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- PDB-3mb6: Human CK2 catalytic domain in complex with a difurane derivative ... -

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Basic information

Entry
Database: PDB / ID: 3mb6
TitleHuman CK2 catalytic domain in complex with a difurane derivative inhibitor (CPA)
ComponentsCasein kinase II subunit alpha
KeywordsTRANSFERASE / kinases / difurane / inhibitor / CK2 / ATP-binding / Kinase / Nucleotide-binding / Serine/threonine-protein kinase
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 / Wnt signaling pathway / Regulation of PTEN stability and activity / 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-01I / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsReiser, J.-B. / Prudent, R. / Claude, C.
CitationJournal: Faseb J. / Year: 2010
Title: New potent dual inhibitors of CK2 and Pim kinases: discovery and structural insights.
Authors: Lopez-Ramos, M. / Prudent, R. / Moucadel, V. / Sautel, C.F. / Barette, C. / Lafanechere, L. / Mouawad, L. / Grierson, D. / Schmidt, F. / Florent, J.C. / Filippakopoulos, P. / Bullock, A.N. / ...Authors: Lopez-Ramos, M. / Prudent, R. / Moucadel, V. / Sautel, C.F. / Barette, C. / Lafanechere, L. / Mouawad, L. / Grierson, D. / Schmidt, F. / Florent, J.C. / Filippakopoulos, P. / Bullock, A.N. / Knapp, S. / Reiser, J.B. / Cochet, C.
History
DepositionMar 25, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0433
Polymers39,6501
Non-polymers3922
Water3,621201
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.776, 45.787, 63.673
Angle α, β, γ (deg.)90.00, 111.65, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 39650.223 Da / Num. of mol.: 1 / Fragment: UNP residues 1-331
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-01I / naphtho[2,1-b:7,6-b']difuran-2,8-dicarboxylic acid


Mass: 296.231 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H8O6
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 2.01 Å3/Da / Density % sol: 38.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 36 % polyethylene glycol 5000 monomethyl ether, 150 mM ammonium sulphate and 100 mM Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 1.0722 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 7, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0722 Å / Relative weight: 1
ReflectionResolution: 1.75→19.84 Å / Num. all: 31145 / Num. obs: 31145 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 17.2
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.408 / Mean I/σ(I) obs: 2.9 / Num. unique all: 2646 / Rsym value: 0.408 / % possible all: 86.9

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Processing

Software
NameVersionClassification
AMoREphasing
REFMAC5.5.0044refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PJK

1pjk


Resolution: 1.75→19.77 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.933 / SU B: 2.658 / SU ML: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.144 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22887 3174 10 %RANDOM
Rwork0.18153 ---
obs0.18621 28558 100 %-
all-28558 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.854 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å2-0.01 Å2
2---0 Å20 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 1.75→19.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2782 0 27 201 3010
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222985
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4851.9594063
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0915360
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.52122.919161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.75315540
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2561528
X-RAY DIFFRACTIONr_chiral_restr0.0930.2419
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212325
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.41721692
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.29532770
X-RAY DIFFRACTIONr_scbond_it1.65921293
X-RAY DIFFRACTIONr_scangle_it2.4631277
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.753→1.798 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 227 -
Rwork0.253 2040 -
obs--100 %

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