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- PDB-3fl5: Protein kinase CK2 in complex with the inhibitor Quinalizarin -

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Basic information

Entry
Database: PDB / ID: 3fl5
TitleProtein kinase CK2 in complex with the inhibitor Quinalizarin
ComponentsCasein kinase II subunit alpha
KeywordsTRANSFERASE / Protein kinase CK2-inhibitor complex / ATP-binding / Kinase / Nucleotide-binding / Serine/threonine-protein kinase
Function / homology
Function and homology information


protein kinase CK2 complex / regulation of cell cycle / non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity / 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
DI(HYDROXYETHYL)ETHER / 1,2,5,8-tetrahydroxyanthracene-9,10-dione / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Rigid body in an isomorphous cell / Resolution: 2.3 Å
AuthorsMazzorana, M. / Franchin, C. / Battistutta, R.
Citation
Journal: Biochem.J. / Year: 2009
Title: Quinalizarin as a potent, selective and cell-permeable inhibitor of protein kinase CK2
Authors: Cozza, G. / Mazzorana, M. / Papinutto, E. / Bain, J. / Elliott, M. / di Maira, G. / Gianoncelli, A. / Pagano, M.A. / Sarno, S. / Ruzzene, M. / Battistutta, R. / Meggio, F. / Moro, S. / Zagotto, G. / Pinna, L.A.
#1: Journal: J.Mol.Biol. / Year: 2008
Title: The catalytic subunit of human protein kinase CK2 structurally deviates from its maize homologue in complex with the nucleotide competitive inhibitor emodin
Authors: Raaf, J. / Klopffleisch, K. / Issinger, O.G. / Niefind, K.
#2: Journal: J.Biol.Chem. / Year: 2000
Title: The replacement of ATP by the competitive inhibitor emodin induces conformational modifications in the catalytic site of protein kinase CK2
Authors: Battistutta, R. / Sarno, S. / De Moliner, E. / Papinutto, E. / Zanotti, G. / Pinna, L.A.
History
DepositionDec 18, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 18, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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

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Assembly

Deposited unit
A: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6853
Polymers39,3071
Non-polymers3782
Water3,873215
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)142.743, 61.078, 44.797
Angle α, β, γ (deg.)90.000, 103.010, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-465-

HOH

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Components

#1: Protein Casein kinase II subunit alpha / Protein kinase CK2 / CK2-alpha / CK II


Mass: 39307.164 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Gene: ACK2 / Plasmid: pT7-7 / Production host: Escherichia coli (E. coli)
References: UniProt: P28523, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-TXQ / 1,2,5,8-tetrahydroxyanthracene-9,10-dione / 1,2,5,8-tetrahydroxy-anthraquinone


Mass: 272.210 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H8O6 / Comment: inhibitor*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.42 Å3/Da / Density % sol: 49.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% PEG 4000, 200mM Na-acetate, 100mM Na-HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 12, 2007 / Details: mirrors
RadiationMonochromator: LN2 cooled Si111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.3→69.541 Å / Num. all: 16853 / Num. obs: 15986 / % possible obs: 95.4 % / Redundancy: 3.1 % / Biso Wilson estimate: 27.7 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 12.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.3-2.423.10.1535717623210.15395.3
2.42-2.573.10.126.2677621830.1295
2.57-2.753.10.1017.4637820550.10195.3
2.75-2.973.10.06710.8602119460.06795.9
2.97-3.253.10.05212.7552217890.05295.6
3.25-3.643.10.03916.6494416020.03995.9
3.64-4.230.04115433814290.04195.7
4.2-5.1430.02820.8371312180.02895.6
5.14-7.2730.02724.127989310.02795.4
7.27-55.92.90.02720.514635120.02792

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
RefinementMethod to determine structure: Rigid body in an isomorphous cell
Resolution: 2.3→69.5 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.895 / SU B: 12.585 / SU ML: 0.168 / Isotropic thermal model: isotropic + TLS parameters / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.41 / ESU R Free: 0.247 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.235 804 5 %RANDOM
Rwork0.183 ---
all0.186 16853 --
obs-15986 94.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.352 Å2
Baniso -1Baniso -2Baniso -3
1--1.38 Å20 Å2-0.73 Å2
2--2.85 Å20 Å2
3----1.8 Å2
Refinement stepCycle: LAST / Resolution: 2.3→69.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2714 0 20 222 2956
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222811
X-RAY DIFFRACTIONr_angle_refined_deg1.0821.973801
X-RAY DIFFRACTIONr_dihedral_angle_1_deg12.8275.061326
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.30123.819144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.2715504
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3321519
X-RAY DIFFRACTIONr_chiral_restr0.0760.2397
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022145
X-RAY DIFFRACTIONr_nbd_refined0.1880.21336
X-RAY DIFFRACTIONr_nbtor_refined0.3010.21888
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.2201
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.20.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1310.218
X-RAY DIFFRACTIONr_mcbond_it0.3641.51680
X-RAY DIFFRACTIONr_mcangle_it0.62222627
X-RAY DIFFRACTIONr_scbond_it0.93431394
X-RAY DIFFRACTIONr_scangle_it1.4954.51174
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 54 -
Rwork0.196 1141 -
obs-1195 94.99 %

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