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- PDB-7at5: Structure of protein kinase ck2 catalytic subunit (csnk2a1 gene p... -

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Basic information

Entry
Database: PDB / ID: 7at5
TitleStructure of protein kinase ck2 catalytic subunit (csnk2a1 gene product) in complex with the bivalent inhibitor KN2
ComponentsCasein kinase II subunit alpha
KeywordsTRANSFERASE / protein kinase CK2 / casein kinase 2 / bivalent inhibitor
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
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
2-(3,4-dichlorophenyl)ethanamine / Chem-RXE / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsLindenblatt, D. / Applegate, V. / Nickelsen, A. / Klussmann, M. / Neundorf, I. / Goetz, C. / Jose, J. / Niefind, K.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)NI 643/4-2 Germany
Citation
Journal: J.Med.Chem. / Year: 2022
Title: Molecular Plasticity of Crystalline CK2 alpha ' Leads to KN2, a Bivalent Inhibitor of Protein Kinase CK2 with Extraordinary Selectivity.
Authors: Lindenblatt, D. / Applegate, V. / Nickelsen, A. / Klussmann, M. / Neundorf, I. / Gotz, C. / Jose, J. / Niefind, K.
#1: Journal: ACS Omega / Year: 2019
Title: Diacritic Binding of an Indenoindole Inhibitor by CK2alpha Paralogs Explored by a Reliable Path to Atomic Resolution CK2alpha' Structures.
Authors: Lindenblatt, D. / Nickelsen, A. / Applegate, V.M. / Hochscherf, J. / Witulski, B. / Bouaziz, Z. / Marminon, C. / Bretner, M. / Le Borgne, M. / Jose, J. / Niefind, K.
#2: Journal: J Med Chem / Year: 2020
Title: Structural and Mechanistic Basis of the Inhibitory Potency of Selected 2-Aminothiazole Compounds on Protein Kinase CK2.
Authors: Lindenblatt, D. / Nickelsen, A. / Applegate, V.M. / Jose, J. / Niefind, K.
History
DepositionOct 29, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 4, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 22, 2021Group: Data collection / Database references / Category: citation / database_2 / pdbx_database_proc
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Feb 9, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)85,87513
Polymers83,3712
Non-polymers2,50511
Water7,548419
1
A: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8455
Polymers41,6851
Non-polymers1,1594
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0318
Polymers41,6851
Non-polymers1,3457
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)127.591, 127.591, 124.520
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 2 through 7 or resid 9...
d_2ens_1(chain "B" and (resid 2 through 7 or resid 9...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1SERSERA1 - 6
d_12ens_1ALAHISA8 - 17
d_13ens_1PROTYRA19 - 135
d_14ens_1TYRALAA138 - 179
d_15ens_1PHESERA182 - 225
d_16ens_1ILEPROA227 - 296
d_17ens_1ALAALAA298 - 319
d_18ens_1GLUALAA322 - 334
d_21ens_1SERSERB1 - 6
d_22ens_1ALAHISB9 - 18
d_23ens_1PROTYRB21 - 137
d_24ens_1TYRALAB139 - 180
d_25ens_1PHESERB182 - 225
d_26ens_1ILEPROB228 - 297
d_27ens_1ALAALAB300 - 321
d_28ens_1GLUALAB323 - 335

NCS oper: (Code: givenMatrix: (0.00537675180962, -0.997077652078, 0.0762052902802), (0.999967954902, 0.00490901668242, -0.00632382189733), (0.00593124844828, 0.0762368498951, 0.997072095192)Vector: - ...NCS oper: (Code: given
Matrix: (0.00537675180962, -0.997077652078, 0.0762052902802), (0.999967954902, 0.00490901668242, -0.00632382189733), (0.00593124844828, 0.0762368498951, 0.997072095192)
Vector: -64.475133916, -62.0630864194, 32.9343878344)

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 41685.426 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

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Non-polymers , 5 types, 430 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-RXE / ~{N}'-[2-(3,4-dichlorophenyl)ethyl]-~{N}-[4-[4,5,6,7-tetrakis(bromanyl)benzimidazol-1-yl]butyl]butanediamide / KN2


Mass: 776.968 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H22Br4Cl2N4O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-42J / 2-(3,4-dichlorophenyl)ethanamine


Mass: 190.070 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H9Cl2N
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 419 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.19 Å3/Da / Density % sol: 61.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: reservoir composition: 30 % (w/v) PEG8000, 0.2 M ammonium sulfate, 0.1 M sodium cacodylate, pH 6.5; crystallization drop composition before equilibration: 0.01 ml reservoir solution plus 0. ...Details: reservoir composition: 30 % (w/v) PEG8000, 0.2 M ammonium sulfate, 0.1 M sodium cacodylate, pH 6.5; crystallization drop composition before equilibration: 0.01 ml reservoir solution plus 0.02 ml enzyme stock solution (6 mg/ml enzyme, 0.5 M NaCl, 25 mM Tris/HCl, pH 8.5); the bivalent inhibitor KN2 was introduced by extensive soaking

