[English] 日本語
Yorodumi
- PDB-6qy9: Human CSNK2A2 bound to a Pyrrolo[2,3-d]pyrimidinyl inhibitor -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6qy9
TitleHuman CSNK2A2 bound to a Pyrrolo[2,3-d]pyrimidinyl inhibitor
ComponentsCasein kinase II subunit alpha'
KeywordsTRANSFERASE / Kinase / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


regulation of mitophagy / regulation of chromosome separation / WNT mediated activation of DVL / Condensation of Prometaphase Chromosomes / protein kinase CK2 complex / positive regulation of protein targeting to mitochondrion / Receptor Mediated Mitophagy / Synthesis of PC / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / Maturation of hRSV A proteins ...regulation of mitophagy / regulation of chromosome separation / WNT mediated activation of DVL / Condensation of Prometaphase Chromosomes / protein kinase CK2 complex / positive regulation of protein targeting to mitochondrion / Receptor Mediated Mitophagy / 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 / negative regulation of ubiquitin-dependent protein catabolic process / acrosomal vesicle / Signal transduction by L1 / liver regeneration / cerebral cortex development / Wnt signaling pathway / Regulation of PTEN stability and activity / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / KEAP1-NFE2L2 pathway / double-strand break repair / spermatogenesis / peptidyl-serine phosphorylation / Regulation of TP53 Activity through Phosphorylation / non-specific serine/threonine protein kinase / cell cycle / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / chromatin / nucleoplasm / ATP binding / nucleus / cytosol
Similarity search - Function
Casein Kinase 2, subunit alpha / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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 ...Casein Kinase 2, subunit alpha / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-JL2 / Casein kinase II subunit alpha'
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsAbdul Azeez, K.R. / Sorrell, F.J. / Krojer, T. / Bountra, C. / Edwards, A.M. / Arrowsmith, C. / Knapp, S. / Elkins, J.M.
CitationJournal: To Be Published
Title: Human CSNK2A2 bound to a Pyrrolo[2,3-d]pyrimidinyl inhibitor
Authors: Abdul Azeez, K.R. / Elkins, J.M.
History
DepositionMar 8, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Casein kinase II subunit alpha'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4955
Polymers39,9331
Non-polymers5624
Water5,116284
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area480 Å2
ΔGint-19 kcal/mol
Surface area14830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.579, 59.460, 83.080
Angle α, β, γ (deg.)90.00, 93.64, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-643-

HOH

21A-720-

HOH

31A-754-

HOH

-
Components

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


Mass: 39932.723 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK2A2, CK2A2 / Details (production host): pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P19784, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-JL2 / 3-[3-[2-[(3,4,5-trimethoxyphenyl)amino]pyrrolo[2,3-d]pyrimidin-7-yl]phenyl]propanenitrile


Mass: 429.471 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H23N5O3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 284 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.09 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 20% PEG3350, 0.2 M potassium nitrate

-
Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.5→82.91 Å / Num. obs: 55567 / % possible obs: 98.3 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.7
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.13 / Mean I/σ(I) obs: 5 / Num. unique obs: 2404 / % possible all: 85.5

-
Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OFM

3ofm


Resolution: 1.5→46 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.966 / SU B: 2.138 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.061 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16477 2671 4.8 %RANDOM
Rwork0.12504 ---
obs0.12699 52894 98.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 20.652 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0 Å2-0.72 Å2
2---0.59 Å2-0 Å2
3---0.69 Å2
Refinement stepCycle: 1 / Resolution: 1.5→46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2728 0 38 284 3050
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0142864
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172518
X-RAY DIFFRACTIONr_angle_refined_deg1.3991.653880
X-RAY DIFFRACTIONr_angle_other_deg1.0151.6335885
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8335334
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.68422.061165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.1315493
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.3591519
X-RAY DIFFRACTIONr_chiral_restr0.0880.2345
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023219
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02565
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.1261.9151330
X-RAY DIFFRACTIONr_mcbond_other3.0831.9131329
X-RAY DIFFRACTIONr_mcangle_it3.5952.8791666
X-RAY DIFFRACTIONr_mcangle_other3.5952.8821667
X-RAY DIFFRACTIONr_scbond_it4.0022.1911534
X-RAY DIFFRACTIONr_scbond_other4.0022.1911534
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3643.1912215
X-RAY DIFFRACTIONr_long_range_B_refined4.32222.9383375
X-RAY DIFFRACTIONr_long_range_B_other4.32122.9413376
X-RAY DIFFRACTIONr_rigid_bond_restr2.00235381
X-RAY DIFFRACTIONr_sphericity_free20.7655181
X-RAY DIFFRACTIONr_sphericity_bonded13.89455409
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.202 175 -
Rwork0.123 3444 -
obs--87.04 %

+
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://pdbjlvh1.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