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- PDB-5mo7: Crystal Structure of CK2alpha with N-(3-(((2-chloro-[1,1'-bipheny... -

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Basic information

Entry
Database: PDB / ID: 5mo7
TitleCrystal Structure of CK2alpha with N-(3-(((2-chloro-[1,1'-biphenyl]-4-yl)methyl)amino)propyl)methanesulfonamide bound
ComponentsCasein kinase II subunit alpha
KeywordsTRANSFERASE / CK2alpha / CK2a / fragment based drug discovery / high concentration screening / selective ATP competitive inhibitors / surface entrophy reduction
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 signal transduction by p53 class mediator / negative regulation of apoptotic signaling pathway / positive regulation of Wnt signaling pathway / negative regulation of double-strand break repair via homologous recombination / : / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / Signal transduction by L1 / Hsp90 protein binding / PML body / Regulation of PTEN stability and activity / Wnt signaling pathway / positive regulation of protein catabolic process / KEAP1-NFE2L2 pathway / kinase activity / rhythmic process / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / double-strand break repair / positive regulation of cell growth / Regulation of TP53 Activity through Phosphorylation / non-specific serine/threonine protein kinase / regulation of cell cycle / negative regulation of translation / protein stabilization / protein serine kinase activity / protein serine/threonine kinase activity / positive regulation of cell population proliferation / apoptotic process / DNA damage response / signal transduction / nucleoplasm / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Casein Kinase 2, subunit alpha / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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
PHOSPHATE ION / Chem-YRA / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.15 Å
AuthorsBrear, P. / De Fusco, C. / Georgiou, K. / Iegre, J. / Sore, H. / Hyvonen, M. / Spring, D.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust090340/Z/09/Z United Kingdom
CitationJournal: Bioorg. Med. Chem. / Year: 2017
Title: A fragment-based approach leading to the discovery of a novel binding site and the selective CK2 inhibitor CAM4066.
Authors: De Fusco, C. / Brear, P. / Iegre, J. / Georgiou, K.H. / Sore, H.F. / Hyvonen, M. / Spring, D.R.
History
DepositionDec 13, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2017Group: Database references
Revision 1.2Jan 17, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)83,5096
Polymers82,9362
Non-polymers5744
Water2,000111
1
A: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9474
Polymers41,4681
Non-polymers4793
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5632
Polymers41,4681
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.350, 66.060, 335.850
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 41467.793 Da / Num. of mol.: 2
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 / Plasmid: pHAT4 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P68400, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-YRA / 3-[(3-chloranyl-4-phenyl-phenyl)methylamino]propanamide


Mass: 288.772 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H17ClN2O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.56 % / Mosaicity: 0 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 112.5mM Mes pH 6.5, 35% glycerol ethoxylate, 180 mM ammonium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.15→55.98 Å / Num. obs: 40251 / % possible obs: 99.8 % / Redundancy: 5.7 % / Biso Wilson estimate: 48.45 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.093 / Net I/σ(I): 9.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.15-2.225.31.0340.6041100
9.66-55.985.10.0420.997199.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.5.1data scaling
PHASERphasing
BUSTERrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CVH

5cvh


Resolution: 2.15→55.98 Å / Cor.coef. Fo:Fc: 0.9391 / Cor.coef. Fo:Fc free: 0.9239 / SU R Cruickshank DPI: 0.234 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.229 / SU Rfree Blow DPI: 0.178 / SU Rfree Cruickshank DPI: 0.181
RfactorNum. reflection% reflectionSelection details
Rfree0.2235 2034 5.06 %RANDOM
Rwork0.1894 ---
obs0.1911 40186 99.06 %-
Displacement parametersBiso max: 164.35 Å2 / Biso mean: 64.71 Å2 / Biso min: 26.7 Å2
Baniso -1Baniso -2Baniso -3
1--6.3902 Å20 Å20 Å2
2---4.6475 Å20 Å2
3---11.0377 Å2
Refine analyzeLuzzati coordinate error obs: 0.371 Å
Refinement stepCycle: final / Resolution: 2.15→55.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5501 0 35 111 5647
Biso mean--72.97 55.99 -
Num. residues----652
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2044SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes144HARMONIC2
X-RAY DIFFRACTIONt_gen_planes848HARMONIC5
X-RAY DIFFRACTIONt_it5755HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion691SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6446SEMIHARMONIC0
X-RAY DIFFRACTIONt_bond_d5755HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg7797HARMONIC21.03
X-RAY DIFFRACTIONt_omega_torsion2.95
X-RAY DIFFRACTIONt_other_torsion17.98
LS refinement shellResolution: 2.15→2.21 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2585 155 5.66 %
Rwork0.2394 2583 -
all0.2405 2738 -
obs--99.06 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6089-0.0201-0.20981.41670.81222.79390.1594-0.2342-0.0573-0.2831-0.19240.0348-0.44030.08480.03290.0986-0.1251-0.005-0.10980.0162-0.110915.333138.958357.372
21.38360.08320.61010.5326-0.05032.4708-0.1965-0.22940.0277-0.24330.1687-0.02640.0703-0.34710.0278-0.078-0.11180.00210.030.0062-0.0998-6.7798149.884398.293
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A2 - 328
2X-RAY DIFFRACTION2{ B|* }B3 - 327

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