+Open data
-Basic information
Entry | Database: PDB / ID: 6q38 | |||||||||
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Title | The Crystal structure of CK2a bound to P1-C4 | |||||||||
Components |
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Keywords | PEPTIDE BINDING PROTEIN / CK2alpha / CK2a / Stapled peptides / high concentration screening / selective ATP competitive inhibitors / surface entrophy reduction | |||||||||
Function / homology | Function and homology information regulation of DNA binding / adiponectin-activated signaling pathway / positive regulation of activin receptor signaling pathway / UTP-C complex / endothelial tube morphogenesis / negative regulation of viral life cycle / regulation of transcription by RNA polymerase III / protein kinase regulator activity / regulation of chromosome separation / positive regulation of aggrephagy ...regulation of DNA binding / adiponectin-activated signaling pathway / positive regulation of activin receptor signaling pathway / UTP-C complex / endothelial tube morphogenesis / negative regulation of viral life cycle / regulation of transcription by RNA polymerase III / protein kinase regulator activity / 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 / Maturation of hRSV A proteins / Receptor Mediated Mitophagy / Sin3-type complex / Synthesis of PC / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / positive regulation of SMAD protein signal transduction / negative regulation of apoptotic signaling pathway / negative regulation of blood vessel endothelial cell migration / 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 / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / positive regulation of protein catabolic process / KEAP1-NFE2L2 pathway / double-strand break repair / rhythmic process / protein-macromolecule adaptor activity / kinase activity / positive regulation of cell growth / peptidyl-serine phosphorylation / protein-containing complex assembly / secretory granule lumen / Regulation of TP53 Activity through Phosphorylation / RNA polymerase II-specific DNA-binding transcription factor binding / ficolin-1-rich granule lumen / negative regulation of translation / protein stabilization / non-specific serine/threonine protein kinase / regulation of cell cycle / cell cycle / protein domain specific binding / negative regulation of cell population proliferation / protein phosphorylation / signaling receptor binding / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / DNA damage response / chromatin binding / chromatin / Neutrophil degranulation / positive regulation of cell population proliferation / signal transduction / extracellular exosome / extracellular region / nucleoplasm / ATP binding / identical protein binding / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.74 Å | |||||||||
Authors | Brear, P. / Iegre, J. / Baker, D. / Tan, Y. / Sore, H. / Donovan, D. / Spring, D. / Chandra, V. / Hyvonen, M. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: Chem Sci / Year: 2019 Title: Efficient development of stable and highly functionalised peptides targeting the CK2 alpha /CK2 beta protein-protein interaction. Authors: Iegre, J. / Brear, P. / Baker, D.J. / Tan, Y.S. / Atkinson, E.L. / Sore, H.F. / O' Donovan, D.H. / Verma, C.S. / 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 | 6q38.cif.gz | 164.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6q38.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6q38.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q3/6q38 ftp://data.pdbj.org/pub/pdb/validation_reports/q3/6q38 | HTTPS FTP |
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-Related structure data
Related structure data | 6q4qC 5otzS 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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Unit cell |
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-Components
#1: Protein | Mass: 39118.617 Da / Num. of mol.: 1 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 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P68400, non-specific serine/threonine protein kinase |
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#2: Protein/peptide | Type: Peptide-like / Class: Inhibitor / Mass: 1345.555 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: BIRD: PRD_002559, UniProt: P67870*PLUS |
#3: Chemical | ChemComp-BEZ / |
#4: Chemical | ChemComp-A1H27 / Type: Peptide-like / Class: Inhibitor / Mass: 284.273 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H12N6O2 / References: BIRD: PRD_002559 |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.04 % / Mosaicity: 0.22 ° |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1 M HEPES 7.5 pH, 10 %w/v PEG 8K, 8 %v/v Ethelyene glycol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 6, 2018 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.74→63.88 Å / Num. obs: 44243 / % possible obs: 99.7 % / Redundancy: 18.8 % / Biso Wilson estimate: 30.7 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.176 / Rpim(I) all: 0.041 / Rrim(I) all: 0.181 / Net I/σ(I): 11.1 / Num. measured all: 833029 / Scaling rejects: 4 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5OTZ Resolution: 1.74→25.48 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.93 / SU R Cruickshank DPI: 0.109 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.109 / SU Rfree Blow DPI: 0.106 / SU Rfree Cruickshank DPI: 0.106
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Displacement parameters | Biso max: 158.32 Å2 / Biso mean: 56.92 Å2 / Biso min: 26.66 Å2
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Refinement step | Cycle: final / Resolution: 1.74→25.48 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.74→1.78 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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