+Open data
-Basic information
Entry | Database: PDB / ID: 7qux | ||||||
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Title | Crystal structure of P7C8 bound to CK2alpha | ||||||
Components |
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Keywords | TRANSFERASE / Stapled peptide / CK2alpha | ||||||
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) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.48 Å | ||||||
Authors | Atkinson, E. / Iegre, J. / Brear, P. / Baker, D. / Sore, H. / Hyvonen, M. / Spring, D. | ||||||
Funding support | 1items
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Citation | Journal: Chem.Commun.(Camb.) / Year: 2022 Title: Development of small cyclic peptides targeting the CK2 alpha / beta interface. Authors: Atkinson, E.L. / Iegre, J. / D'Amore, C. / Brear, P. / Salvi, M. / 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 | 7qux.cif.gz | 99.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7qux.ent.gz | 70.8 KB | Display | PDB format |
PDBx/mmJSON format | 7qux.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7qux_validation.pdf.gz | 924.7 KB | Display | wwPDB validaton report |
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Full document | 7qux_full_validation.pdf.gz | 934.2 KB | Display | |
Data in XML | 7qux_validation.xml.gz | 18.1 KB | Display | |
Data in CIF | 7qux_validation.cif.gz | 26.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qu/7qux ftp://data.pdbj.org/pub/pdb/validation_reports/qu/7qux | HTTPS FTP |
-Related structure data
Related structure data | 6yzhC 6z19C 5cvhS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein / Protein/peptide , 2 types, 2 molecules AD
#1: Protein | Mass: 41697.867 Da / Num. of mol.: 1 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 | Mass: 1074.299 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others) |
-Non-polymers , 6 types, 296 molecules
#3: Chemical | ChemComp-ADP / | ||||||||
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#4: Chemical | #5: Chemical | #6: Chemical | ChemComp-SO4 / | #7: Chemical | ChemComp-OUT / | #8: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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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: 2.36 Å3/Da / Density % sol: 47.99 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.2 M Ammonium sulfate, 30 % w/v PEG 4000 |
-Data collection
Diffraction | Mean temperature: 88 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 9, 2021 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.48→55.66 Å / Num. obs: 66333 / % possible obs: 99.8 % / Redundancy: 17.1 % / CC1/2: 1 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.019 / Rrim(I) all: 0.079 / Net I/σ(I): 18 / Num. measured all: 1135548 / Scaling rejects: 1 | ||||||||||||||||||||||||||||||
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: 5CVH Resolution: 1.48→55.66 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.903 / SU ML: 0.066 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.069 / ESU R Free: 0.07 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 124.49 Å2 / Biso mean: 33.211 Å2 / Biso min: 16.21 Å2
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Refinement step | Cycle: final / Resolution: 1.48→55.66 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.48→1.518 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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