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- PDB-6f1w: Crystal structure of human Casein Kinase I delta in complex with ... -

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Basic information

Entry
Database: PDB / ID: 6f1w
TitleCrystal structure of human Casein Kinase I delta in complex with compound 31a
Components(Casein kinase I isoform delta) x 2
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 / tau-protein kinase / midbrain dopaminergic neuron differentiation / 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 / tau-protein kinase / midbrain dopaminergic neuron differentiation / 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 / regulation of circadian rhythm / spindle / Wnt signaling pathway / endocytosis / : / Regulation of PLK1 Activity at G2/M Transition / positive regulation of canonical Wnt signaling pathway / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / actin cytoskeleton / protein phosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / cilium / ciliary basal body / 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 / cytoplasm / cytosol
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-CG5 / Casein kinase I isoform delta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.864 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 1.1Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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)75,52419
Polymers72,8362
Non-polymers2,68817
Water7,476415
1
A: Casein kinase I isoform delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7549
Polymers36,4581
Non-polymers1,2968
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Casein kinase I isoform delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,77010
Polymers36,3781
Non-polymers1,3929
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.549, 105.872, 71.687
Angle α, β, γ (deg.)90.00, 108.93, 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: 36457.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK1D, HCKID / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (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.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK1D, HCKID / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): TAKARA 2
References: UniProt: P48730, non-specific serine/threonine protein kinase, tau-protein kinase
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CG5 / (9~{R},10~{R},11~{S})-~{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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 415 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.54 Å3/Da / Density % sol: 51.58 %
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: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9889 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9889 Å / Relative weight: 1
ReflectionResolution: 1.864→67.81 Å / Num. obs: 58776 / % possible obs: 97 % / Redundancy: 3.3 % / Net I/σ(I): 11.42
Reflection shellResolution: 1.864→1.931 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 1.19 / Num. unique obs: 4416 / % possible all: 72

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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 / Resolution: 1.864→67.81 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 22.03
RfactorNum. reflection% reflection
Rfree0.2064 1904 3.24 %
Rwork0.1809 --
obs0.1818 58768 96.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.864→67.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4578 0 167 415 5160
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064935
X-RAY DIFFRACTIONf_angle_d0.786675
X-RAY DIFFRACTIONf_dihedral_angle_d14.1822880
X-RAY DIFFRACTIONf_chiral_restr0.071682
X-RAY DIFFRACTIONf_plane_restr0.003835
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.864-1.91060.417920.33222690X-RAY DIFFRACTION64
1.9106-1.96230.28771330.30584075X-RAY DIFFRACTION98
1.9623-2.020.30351370.25424144X-RAY DIFFRACTION100
2.02-2.08530.26441370.23124156X-RAY DIFFRACTION100
2.0853-2.15980.24161430.2044189X-RAY DIFFRACTION100
2.1598-2.24630.20471500.18754164X-RAY DIFFRACTION100
2.2463-2.34850.20981330.18424184X-RAY DIFFRACTION100
2.3485-2.47230.21891410.17664159X-RAY DIFFRACTION100
2.4723-2.62720.20611400.17824150X-RAY DIFFRACTION100
2.6272-2.83010.21751390.17824194X-RAY DIFFRACTION100
2.8301-3.11490.19931350.17924184X-RAY DIFFRACTION100
3.1149-3.56560.20331390.1694178X-RAY DIFFRACTION100
3.5656-4.49220.15991420.14644170X-RAY DIFFRACTION99
4.4922-67.85550.19111430.17124227X-RAY DIFFRACTION99

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