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- PDB-3mb6: Human CK2 catalytic domain in complex with a difurane derivative ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3mb6 | ||||||
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Title | Human CK2 catalytic domain in complex with a difurane derivative inhibitor (CPA) | ||||||
![]() | Casein kinase II subunit alpha | ||||||
![]() | TRANSFERASE / kinases / difurane / inhibitor / CK2 / ATP-binding / Kinase / Nucleotide-binding / Serine/threonine-protein kinase | ||||||
Function / homology | ![]() 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 / Sin3-type complex / Synthesis of PC / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known ...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 / Sin3-type complex / Synthesis of PC / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / Maturation of hRSV A proteins / 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 / negative regulation of ubiquitin-dependent protein catabolic process / Signal transduction by L1 / peptidyl-threonine phosphorylation / Hsp90 protein binding / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / PML body / Wnt signaling pathway / Regulation of PTEN stability and activity / positive regulation of protein catabolic process / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / KEAP1-NFE2L2 pathway / double-strand break repair / rhythmic process / kinase activity / positive regulation of cell growth / peptidyl-serine phosphorylation / Regulation of TP53 Activity through Phosphorylation / protein stabilization / negative regulation of translation / non-specific serine/threonine protein kinase / regulation of cell cycle / cell cycle / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / DNA damage response / positive regulation of cell population proliferation / signal transduction / nucleoplasm / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Reiser, J.-B. / Prudent, R. / Claude, C. | ||||||
![]() | ![]() Title: New potent dual inhibitors of CK2 and Pim kinases: discovery and structural insights. Authors: Lopez-Ramos, M. / Prudent, R. / Moucadel, V. / Sautel, C.F. / Barette, C. / Lafanechere, L. / Mouawad, L. / Grierson, D. / Schmidt, F. / Florent, J.C. / Filippakopoulos, P. / Bullock, A.N. / ...Authors: Lopez-Ramos, M. / Prudent, R. / Moucadel, V. / Sautel, C.F. / Barette, C. / Lafanechere, L. / Mouawad, L. / Grierson, D. / Schmidt, F. / Florent, J.C. / Filippakopoulos, P. / Bullock, A.N. / Knapp, S. / Reiser, J.B. / Cochet, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 89 KB | Display | ![]() |
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PDB format | ![]() | 66.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 708.6 KB | Display | ![]() |
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Full document | ![]() | 715.3 KB | Display | |
Data in XML | ![]() | 16.9 KB | Display | |
Data in CIF | ![]() | 24.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3ma3C ![]() 3mb7C ![]() 1pjkS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 39650.223 Da / Num. of mol.: 1 / Fragment: UNP residues 1-331 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P68400, non-specific serine/threonine protein kinase |
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#2: Chemical | ChemComp-01I / |
#3: Chemical | ChemComp-SO4 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.76 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 36 % polyethylene glycol 5000 monomethyl ether, 150 mM ammonium sulphate and 100 mM Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 7, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0722 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→19.84 Å / Num. all: 31145 / Num. obs: 31145 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 17.2 |
Reflection shell | Resolution: 1.75→1.81 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.408 / Mean I/σ(I) obs: 2.9 / Num. unique all: 2646 / Rsym value: 0.408 / % possible all: 86.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1PJK Resolution: 1.75→19.77 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.933 / SU B: 2.658 / SU ML: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.144 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.854 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→19.77 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.753→1.798 Å / Total num. of bins used: 20
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