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- PDB-5ctp: Crystal structure of CK2alpha with N-(3-(3-chloro-4-(phenyl)benzy... -

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Basic information

Entry
Database: PDB / ID: 5ctp
TitleCrystal structure of CK2alpha with N-(3-(3-chloro-4-(phenyl)benzylamino)propyl)acetamide 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
Chem-54R / ACETATE ION / PHOSPHATE ION / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.033 Å
AuthorsBrear, P. / De Fusco, C. / Georgiou, K.H. / Spring, D. / Hyvonen, M.
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
DepositionJul 24, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 30, 2016Provider: repository / Type: Initial release
Revision 1.1May 24, 2017Group: Database references
Revision 1.2Jun 7, 2017Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / 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)83,9009
Polymers82,9362
Non-polymers9657
Water3,819212
1
A: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8443
Polymers41,4681
Non-polymers3762
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0576
Polymers41,4681
Non-polymers5895
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.067, 68.858, 333.876
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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-54R / N-(3-{[(2-chlorobiphenyl-4-yl)methyl]amino}propyl)acetamide


Mass: 316.825 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H21ClN2O
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / 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: 2.25 Å3/Da / Density % sol: 45.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 107mM Mes pH 6.5, 29% glycerol ethoxylate, 1 M ammonium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.033→83.47 Å / Num. obs: 48911 / % possible obs: 100 % / Redundancy: 6.2 % / Biso Wilson estimate: 39.38 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.04 / Rsym value: 0.09 / Net I/σ(I): 12 / Num. measured all: 300842
Reflection shellResolution: 2.033→2.039 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.737 / Mean I/σ(I) obs: 2.3 / Num. measured all: 42948 / Num. unique all: 7036 / CC1/2: 0.833 / Rpim(I) all: 0.288 / Rsym value: 0.737 / Rejects: 0 / % possible all: 98.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.2.14data scaling
PHASERphasing
BUSTER-TNTrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WAR

3war


Resolution: 2.033→83.47 Å / Cor.coef. Fo:Fc: 0.9483 / Cor.coef. Fo:Fc free: 0.945 / SU R Cruickshank DPI: 0.179 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.177 / SU Rfree Blow DPI: 0.137 / SU Rfree Cruickshank DPI: 0.139
RfactorNum. reflection% reflectionSelection details
Rfree0.1989 2482 5.08 %RANDOM
Rwork0.1848 ---
obs0.1855 48830 98.68 %-
Displacement parametersBiso max: 209.21 Å2 / Biso mean: 56.12 Å2 / Biso min: 17.41 Å2
Baniso -1Baniso -2Baniso -3
1-0.7747 Å20 Å20 Å2
2---4.898 Å20 Å2
3---4.1232 Å2
Refine analyzeLuzzati coordinate error obs: 0.275 Å
Refinement stepCycle: final / Resolution: 2.033→83.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5500 0 87 212 5799
Biso mean--81.2 49.68 -
Num. residues----651
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2048SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes144HARMONIC2
X-RAY DIFFRACTIONt_gen_planes875HARMONIC5
X-RAY DIFFRACTIONt_it5771HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion688SEMIHARMONIC5
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_contact6445SEMIHARMONIC0
X-RAY DIFFRACTIONt_bond_d5771HARMONIC20.013
X-RAY DIFFRACTIONt_angle_deg7802HARMONIC21.12
X-RAY DIFFRACTIONt_omega_torsion2.92
X-RAY DIFFRACTIONt_other_torsion17.39
LS refinement shellResolution: 2.02→2.08 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2285 166 5.46 %
Rwork0.1997 2874 -
all0.2013 3040 -
obs--98.68 %
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)
13.05780.12941.17670.7378-0.12073.086-0.059-0.7889-0.0172-0.11290.0939-0.11430.1019-0.8915-0.035-0.17980.02610.04050.14690.0309-0.3187-6.2375155.444395.91
20.47870.05040.11430.7465-0.28241.09460.0606-0.0527-0.01520.0389-0.03120.0152-0.0430.0217-0.0293-0.1323-0.03350.0085-0.1477-0.0229-0.14916.389144.555355.427
32.01480.45670.09662.91563.87587.44220.04520.4229-0.26840.1916-0.0212-0.5132-0.252-0.2392-0.024-0.03-0.1298-0.1595-0.44910.1407-0.16573.8586148.276368.388
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A4 - 327
2X-RAY DIFFRACTION2{ B|* }B3 - 329
3X-RAY DIFFRACTION3{ D|* }D1 - 2

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