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PDB | 3NGA | Human CK2 catalytic domain in complex with CX-4945

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Internal ID
72514
PDB Entry ID
3NGA
Title
Human CK2 catalytic domain in complex with CX-4945
Authors
Primary Citation
AuthorsFerguson, A.D., Sheth, P.R., Basso, A.D., Paliwal, S., Gray, K., Fischmann, T.O., Le, H.V.
TitleStructural basis of CX-4945 binding to human protein kinase CK2.
JournalFebs Lett., v.585, pp.104 - 110, 2011
AbstractView
Pubmed21093442
DOI10.1016/j.febslet.2010.11.019
 
History
Deposition: 2010-06-11Release: 2010-12-15Last Modified: 2011-02-02
Experimental Method
TypeX-RAY DIFFRACTION
Parameters
Resolution [Å]R-Value (Obs.)R-Value (Work)R-FreeSpace Group
2.710.1890.1880.218P 43 21 2
Unit Cell
Length [Å]a127.64b127.64c125.75
Angles [°]alpha90.00beta90.00gamma90.00
Molecular Description
PolymerMoleculeMutationFragmentChainsEC NumberOther details
1Casein kinase II subunit alphaUNP residues 1-333A, B2.7.11.1
Functional Class
Source
PolymerScientific NameCommon NameExpression System
1Homo sapienshumanEscherichia coli
Chemical Component
IdentifierNameFormulaLigand StructureLigand Interaction
3NG5-[(3-CHLOROPHENYL)AMINO]BENZO[C][2,6]NAPHTHYRIDINE-8-CARBOXYLIC ACIDC19H12ClN3O2[View][View]
SO4SULFATE IONO4S2[View][View]
SCOP Classification
CATH Classification
Structural Details
KeywordTRANSFERASE/TRANSFERASE INHIBITOR
TextKinase, CK2, inhibitor, TRANSFERASE-TRANSFERASE INHIBITOR complex
 
Polymeric Molecules
Chain A
DescriptionCasein kinase II subunit alpha
FragmentUNP residues 1-333
Polymer typepolypeptide
Formula Weight39878.9
Source Methodgenetically manipulated
Entity NameCK II alpha
Entity Name Sysn/a
 
Chain B
DescriptionCasein kinase II subunit alpha
FragmentUNP residues 1-333
Polymer typepolypeptide
Formula Weight39878.9
Source Methodgenetically manipulated
Entity NameCK II alpha
Entity Name Sysn/a
 
Entity Poly
EntityChiralityLinkageMonomer# Mon.StrandTypeDetails
1n/anonon/aA,Bpolypeptide(L)n/a
Ligands And Prosthetic Groups
IDNameFormulaWeightLigand Structure
3NG5-[(3-CHLOROPHENYL)AMINO]BENZO[C][2,6]NAPHTHYRIDINE-8-CARBOXYLIC ACIDC19H12ClN3O2349.776View
SO4SULFATE IONO4S296.058View
EC and Associated Pathways
ChainsIUBMBKEGG EnzymeMetaCycReactome
A, B2.7.11.12.7.11.12.7.11.12.7.11.1
Natural/Genetically Modified Source
Common Namehuman
Scientific NameHomo sapiens
Source Genusn/a
GeneCK2, CK2A1, CSNK2A1
Host Common Namen/a
Host Scientific NameEscherichia coli
Host Genusn/a
Host Cell Linen/a
Host StrainBL21(DE3)
Host Vector TypePLASMID
Host PlasmidpDEST14
 
Crystallization Experiments
MethodVAPOR DIFFUSION, HANGING DROP
PH6.0
Temperature293.0
Details20-26% PEG 4000, 0.2 M ammonium sulfate, 0.1 M sodium citrate pH 6, 1 mM MgCl2 and 10 mM AMPPNP, VAPOR DIFFUSION, HANGING DROP, temperature 293K
 
Unit Cell
Length a (Å)Length b Å)Length c (Å)
127.64127.64125.75
Angle Alpha (°)Angle Beta (°)Angle Gamma (°)
90.0090.0090.00
Space Group
P 43 21 2
Diffraction Detector
DetectorCCD
TypeMARRESEARCH
Detailsn/a
Collection Date2009-10-19
 
Diffraction Radiation
MonochromatorGRAPHITE
Diffraction ProtocolSINGLE WAVELENGTH
Wavelengthn/a
Wavelength List0.9999
 
Diffraction Source
SourceSYNCHROTRON
TypeAPS BEAMLINE 17-BM
SiteAPS
Beamline17-BM
 