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9202 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9202 Å / Relative weight: 1
ReflectionResolution: 1.763→89.115 Å / Num. obs: 74986 / % possible obs: 74 % / Redundancy: 26.5 % / Biso Wilson estimate: 29.81 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.022 / Rrim(I) all: 0.113 / Rsym value: 0.111 / Net I/σ(I): 20.4
Reflection shellResolution: 1.763→1.921 Å / Redundancy: 27.9 % / Rmerge(I) obs: 2.229 / Num. unique obs: 3749 / CC1/2: 0.697 / Rpim(I) all: 0.428 / Rrim(I) all: 2.27 / Rsym value: 2.229 / % possible all: 16.4

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
PHENIX1.18.2_3874refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6TEI

6tei


Resolution: 1.77→73.06 Å / SU ML: 0.1323 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.3954
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1947 1476 1.97 %
Rwork0.1739 73483 -
obs0.1743 74959 74.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.29 Å2
Refinement stepCycle: LAST / Resolution: 1.77→73.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5597 0 124 419 6140
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00475939
X-RAY DIFFRACTIONf_angle_d0.71298036
X-RAY DIFFRACTIONf_chiral_restr0.05814
X-RAY DIFFRACTIONf_plane_restr0.00451031
X-RAY DIFFRACTIONf_dihedral_angle_d21.68252254
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.57703428137 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.77-1.830.2714160.2727749X-RAY DIFFRACTION8.51
1.83-1.890.2767390.2531841X-RAY DIFFRACTION21.08
1.89-1.970.2618610.23142996X-RAY DIFFRACTION33.96
1.97-2.060.25381060.22785566X-RAY DIFFRACTION62.94
2.06-2.170.24711640.20528332X-RAY DIFFRACTION94.21
2.17-2.30.22291760.18268830X-RAY DIFFRACTION99.97
2.3-2.480.19761780.17498884X-RAY DIFFRACTION99.98
2.48-2.730.21161860.18218905X-RAY DIFFRACTION99.99
2.73-3.120.20321790.17898969X-RAY DIFFRACTION100
3.12-3.940.18361830.15899032X-RAY DIFFRACTION100
3.94-73.060.17111880.16349379X-RAY DIFFRACTION99.87
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)
13.72102724445-0.7739790521661.996938072140.754897265063-0.5836613181942.351008895220.06474597779350.220329171526-0.143900524684-0.0794727506327-0.03313485398740.001765363761390.1703444204750.249860404518-0.04126416614230.2020977322870.01435718797930.04155340657750.209222235653-0.02459531704440.195716156352.1137933876-48.642587930415.6925706609
21.68368838665-1.22297119148-1.570671387830.8742661702661.254560584931.75798208751-0.556519193248-0.6821311626530.359304877980.6790329486540.407123961429-0.2128019182260.09238592232260.406480086740.2090519838890.4864252270330.190223516961-0.1409034993670.507187950247-0.1181423883810.3513784833032.81731075919-37.99431972832.4988171733
31.5279605236-0.669038335319-0.2010100477461.529893957520.1359138518542.1038012069-0.112896083667-0.1665211412620.04481475464680.14840854450.1774053187860.06926891839460.0132524143092-0.175643142405-0.02741823924180.1209397143350.04125619965380.01028447632960.1886976364640.01985981168510.162101442874-16.9895124837-37.994424279726.0053229342
40.7557801869350.8369516108320.6217810437793.785570467731.844201025052.48938142012-0.1017891328490.1126085685590.0228013306668-0.1548205757040.140203886091-0.113767676633-0.3236587348920.125294732127-0.04361381979820.12052308388-0.004052575418310.0186666590590.156694706545-0.004452481250550.143561983965-15.2955675699-61.72875605344.7426318373
52.017491884060.526606342961-0.6807454325422.21766968821-0.2114474469652.084625837120.126604060715-0.2747014765320.06762098398830.279775508388-0.200472755537-0.0837485764787-0.317972858645-0.0161241321680.06441637773390.251276726161-0.04436007371330.004733674093650.257815359305-0.04238545285650.21602813157-18.1039354974-59.17639988351.378726384
61.730718647770.682063788163-0.4633059247721.80419747863-0.3917448575131.880866683330.135117195579-0.259104744529-0.06794982506010.215886213712-0.08630173284810.06055048441340.05529943743930.050299078544-0.02884423352970.150863266121-0.0657157037511-0.002558882810310.231396754152-0.02986477623370.171319336455-24.6123398633-79.514918903156.0599242085
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 108 )AA2 - 1081 - 107
22chain 'A' and (resid 109 through 129 )AA109 - 129108 - 128
33chain 'A' and (resid 130 through 333 )AA130 - 333129 - 335
44chain 'B' and (resid 2 through 74 )BB2 - 741 - 75
55chain 'B' and (resid 75 through 129 )BB75 - 12976 - 130
66chain 'B' and (resid 130 through 332 )BB130 - 332131 - 335

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