[English] 日本語
Yorodumi
- PDB-6z84: CK2 alpha bound to chemical probe SGC-CK2-1 derivative -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6z84
TitleCK2 alpha bound to chemical probe SGC-CK2-1 derivative
ComponentsCasein kinase II subunit alphaCasein kinase 2
KeywordsTRANSFERASE / Kinase / Inhibitor / Chemical probe / Structural Genomics / Structural Genomics Consortium / SGC
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 / negative regulation of apoptotic signaling pathway / positive regulation of Wnt signaling pathway / chaperone-mediated protein folding / negative regulation of ubiquitin-dependent protein catabolic process / Signal transduction by L1 / Hsp90 protein binding / peptidyl-threonine phosphorylation / 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 / rhythmic process / KEAP1-NFE2L2 pathway / double-strand break repair / kinase activity / positive regulation of cell growth / peptidyl-serine phosphorylation / Regulation of TP53 Activity through Phosphorylation / negative regulation of translation / protein stabilization / regulation of cell cycle / non-specific serine/threonine protein kinase / 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
Casein Kinase 2, subunit alpha / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Chem-QB8 / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKraemer, A. / Wells, C. / Drewry, D.H. / Pickett, J.E. / Axtman, A.D. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: Cell Chem Biol / Year: 2021
Title: Development of a potent and selective chemical probe for the pleiotropic kinase CK2.
Authors: Wells, C.I. / Drewry, D.H. / Pickett, J.E. / Tjaden, A. / Kramer, A. / Muller, S. / Gyenis, L. / Menyhart, D. / Litchfield, D.W. / Knapp, S. / Axtman, A.D.
History
DepositionJun 2, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 28, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: Casein kinase II subunit alpha
BBB: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,55216
Polymers80,6562
Non-polymers1,89614
Water3,189177
1
AAA: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,46810
Polymers40,3281
Non-polymers1,1409
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0846
Polymers40,3281
Non-polymers7565
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)126.352, 126.352, 124.514
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein Casein kinase II subunit alpha / Casein kinase 2 / CK II alpha


Mass: 40327.977 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK2A1, CK2A1 / Production host: Escherichia coli (E. coli)
References: UniProt: P68400, non-specific serine/threonine protein kinase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-QB8 / ~{N}-[1-[3-cyano-7-(cyclopropylamino)pyrazolo[1,5-a]pyrimidin-5-yl]indol-6-yl]ethanamide


Mass: 371.395 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H17N7O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 177 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.08 Å3/Da / Density % sol: 60.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M bis-tris pH 5.5 23-26% (v/v) PEG 3350 0.2 M ammonia sulphate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.99999 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: May 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 2.5→44.67 Å / Num. obs: 35531 / % possible obs: 100 % / Redundancy: 13.2 % / CC1/2: 0.998 / Rpim(I) all: 0.056 / Net I/σ(I): 12.7
Reflection shellResolution: 2.5→2.6 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 3947 / CC1/2: 0.845 / Rpim(I) all: 0.415

-
Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6yul

6yul


Resolution: 2.5→44.67 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.903 / SU B: 10.167 / SU ML: 0.216 / Cross valid method: FREE R-VALUE / ESU R: 0.398 / ESU R Free: 0.262
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2501 1850 5.215 %
Rwork0.215 33625 -
all0.217 --
obs-35475 99.969 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 39.771 Å2
Baniso -1Baniso -2Baniso -3
1-2.362 Å2-0 Å2-0 Å2
2--2.362 Å2-0 Å2
3----4.723 Å2
Refinement stepCycle: LAST / Resolution: 2.5→44.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5415 0 116 177 5708
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0135675
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175051
X-RAY DIFFRACTIONr_ext_dist_refined_d0.0510.018358
X-RAY DIFFRACTIONr_angle_refined_deg1.4061.6427710
X-RAY DIFFRACTIONr_angle_other_deg1.491.5911650
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2485652
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.02121.601331
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.50215932
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4791541
X-RAY DIFFRACTIONr_chiral_restr0.0880.2689
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026553
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021286
X-RAY DIFFRACTIONr_nbd_refined0.2180.21097
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1810.24822
X-RAY DIFFRACTIONr_nbtor_refined0.180.22740
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.22596
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1180.2174
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1870.218
X-RAY DIFFRACTIONr_nbd_other0.2110.252
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1240.26
X-RAY DIFFRACTIONr_mcbond_it1.5564.2852619
X-RAY DIFFRACTIONr_mcbond_other1.5564.2842617
X-RAY DIFFRACTIONr_mcangle_it2.6676.423266
X-RAY DIFFRACTIONr_mcangle_other2.6676.4223267
X-RAY DIFFRACTIONr_scbond_it1.4824.4513056
X-RAY DIFFRACTIONr_scbond_other1.4824.4263031
X-RAY DIFFRACTIONr_scangle_it2.566.6274438
X-RAY DIFFRACTIONr_scangle_other2.5636.5884402
X-RAY DIFFRACTIONr_lrange_it4.58785.25311892
X-RAY DIFFRACTIONr_lrange_other4.52585.28811874
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.5650.3351160.3092467X-RAY DIFFRACTION100
2.565-2.6350.3641420.2992374X-RAY DIFFRACTION99.9206
2.635-2.7110.3351190.2792326X-RAY DIFFRACTION100
2.711-2.7950.3081240.2672245X-RAY DIFFRACTION100
2.795-2.8860.2511020.2362199X-RAY DIFFRACTION100
2.886-2.9880.2371340.2372105X-RAY DIFFRACTION100
2.988-3.10.2691200.2392043X-RAY DIFFRACTION100
3.1-3.2270.2711140.2251969X-RAY DIFFRACTION100
3.227-3.370.215960.2081908X-RAY DIFFRACTION100
3.37-3.5340.2911290.2011775X-RAY DIFFRACTION100
3.534-3.7250.2461120.2011734X-RAY DIFFRACTION100
3.725-3.9510.21920.1841641X-RAY DIFFRACTION100
3.951-4.2230.23960.1731544X-RAY DIFFRACTION100
4.223-4.560.197610.1581466X-RAY DIFFRACTION100
4.56-4.9940.159620.1591356X-RAY DIFFRACTION100
4.994-5.5820.201610.1971232X-RAY DIFFRACTION100
5.582-6.4410.264770.2341075X-RAY DIFFRACTION100
6.441-7.8780.259530.227940X-RAY DIFFRACTION100

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more