+Open data
-Basic information
Entry | Database: PDB / ID: 6yzh | |||||||||||||||
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Title | Crystal structure of P8C9 bound to CK2alpha | |||||||||||||||
Components |
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Keywords | TRANSFERASE / BTK / Covalent fragments / surface entrophy reduction / crystal engineering | |||||||||||||||
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 / molecular replacement / Resolution: 1.19 Å | |||||||||||||||
Authors | Atkinson, E. / Iegre, J. / Brear, P. / Baker, D. / Sore, H. / Hyvonen, M. / Spring, D. | |||||||||||||||
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 | 6yzh.cif.gz | 106.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6yzh.ent.gz | 76.3 KB | Display | PDB format |
PDBx/mmJSON format | 6yzh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6yzh_validation.pdf.gz | 472.8 KB | Display | wwPDB validaton report |
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Full document | 6yzh_full_validation.pdf.gz | 476.5 KB | Display | |
Data in XML | 6yzh_validation.xml.gz | 19.1 KB | Display | |
Data in CIF | 6yzh_validation.cif.gz | 29.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yz/6yzh ftp://data.pdbj.org/pub/pdb/validation_reports/yz/6yzh | HTTPS FTP |
-Related structure data
Related structure data | 6z19C 7quxC 5cu6S 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
-Protein / Protein/peptide , 2 types, 2 molecules AD
#1: Protein | Mass: 46719.570 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK2A1, CK2A1 / Plasmid: pHAT4 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P68400, non-specific serine/threonine protein kinase |
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#2: Protein/peptide | Mass: 1157.411 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) |
-Non-polymers , 5 types, 359 molecules
#3: Chemical | #4: Chemical | ChemComp-ADP / | #5: Chemical | ChemComp-GOL / | #6: Chemical | ChemComp-NA / | #7: Water | ChemComp-HOH / | |
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-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: 2.12 Å3/Da / Density % sol: 42.02 % / Mosaicity: 0.09 ° |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.2 / Details: 12 %v/v PEGSH, 0.1 M Mg Acet, 0.1 M KCl,0.1 M MES |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Sep 23, 2019 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.19→55.19 Å / Num. obs: 116431 / % possible obs: 91.9 % / Redundancy: 14.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.029 / Rrim(I) all: 0.114 / Net I/σ(I): 12.9 / Num. measured all: 1689252 / Scaling rejects: 2114 | ||||||||||||||||||||||||||||||
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: 5CU6 Resolution: 1.19→55.19 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.968 / SU B: 0.732 / SU ML: 0.031 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.041 / ESU R Free: 0.042 / 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: 108.66 Å2 / Biso mean: 20.316 Å2 / Biso min: 8.28 Å2
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Refinement step | Cycle: final / Resolution: 1.19→55.19 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.192→1.223 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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