- PDB-9eq0: Crystal structure of human Casein Kinase II subunit alpha (CK2a1)... -
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Basic information
Entry
Database: PDB / ID: 9eq0
Title
Crystal structure of human Casein Kinase II subunit alpha (CK2a1) in complex with allosteric ligand FGJG12
Components
Casein kinase II subunit alpha
Keywords
TRANSFERASE / CK2 / Kinase / Chemical / allosteric Inhibitor
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 / Maturation of hRSV A proteins / negative regulation of apoptotic signaling pathway / positive regulation of Wnt signaling pathway / negative regulation of double-strand break repair via homologous recombination / chaperone-mediated protein folding / negative regulation of ubiquitin-dependent protein catabolic process / Signal transduction by L1 / peptidyl-threonine phosphorylation / Hsp90 protein binding / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / PML body / Wnt signaling pathway / Regulation of PTEN stability and activity / positive regulation of protein catabolic process / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / KEAP1-NFE2L2 pathway / double-strand break repair / rhythmic process / kinase activity / positive regulation of cell growth / peptidyl-serine phosphorylation / Regulation of TP53 Activity through Phosphorylation / protein stabilization / negative regulation of translation / non-specific serine/threonine protein kinase / regulation of cell cycle / 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 / 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 Similarity search - Domain/homology
A: Casein kinase II subunit alpha hetero molecules
defined by author
Evidence: gel filtration
41.1 kDa, 1 polymers
Theoretical mass
Number of molelcules
Total (without water)
41,096
5
Polymers
40,328
1
Non-polymers
768
4
Water
18
1
Type
Name
Symmetry operation
Number
identity operation
1_555
x,y,z
1
2
B: Casein kinase II subunit alpha hetero molecules
defined by author
41.1 kDa, 1 polymers
Theoretical mass
Number of molelcules
Total (without water)
41,096
5
Polymers
40,328
1
Non-polymers
768
4
Water
18
1
Type
Name
Symmetry operation
Number
identity operation
1_555
x,y,z
1
Unit cell
Length a, b, c (Å)
126.497, 126.497, 126.444
Angle α, β, γ (deg.)
90.00, 90.00, 90.00
Int Tables number
96
Space group name H-M
P43212
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Components
#1: Protein
CaseinkinaseIIsubunitalpha / CK II alpha
Mass: 40327.977 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK2A1, CK2A1 / Production host: Escherichia coli (E. coli) References: UniProt: P68400, non-specific serine/threonine protein kinase
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.999998 Å / Relative weight: 1
Reflection
Resolution: 3.15→44.76 Å / Num. obs: 18361 / % possible obs: 100 % / Redundancy: 26.3 % / CC1/2: 0.99 / Net I/σ(I): 7.8
Reflection shell
Resolution: 3.15→3.37 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3253 / CC1/2: 0.684
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Processing
Software
Name
Version
Classification
REFMAC
5.8.0419
refinement
Aimless
datascaling
XDS
datareduction
MOLREP
phasing
Refinement
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.15→44.76 Å / Cor.coef. Fo:Fc: 0.896 / Cor.coef. Fo:Fc free: 0.894 / SU B: 58.921 / SU ML: 0.445 / Cross valid method: THROUGHOUT / ESU R Free: 0.487 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.27446
962
5.3 %
RANDOM
Rwork
0.25513
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obs
0.25616
17351
99.94 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK