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- PDB-6f26: Crystal structure of human Casein Kinase I delta in complex with ... -

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Basic information

Entry
Database: PDB / ID: 6f26
TitleCrystal structure of human Casein Kinase I delta in complex with compound 31b
ComponentsCasein kinase I isoform delta
KeywordsTRANSFERASE / Kinase / Inhibitor / Complex / CK1
Function / homology
Function and homology information


positive regulation of non-canonical Wnt signaling pathway / protein localization to Golgi apparatus / COPII vesicle coating / midbrain dopaminergic neuron differentiation / tau-protein kinase / microtubule nucleation / protein localization to cilium / non-motile cilium assembly / protein localization to centrosome / COPII-mediated vesicle transport ...positive regulation of non-canonical Wnt signaling pathway / protein localization to Golgi apparatus / COPII vesicle coating / midbrain dopaminergic neuron differentiation / tau-protein kinase / microtubule nucleation / protein localization to cilium / non-motile cilium assembly / 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 / endoplasmic reticulum-Golgi intermediate compartment membrane / 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 / AURKA Activation by TPX2 / spindle microtubule / circadian regulation of gene expression / cellular response to nerve growth factor stimulus / regulation of circadian rhythm / spindle / Wnt signaling pathway / endocytosis / positive regulation of canonical Wnt signaling pathway / : / Regulation of PLK1 Activity at G2/M Transition / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / actin cytoskeleton / 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 / protein kinase activity / ciliary basal body / cilium / protein phosphorylation / cadherin binding / 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 / cytoplasm
Similarity search - Function
: / 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 ...: / 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-C9Z / Casein kinase I isoform delta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsPichlo, C. / Brunstein, E. / Baumann, U.
CitationJournal: Molecules / Year: 2019
Title: Design, Synthesis and Biological Evaluation of Isoxazole-Based CK1 Inhibitors Modified with Chiral Pyrrolidine Scaffolds.
Authors: Luxenburger, A. / Schmidt, D. / Ianes, C. / Pichlo, C. / Kruger, M. / von Drathen, T. / Brunstein, E. / Gainsford, G.J. / Baumann, U. / Knippschild, U. / Peifer, C.
History
DepositionNov 23, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,82823
Polymers72,7562
Non-polymers3,07321
Water6,593366
1
A: Casein kinase I isoform delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,25015
Polymers36,3781
Non-polymers1,87214
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Casein kinase I isoform delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5788
Polymers36,3781
Non-polymers1,2007
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.075, 72.956, 90.015
Angle α, β, γ (deg.)90.00, 90.15, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: 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 / Plasmid: pET28a / 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: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-C9Z / (9~{S},10~{S},11~{R})-~{N}-[4-[3-(4-fluorophenyl)-5-propan-2-yl-1,2-oxazol-4-yl]pyridin-2-yl]-4-(4-methoxyphenyl)-10,11-bis(oxidanyl)-1,7-diazatricyclo[7.3.0.0^{3,7}]dodeca-3,5-diene-6-carboxamide


Mass: 623.673 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C35H34FN5O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 366 / 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: 2.53 Å3/Da / Density % sol: 51.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M MES pH 5.5, 10 % (w/v) PEG 4000, 0.2 M lithium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Aug 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.83→47.651 Å / Num. obs: 63861 / % possible obs: 99 % / Redundancy: 5 % / Net I/σ(I): 13.12
Reflection shellResolution: 1.83→1.895 Å / Mean I/σ(I) obs: 2.41 / Num. unique obs: 4416 / CC1/2: 0.785 / % possible all: 97

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDS20170720data reduction
XSCALE20170720data scaling
PHENIX(1.12_2829)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TWC

4twc


Resolution: 1.83→47.651 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.46 / Phase error: 21.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2087 1949 3.05 %
Rwork0.1895 --
obs0.1901 63822 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.83→47.651 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4559 0 187 366 5112
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054872
X-RAY DIFFRACTIONf_angle_d0.7836583
X-RAY DIFFRACTIONf_dihedral_angle_d13.3832819
X-RAY DIFFRACTIONf_chiral_restr0.146672
X-RAY DIFFRACTIONf_plane_restr0.004816
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.83-1.87580.29061420.26194437X-RAY DIFFRACTION100
1.8758-1.92650.28781390.24914380X-RAY DIFFRACTION99
1.9265-1.98320.29241400.2344388X-RAY DIFFRACTION100
1.9832-2.04720.20541360.21684425X-RAY DIFFRACTION100
2.0472-2.12040.24531400.20174384X-RAY DIFFRACTION99
2.1204-2.20530.21981440.1944395X-RAY DIFFRACTION100
2.2053-2.30560.2231400.19094435X-RAY DIFFRACTION100
2.3056-2.42720.20251390.18624424X-RAY DIFFRACTION100
2.4272-2.57920.21431350.19374420X-RAY DIFFRACTION100
2.5792-2.77840.18741390.19434416X-RAY DIFFRACTION100
2.7784-3.05790.19681350.1934449X-RAY DIFFRACTION100
3.0579-3.50030.22031370.18444405X-RAY DIFFRACTION99
3.5003-4.40950.1641370.15534410X-RAY DIFFRACTION99
4.4095-47.66760.20821460.1854505X-RAY DIFFRACTION99

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