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- PDB-3kxg: Crystal structure of Z. mays CK2 kinase alpha subunit in complex ... -

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Basic information

Entry
Database: PDB / ID: 3kxg
TitleCrystal structure of Z. mays CK2 kinase alpha subunit in complex with the inhibitor 3,4,5,6,7-pentabromo-1H-indazole (K64)
ComponentsCasein kinase II subunit alpha
KeywordsTransferase/Transferase inhibitor / Protein kinase CK2-inhibitor complex / ATP-binding / Kinase / Nucleotide-binding / Serine/threonine-protein kinase / Transferase / Transferase-Transferase inhibitor complex
Function / homology
Function and homology information


protein kinase CK2 complex / non-specific serine/threonine protein kinase / regulation of cell cycle / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / ATP binding / nucleus / 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
3,4,5,6,7-pentabromo-1H-indazole / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Rigid body in an isomorphous cell / Resolution: 1.7 Å
AuthorsPapinutto, E. / Franchin, C. / Battistutta, R.
Citation
#1: Journal: Chem.Biol. / Year: 2005
Title: Inspecting the structure-activity relationship of protein kinase CK2 inhibitors derived from tetrabromo-benzimidazole.
Authors: Battistutta, R. / Mazzorana, M. / Sarno, S. / Kazimierczuk, Z. / Zanotti, G. / Pinna, L.A.
#2: Journal: Chembiochem / Year: 2007
Title: The ATP-binding site of protein kinase CK2 holds a positive electrostatic area and conserved water molecules.
Authors: Battistutta, R. / Mazzorana, M. / Cendron, L. / Bortolato, A. / Sarno, S. / Kazimierczuk, Z. / Zanotti, G. / Moro, S. / Pinna, L.A.
History
DepositionDec 3, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Oct 30, 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

Downloads & links

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Assembly

Deposited unit
A: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2022
Polymers38,6891
Non-polymers5131
Water4,792266
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)142.467, 60.370, 45.514
Angle α, β, γ (deg.)90.00, 103.13, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-339-

HOH

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Components

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


Mass: 38689.395 Da / Num. of mol.: 1 / Fragment: ALPHA SUBUNIT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Gene: ACK2 / Production host: Escherichia coli (E. coli)
References: UniProt: P28523, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-K6X / 3,4,5,6,7-pentabromo-1H-indazole


Mass: 512.616 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7HBr5N2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / 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: 2.46 Å3/Da / Density % sol: 50.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 20% PEG 4000, 0.2M Na-acetate, 0.1M Tris, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.972991 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 6, 2008 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972991 Å / Relative weight: 1
ReflectionResolution: 1.7→69.34 Å / Num. all: 41479 / Num. obs: 41272 / % possible obs: 99.5 % / Redundancy: 4 % / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 16.3
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 4 % / Rmerge(I) obs: 0.441 / Mean I/σ(I) obs: 2.3 / Rsym value: 0.441 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: Rigid body in an isomorphous cell
Resolution: 1.7→69.34 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.928 / SU B: 6.099 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.124 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26263 2079 5 %RANDOM
Rwork0.21432 ---
obs0.21678 39192 99.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.519 Å2
Baniso -1Baniso -2Baniso -3
1--1.78 Å2-0 Å2-0.82 Å2
2---0.2 Å20 Å2
3---1.61 Å2
Refinement stepCycle: LAST / Resolution: 1.7→69.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2728 0 14 266 3008
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222817
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7541.9643812
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg12.6245.061330
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.56523.904146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.61915507
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3561519
X-RAY DIFFRACTIONr_chiral_restr0.120.2400
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022155
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2240.21382
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.21915
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2236
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2370.246
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1570.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0141.51683
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.46722647
X-RAY DIFFRACTIONr_scbond_it2.45331338
X-RAY DIFFRACTIONr_scangle_it3.4054.51164
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 150 -
Rwork0.329 2921 -
obs--100 %

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