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- PDB-4anm: Complex of CK2 with a CDC7 inhibitor -

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Basic information

Entry
Database: PDB / ID: 4anm
TitleComplex of CK2 with a CDC7 inhibitor
ComponentsCASEIN KINASE II SUBUNIT ALPHA
KeywordsTRANSFERASE
Function / homology
Function and homology information


protein kinase CK2 complex / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity ...protein kinase CK2 complex / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / 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
Chem-WUL / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesZEA MAYS (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsStout, T.J.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2012
Title: Discovery of Xl413, a Potent and Selective Cdc7 Inhibitor.
Authors: Koltun, E.S. / Tsuhako, A.L. / Brown, D.S. / Aay, N. / Arcalas, A. / Chan, V. / Du, H. / Engst, S. / Ferguson, K. / Franzini, M. / Galan, A. / Holst, C.R. / Huang, P. / Kane, B. / Kim, M.H. ...Authors: Koltun, E.S. / Tsuhako, A.L. / Brown, D.S. / Aay, N. / Arcalas, A. / Chan, V. / Du, H. / Engst, S. / Ferguson, K. / Franzini, M. / Galan, A. / Holst, C.R. / Huang, P. / Kane, B. / Kim, M.H. / Li, J. / Markby, D. / Mohan, M. / Noson, K. / Plonowski, A. / Richards, S.J. / Robertson, S. / Shaw, K. / Stott, G. / Stout, T.J. / Young, J. / Yu, P. / Zaharia, C.A. / Zhang, W. / Zhou, P. / Nuss, J.M. / Xu, W. / Kearney, P.C.
History
DepositionMar 20, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 23, 2012Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _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)39,9452
Polymers39,5801
Non-polymers3641
Water6,413356
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)142.061, 60.549, 44.747
Angle α, β, γ (deg.)90.00, 102.92, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2167-

HOH

21A-2322-

HOH

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Components

#1: Protein CASEIN KINASE II SUBUNIT ALPHA / CK II / CK2-ALPHA / CK2


Mass: 39580.383 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, RESIDUES 2-332
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ZEA MAYS (maize) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: P28523, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-WUL / 8-BROMANYL-2-[[(3S)-3-OXIDANYLPYRROLIDIN-1-YL]METHYL]-3H-[1]BENZOFURO[3,2-D]PYRIMIDIN-4-ONE / (S)-8-BROMO-2-((3-HYDROXYPYRROLIDIN-1-YL)METHYL)


Mass: 364.194 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H14BrN3O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 356 / 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: 2.32 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growpH: 8 / Details: 20% PEG4K, 200 MM NAOAC, 100 MM TRIS, PH 8.0

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Data collection

DiffractionMean temperature: 155 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.97946
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 21, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.7→36.71 Å / Num. obs: 40017 / % possible obs: 97.9 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 31.58
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.13 / Mean I/σ(I) obs: 7.9 / % possible all: 91.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: IN-HOUSE CK2 APO STRUCTURE

Resolution: 1.7→36.71 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.945 / SU B: 1.839 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.1 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.20184 2000 5 %RANDOM
Rwork0.16444 ---
obs0.16636 38012 97.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.738 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.7→36.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2733 0 22 356 3111
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0320.0222843
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.3731.9683850
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0545333
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.44223.904146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.68615514
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2711519
X-RAY DIFFRACTIONr_chiral_restr0.2950.2405
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.022169
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2290.21403
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3220.21949
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.2286
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4030.249
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3750.224
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8211.51708
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.43522667
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.27531385
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.844.51180
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
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
Rfree0.283 127 -
Rwork0.203 2480 -
obs--86.41 %

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