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- PDB-5okt: Crystal structure of human Casein Kinase I delta in complex with IWP-2 -

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Basic information

Entry
Database: PDB / ID: 5okt
TitleCrystal structure of human Casein Kinase I delta in complex with IWP-2
Components(Casein kinase I isoform ...) x 2
KeywordsTRANSFERASE / CK1D / Kinase-inhibitor complex / Kinase
Function / homology
Function and homology information


positive regulation of non-canonical Wnt signaling pathway / protein localization to Golgi apparatus / midbrain dopaminergic neuron differentiation / COPII vesicle coating / microtubule nucleation / tau-protein kinase / non-motile cilium assembly / protein localization to cilium / protein localization to centrosome / COPII-mediated vesicle transport ...positive regulation of non-canonical Wnt signaling pathway / protein localization to Golgi apparatus / midbrain dopaminergic neuron differentiation / COPII vesicle coating / microtubule nucleation / tau-protein kinase / non-motile cilium assembly / protein localization to cilium / protein localization to centrosome / COPII-mediated vesicle transport / tau-protein kinase activity / Golgi organization / Major pathway of rRNA processing in the nucleolus and cytosol / spindle assembly / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / endoplasmic reticulum-Golgi intermediate compartment membrane / AURKA Activation by TPX2 / cellular response to nerve growth factor stimulus / ciliary basal body / circadian regulation of gene expression / spindle microtubule / regulation of circadian rhythm / Wnt signaling pathway / spindle / endocytosis / Regulation of PLK1 Activity at G2/M Transition / Circadian Clock / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / positive regulation of canonical Wnt signaling pathway / non-specific serine/threonine protein kinase / protein kinase activity / cadherin binding / positive regulation of protein phosphorylation / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / perinuclear region of cytoplasm / Golgi apparatus / signal transduction / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol
Similarity search - Function
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. ...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-9XK / ACETATE ION / Casein kinase I isoform delta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsPichlo, C. / Brunstein, E. / Baumann, U.
CitationJournal: J. Med. Chem. / Year: 2018
Title: Discovery of Inhibitor of Wnt Production 2 (IWP-2) and Related Compounds As Selective ATP-Competitive Inhibitors of Casein Kinase 1 (CK1) delta / epsilon.
Authors: Garcia-Reyes, B. / Witt, L. / Jansen, B. / Karasu, E. / Gehring, T. / Leban, J. / Henne-Bruns, D. / Pichlo, C. / Brunstein, E. / Baumann, U. / Wesseler, F. / Rathmer, B. / Schade, D. / ...Authors: Garcia-Reyes, B. / Witt, L. / Jansen, B. / Karasu, E. / Gehring, T. / Leban, J. / Henne-Bruns, D. / Pichlo, C. / Brunstein, E. / Baumann, U. / Wesseler, F. / Rathmer, B. / Schade, D. / Peifer, C. / Knippschild, U.
History
DepositionJul 25, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 25, 2018Provider: repository / Type: Initial release
Revision 1.1May 23, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.3Jan 17, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Casein kinase I isoform delta
B: Casein kinase I isoform delta
C: Casein kinase I isoform delta
D: Casein kinase I isoform delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,85033
Polymers145,6724
Non-polymers4,17829
Water6,539363
1
A: Casein kinase I isoform delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5239
Polymers36,4581
Non-polymers1,0658
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Casein kinase I isoform delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3056
Polymers36,4581
Non-polymers8475
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Casein kinase I isoform delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,60510
Polymers36,3781
Non-polymers1,2279
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Casein kinase I isoform delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4178
Polymers36,3781
Non-polymers1,0397
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.110, 82.730, 89.640
Angle α, β, γ (deg.)89.73, 74.14, 86.57
Int Tables number1
Space group name H-MP1

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Components

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Casein kinase I isoform ... , 2 types, 4 molecules ABCD

#1: Protein Casein kinase I isoform delta / CKId / Tau-protein kinase CSNK1D


Mass: 36457.867 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK1D, HCKID / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): TAKARA 2
References: UniProt: P48730, non-specific serine/threonine protein kinase, tau-protein kinase
#2: Protein Casein kinase I isoform delta / CKId / Tau-protein kinase CSNK1D


Mass: 36377.887 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK1D, HCKID / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): TAKARA 2
References: UniProt: P48730, non-specific serine/threonine protein kinase, tau-protein kinase

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Non-polymers , 5 types, 392 molecules

#3: Chemical
ChemComp-9XK / ~{N}-(6-methyl-1,3-benzothiazol-2-yl)-2-[(4-oxidanylidene-3-phenyl-6,7-dihydrothieno[3,2-d]pyrimidin-2-yl)sulfanyl]ethanamide


Mass: 466.599 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C22H18N4O2S3
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 363 / 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: 2.4 Å3/Da / Density % sol: 48.76 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium sulfate, 0.1 M sodium acetate pH 5.0 and 5 % (w/v) PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.13→47.155 Å / Num. obs: 74219 / % possible obs: 98 % / Redundancy: 3.5 % / Net I/σ(I): 14.1

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MQV

5mqv


Resolution: 2.13→47.155 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 2.13 / Phase error: 26.55
RfactorNum. reflection% reflection
Rfree0.2206 2010 2.71 %
Rwork0.1932 --
obs0.1939 74160 97.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.13→47.155 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9128 0 251 363 9742
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0049596
X-RAY DIFFRACTIONf_angle_d0.71512934
X-RAY DIFFRACTIONf_dihedral_angle_d16.9833510
X-RAY DIFFRACTIONf_chiral_restr0.0431329
X-RAY DIFFRACTIONf_plane_restr0.0031622
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.13-2.18330.32751450.29925098X-RAY DIFFRACTION97
2.1833-2.24230.34211320.28415161X-RAY DIFFRACTION97
2.2423-2.30830.31281440.25155077X-RAY DIFFRACTION97
2.3083-2.38280.27951350.23875103X-RAY DIFFRACTION98
2.3828-2.46790.23841550.22755192X-RAY DIFFRACTION98
2.4679-2.56670.25481320.22035110X-RAY DIFFRACTION98
2.5667-2.68350.24881450.21885147X-RAY DIFFRACTION98
2.6835-2.8250.24131480.20485188X-RAY DIFFRACTION98
2.825-3.0020.23421430.20475177X-RAY DIFFRACTION98
3.002-3.23370.19831390.19935171X-RAY DIFFRACTION98
3.2337-3.5590.22991520.18855186X-RAY DIFFRACTION98
3.559-4.07380.22131490.16325196X-RAY DIFFRACTION98
4.0738-5.13160.16191450.14525159X-RAY DIFFRACTION99
5.1316-47.16640.18471460.18095185X-RAY DIFFRACTION98

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