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- PDB-3pe2: Crystal structure of human protein kinase CK2 in complex with the... -

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Basic information

Entry
Database: PDB / ID: 3pe2
TitleCrystal structure of human protein kinase CK2 in complex with the inhibitor CX-5011
ComponentsCasein kinase II subunit alphaCasein kinase 2
Keywordstransferase/transferase inhibitor / Kinase / CK2-inhibitor complex / TRANSFERASE / transferase-transferase inhibitor complex
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 / negative regulation of apoptotic signaling pathway / positive regulation of Wnt signaling pathway / chaperone-mediated protein folding / negative regulation of ubiquitin-dependent protein catabolic process / Signal transduction by L1 / Hsp90 protein binding / peptidyl-threonine phosphorylation / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / PML body / Wnt signaling pathway / Regulation of PTEN stability and activity / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / positive regulation of protein catabolic process / rhythmic process / KEAP1-NFE2L2 pathway / double-strand break repair / kinase activity / positive regulation of cell growth / peptidyl-serine phosphorylation / Regulation of TP53 Activity through Phosphorylation / negative regulation of translation / protein stabilization / regulation of cell cycle / non-specific serine/threonine protein kinase / 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 / 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
Chem-E1B / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBattistutta, R. / Papinutto, E. / Lolli, G. / Pierre, F. / Haddach, M. / Ryckman, D.M.
Citation
Journal: Biochemistry / Year: 2011
Title: Unprecedented selectivity and structural determinants of a new class of protein kinase CK2 inhibitors in clinical trials for the treatment of cancer.
Authors: Battistutta, R. / Cozza, G. / Pierre, F. / Papinutto, E. / Lolli, G. / Sarno, S. / O'Brien, S.E. / Siddiqui-Jain, A. / Haddach, M. / Anderes, K. / Ryckman, D.M. / Meggio, F. / Pinna, L.A.
#1: 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.
History
DepositionOct 25, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 4, 2012Group: Database references
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

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Assembly

Deposited unit
A: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8695
Polymers40,2411
Non-polymers6294
Water5,170287
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.510, 46.437, 63.585
Angle α, β, γ (deg.)90.000, 111.730, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Casein kinase II subunit alpha / Casein kinase 2 / CK II alpha


Mass: 40240.902 Da / Num. of mol.: 1 / Fragment: unp residues 1-337
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK2A1, CK2A1 / Plasmid: pT7-7 / Production host: Escherichia coli (E. coli)
References: UniProt: P68400, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-E1B / 5-[(3-ethynylphenyl)amino]pyrimido[4,5-c]quinoline-8-carboxylic acid


Mass: 340.335 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H12N4O2
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 287 / 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: 1.99 Å3/Da / Density % sol: 38.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 32% PEG 4000, 0.2M Li2SO4, 0.1M Tris pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: PILATUS 2M / Detector: PIXEL / Date: Jul 6, 2010 / Details: Mirrors
RadiationMonochromator: Double Crystal Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→46.44 Å / Num. all: 25295 / Num. obs: 24941 / % possible obs: 98.6 % / Redundancy: 3.4 % / Biso Wilson estimate: 21.62 Å2 / Rmerge(I) obs: 0.089 / Rsym value: 0.089 / Net I/σ(I): 10.9
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.594 / Mean I/σ(I) obs: 2 / Num. unique all: 3536 / Rsym value: 0.594 / % possible all: 96.5

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Processing

Software
NameVersionClassificationNB
PHENIX1.6.2_432refinement
PDB_EXTRACT3.1data extraction
ElettraXRD1 in house softwaredata collection
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2PVR

2pvr


Resolution: 1.9→34.135 Å / Occupancy max: 1 / Occupancy min: 0.48 / FOM work R set: 0.8607 / SU ML: 0.24 / Isotropic thermal model: Isotropic + TLS parameters / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 21.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2219 1269 5.09 %RANDOM
Rwork0.178 ---
obs0.1803 24914 98.45 %-
Solvent computationShrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.577 Å2 / ksol: 0.364 e/Å3
Displacement parametersBiso max: 72.48 Å2 / Biso mean: 24.9724 Å2 / Biso min: 9.6 Å2
Baniso -1Baniso -2Baniso -3
1--7.7494 Å2-0 Å2-1.1025 Å2
2--5.4793 Å20 Å2
3---2.2701 Å2
Refinement stepCycle: LAST / Resolution: 1.9→34.135 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2765 0 41 287 3093
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072893
X-RAY DIFFRACTIONf_angle_d1.0573919
X-RAY DIFFRACTIONf_chiral_restr0.078401
X-RAY DIFFRACTIONf_plane_restr0.004500
X-RAY DIFFRACTIONf_dihedral_angle_d14.8891091
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.899-1.9750.32661420.2712517265995
1.975-2.06490.27271250.21922667279299
2.0649-2.17380.26071380.20062605274399
2.1738-2.30990.27681520.18892616276899
2.3099-2.48820.23951340.18442605273998
2.4882-2.73850.2371500.18682628277898
2.7385-3.13460.2081430.17442637278099
3.1346-3.94830.19731520.15482642279499
3.9483-34.14080.17871330.15842728286199
Refinement TLS params.

S33: 0 Å ° / 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 °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.25670.06680.12840.1149-0.14560.3794-0.01940.0611-0.18810.04230.0054-0.06830.06920.01510.15910.00580.02730.1542-0.06310.226321.8488-46.834111.8132
20.46810.3165-0.02040.2166-0.04490.29670.02720.0136-0.02980.0571-0.04950.0013-0.0104-0.02270.1261-0.005-0.00480.1553-0.03250.140726.1451-35.05613.2427
30.72210.0324-0.22860.3634-0.05310.2216-0.03180.1256-0.02260.03540.0362-0.05360.0094-0.10190.11940.0117-0.00610.1163-0.00030.09722.032-36.409917.1239
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 3:47)A3 - 47
2X-RAY DIFFRACTION2(chain A and resid 48:126)A48 - 126
3X-RAY DIFFRACTION3(chain A and resid 127:329)A127 - 329

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