ftp://data.pdbj.org/pub/pdb/validation_reports/lq/5lqf | HTTPS FTP |
-Related structure data
Related structure data | 5nevC 4yc3S 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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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 34553.883 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CDK1, CDC2, CDC28A, CDKN1, P34CDC2 / Production host: Escherichia coli (E. coli) References: UniProt: P06493, cyclin-dependent kinase, [RNA-polymerase]-subunit kinase #2: Protein | Mass: 31369.682 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CCNB1, CCNB / Production host: Escherichia coli (E. coli) / References: UniProt: P14635 #3: Protein | Mass: 10290.819 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CKS2 / Production host: Escherichia coli (E. coli) / References: UniProt: P33552 #4: Chemical | #5: 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: 2.39 Å3/Da / Density % sol: 48.46 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.7 Details: 0.1M MES/IMIDAZOLE BUFFER (PH6.7), 6.5% MPD, 5% PEG4K, 10% PEG1K PROTEIN AT 10-12 MG/ML |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.989 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 22, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.989 Å / Relative weight: 1 |
Reflection | Resolution: 2.06→65.7 Å / Num. obs: 84841 / % possible obs: 97.3 % / Redundancy: 2 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 6.2 |
Reflection shell | Resolution: 2.06→2.1 Å / Redundancy: 2 % / Rmerge(I) obs: 1.16 / % possible all: 95.5 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4YC3 Resolution: 2.06→65.7 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.932 / SU B: 16.73 / SU ML: 0.21 / Cross valid method: THROUGHOUT / ESU R: 0.219 / ESU R Free: 0.194 / 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: 47.072 Å2
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Refinement step | Cycle: 1 / Resolution: 2.06→65.7 Å
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