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Yorodumi- PDB-5mmr: Crystal Structure of CK2alpha with N-((2-chloro-[1,1'-biphenyl]-4... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5mmr | ||||||
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Title | Crystal Structure of CK2alpha with N-((2-chloro-[1,1'-biphenyl]-4-yl)methyl)butane-1,4-diamine bound | ||||||
Components | Casein kinase II subunit alpha | ||||||
Keywords | TRANSFERASE / CK2alpha / CK2a / fragment based drug discovery / high concentration screening / selective ATP competitive inhibitors / surface entrophy reduction | ||||||
Function / homology | Function and homology information regulation of chromosome separation / positive regulation of aggrephagy / WNT mediated activation of DVL / Condensation of Prometaphase Chromosomes / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body / Receptor Mediated Mitophagy / Synthesis of PC / Sin3-type complex / Maturation of hRSV A proteins ...regulation of chromosome separation / positive regulation of aggrephagy / WNT mediated activation of DVL / Condensation of Prometaphase Chromosomes / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body / Receptor Mediated Mitophagy / Synthesis of PC / Sin3-type complex / Maturation of hRSV A proteins / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / negative regulation of apoptotic signaling pathway / positive regulation of Wnt signaling pathway / negative regulation of double-strand break repair via homologous recombination / chaperone-mediated protein folding / Signal transduction by L1 / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / peptidyl-threonine phosphorylation / Hsp90 protein binding / PML body / Wnt signaling pathway / Regulation of PTEN stability and activity / positive regulation of protein catabolic process / rhythmic process / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / KEAP1-NFE2L2 pathway / double-strand break repair / kinase activity / peptidyl-serine phosphorylation / positive regulation of cell growth / Regulation of TP53 Activity through Phosphorylation / protein stabilization / regulation of cell cycle / non-specific serine/threonine protein kinase / negative regulation of translation / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / positive regulation of cell population proliferation / DNA damage response / apoptotic process / signal transduction / nucleoplasm / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å | ||||||
Authors | Brear, P. / De Fusco, C. / Georgiou, K. / Iegre, J. / Sore, H. / Hyvonen, M. / Spring, D. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Bioorg. Med. Chem. / Year: 2017 Title: A fragment-based approach leading to the discovery of a novel binding site and the selective CK2 inhibitor CAM4066. Authors: De Fusco, C. / Brear, P. / Iegre, J. / Georgiou, K.H. / Sore, H.F. / Hyvonen, M. / Spring, D.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5mmr.cif.gz | 292.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mmr.ent.gz | 238.5 KB | Display | PDB format |
PDBx/mmJSON format | 5mmr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5mmr_validation.pdf.gz | 952.2 KB | Display | wwPDB validaton report |
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Full document | 5mmr_full_validation.pdf.gz | 927.6 KB | Display | |
Data in XML | 5mmr_validation.xml.gz | 28 KB | Display | |
Data in CIF | 5mmr_validation.cif.gz | 40.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mm/5mmr ftp://data.pdbj.org/pub/pdb/validation_reports/mm/5mmr | HTTPS FTP |
-Related structure data
Related structure data | 5ct0C 5ctpC 5cu0C 5cu2C 5cx9C 5mmfC 5mo5C 5mo6C 5mo7C 5mo8C 5modC 5moeC 5mohC 5motC 5movC 5mowC 5mp8C 5mpjC 5cvhS 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: 41467.793 Da / Num. of mol.: 2 Fragment: residues 2-329 and N-terminal extension GSMDIEFDDDADDDGSGSGSGSGS Mutation: R21S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK2A1, CK2A1 / Plasmid: pHAT4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P68400, non-specific serine/threonine protein kinase #2: Chemical | #3: Chemical | ChemComp-ACT / #4: Chemical | ChemComp-PO4 / | #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: 2.2 Å3/Da / Density % sol: 44.07 % / Mosaicity: 0.14 ° |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 112.5mM Mes pH 6.5, 35% glycerol ethoxylate, 180 mM ammonium acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9174 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 22, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9174 Å / Relative weight: 1 |
Reflection | Resolution: 1.996→46.65 Å / Num. obs: 50014 / % possible obs: 99.1 % / Redundancy: 6.4 % / Biso Wilson estimate: 28.41 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.147 / Rsym value: 0.147 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 1.996→2.002 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.849 / Mean I/σ(I) obs: 2.1 / Num. measured all: 44428 / Num. unique all: 7226 / CC1/2: 0.869 / Rpim(I) all: 0.327 / Rrim(I) all: 0.821 / Rsym value: 0.849 / Net I/σ(I) obs: 2.8 / % possible all: 98.1 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5CVH Resolution: 2→46.65 Å / Cor.coef. Fo:Fc: 0.9287 / Cor.coef. Fo:Fc free: 0.9071 / SU R Cruickshank DPI: 0.186 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.19 / SU Rfree Blow DPI: 0.156 / SU Rfree Cruickshank DPI: 0.156
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Displacement parameters | Biso max: 150.25 Å2 / Biso mean: 38.24 Å2 / Biso min: 6.71 Å2
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Refine analyze | Luzzati coordinate error obs: 0.245 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2→46.65 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.05 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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