Reflection Details
Observed Criterion Sigma (F)0.0
Observed Criterion Sigma (I)0.0
Resolution (High)2.71
Resolution (Low)36.00
Number Reflections (All) 28836
Number Reflections (Observed)28836
Percent Possible (Observed)100.0
R Merge I (Observed)n/a
Net I Over Average Sigma (I)n/a
B (Isotropic) From Wilson Plot72.5
Redundancy15.0
 
Refinement Statistics
Structure Solution MethodMOLECULAR REPLACEMENT
Resolution (High)2.71
Resolution (Low)33.67
Cut-off Sigma (F)0.0
Cut-off Sigma (I)0.0
Number of Reflections (All)28751
Number of Reflections (Observed)28751
Number of Reflections (R-Free) 1456
Percent Reflections (Observed)99.85
R-Factor (All)0.189
R-Factor (Observed)0.189
R-Work0.1875
R-Free0.2176
R-Free Selection DetailsRANDOM
 
Temperature Factor Modeling
Isotropic Thermal Modeln/a
Mean Isotropic B Value54.090
Anisotropic B[1][1]-4.38
Anisotropic B[1][2]0.00
Anisotropic B[1][3]0.00
Anisotropic B[2][2]-4.38
Anisotropic B[2][3]0.00
Anisotropic B[3][3]8.76
 
Resolution Shells
Shell Resol (High)2.71
Shell Resolution (Low)n/a
Number of Reflections (Observed)n/a
Number of Reflections (R-Free)157
Number of Reflections (R-Work)2753
R-Factor (R-Work)0.211
R-Factor (R-Free)0.283
R-Free Errorn/a
Percent Reflections (Observed)99.85
 
RMS Deviations
Parameter TypeDeviation From Ideal
t_bond_d0.010
t_angle_deg1.04
t_dihedral_angle_d0
t_trig_c_planes0
t_gen_planes0
t_it0
t_omega_torsion3.16
t_other_torsion18.61
t_chiral_improper_torsion0
t_ideal_dist_contact0
Coordinate Error
Luzzati ESD (Observed)0.34
Luzzati Sigma A (Observed)n/a
Luzzati Resolution Cutoff (Low)n/a
Luzzati ESD (R-Free Set)n/a
Luzzati Sigma A (R-Free Set)n/a
 
Number of Non-Hydrogen Atoms Used in Refinement
Protein Atoms5586
Nucleic Acid Atoms0
Heterogen Atoms85
Solvent Atoms116
 
Programs
Data CollectionCrystalClear
Data Reduction (intensity integration)XDS
Data Reduction (data scaling)SCALA
Structure SolutionMolrep
Structure RefinementBUSTER 2.9.4
 
Software
Classificationdata collection
Software NameCrystalClear
 
Classificationmodel building
Software NameMolrep
 
Classificationrefinement
Software NameBUSTER
Software Version 2.9.4
 
Sequence Chain
A
Sequence
  1   MSGPVPSRAR  VYTDVNTHRP  REYWDYESHV  VEWGNQDDYQ  LVRKLGRGKY  SEVFEAINIT

 61   NNEKVVVKIL  KPVKKKKIKR  EIKILENLRG  GPNIITLADI  VKDPVSRTPA  LVFEHVNNTD

121   FKQLYQTLTD  YDIRFYMYEI  LKALDYCHSM  GIMHRDVKPH  NVMIDHEHRK  LRLIDWGLAE

181   FYHPGQEYNV  RVASRYFKGP  ELLVDYQMYD  YSLDMWSLGC  MLASMIFRKE  PFFHGHDNYD

241   QLVRIAKVLG  TEDLYDYIDK  YNIELDPRFN  DILGRHSRKR  WERFVHSENQ  HLVSPEALDF

301   LDKLLRYDHQ  SRLTAREAME  HPYFYTVVKD  QAR  

Sequence Chain
B
Sequence
  1   MSGPVPSRAR  VYTDVNTHRP  REYWDYESHV  VEWGNQDDYQ  LVRKLGRGKY  SEVFEAINIT

 61   NNEKVVVKIL  KPVKKKKIKR  EIKILENLRG  GPNIITLADI  VKDPVSRTPA  LVFEHVNNTD

121   FKQLYQTLTD  YDIRFYMYEI  LKALDYCHSM  GIMHRDVKPH  NVMIDHEHRK  LRLIDWGLAE

181   FYHPGQEYNV  RVASRYFKGP  ELLVDYQMYD  YSLDMWSLGC  MLASMIFRKE  PFFHGHDNYD

241   QLVRIAKVLG  TEDLYDYIDK  YNIELDPRFN  DILGRHSRKR  WERFVHSENQ  HLVSPEALDF

301   LDKLLRYDHQ  SRLTAREAME  HPYFYTVVKD  QAR