+Open data
-Basic information
Entry | Database: PDB / ID: 6gmd | |||||||||
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Title | The crystal structure of CK2alpha in complex with compound 3 | |||||||||
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 / 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 | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å | |||||||||
Authors | Brear, P. / Iegre, J. / North, A. / De Fusco, C. / Georgiou, K. / Lubin, A. / Carro, L. / Sore, H. / Hyvonen, M. / Spring, D. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: Bioorg. Med. Chem. / Year: 2018 Title: Novel non-ATP competitive small molecules targeting the CK2 alpha / beta interface. Authors: Brear, P. / North, A. / Iegre, J. / Hadje Georgiou, K. / Lubin, A. / Carro, L. / Green, W. / 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 | 6gmd.cif.gz | 164.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6gmd.ent.gz | 127.3 KB | Display | PDB format |
PDBx/mmJSON format | 6gmd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6gmd_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 6gmd_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 6gmd_validation.xml.gz | 28.5 KB | Display | |
Data in CIF | 6gmd_validation.cif.gz | 42 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gm/6gmd ftp://data.pdbj.org/pub/pdb/validation_reports/gm/6gmd | HTTPS FTP |
-Related structure data
Related structure data | 6gihC 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: pHAT2 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P68400, non-specific serine/threonine protein kinase #2: Chemical | ChemComp-ACT / #3: Chemical | #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: 2.38 Å3/Da / Density % sol: 48.31 % / Mosaicity: 0 ° |
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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: I24 / Wavelength: 0.96862 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 22, 2015 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.96862 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.66→66.65 Å / Num. obs: 88560 / % possible obs: 100 % / Redundancy: 7.8 % / Biso Wilson estimate: 18.05 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.05 / Rrim(I) all: 0.139 / Net I/σ(I): 8.1 / Num. measured all: 687678 / Scaling rejects: 2317 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5CVH Resolution: 1.66→55.54 Å / Cor.coef. Fo:Fc: 0.9156 / Cor.coef. Fo:Fc free: 0.9018 / SU R Cruickshank DPI: 0.113 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.115 / SU Rfree Blow DPI: 0.108 / SU Rfree Cruickshank DPI: 0.108
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Displacement parameters | Biso mean: 25.53 Å2
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Refine analyze | Luzzati coordinate error obs: 0.264 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.66→55.54 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.66→1.7 Å / Total num. of bins used: 20
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