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- PDB-7nzy: Crystal structure of human Casein Kinase I delta in complex with ... -

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Basic information

Entry
Database: PDB / ID: 7nzy
TitleCrystal structure of human Casein Kinase I delta in complex with CGS-15943
ComponentsCasein kinase I isoform delta
KeywordsTRANSFERASE / Kinase / Inhibitor / Complex / ATP-competitive
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
: / 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
MALONATE ION / PHOSPHATE ION / Chem-UX2 / Casein kinase I isoform delta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsPichlo, C. / Baumann, U.
CitationJournal: J.Med.Chem. / Year: 2022
Title: Phenotypic Discovery of Triazolo[1,5- c ]quinazolines as a First-In-Class Bone Morphogenetic Protein Amplifier Chemotype.
Authors: Wesseler, F. / Lohmann, S. / Riege, D. / Halver, J. / Roth, A. / Pichlo, C. / Weber, S. / Takamiya, M. / Muller, E. / Ketzel, J. / Flegel, J. / Gihring, A. / Rastegar, S. / Bertrand, J. / ...Authors: Wesseler, F. / Lohmann, S. / Riege, D. / Halver, J. / Roth, A. / Pichlo, C. / Weber, S. / Takamiya, M. / Muller, E. / Ketzel, J. / Flegel, J. / Gihring, A. / Rastegar, S. / Bertrand, J. / Baumann, U. / Knippschild, U. / Peifer, C. / Sievers, S. / Waldmann, H. / Schade, D.
History
DepositionMar 24, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)147,76216
Polymers145,8314
Non-polymers1,93112
Water11,944663
1
A: Casein kinase I isoform delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9484
Polymers36,4581
Non-polymers4903
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Casein kinase I isoform delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8393
Polymers36,4581
Non-polymers3812
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Casein kinase I isoform delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9334
Polymers36,4581
Non-polymers4763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Casein kinase I isoform delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0435
Polymers36,4581
Non-polymers5854
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.938, 82.081, 89.556
Angle α, β, γ (deg.)87.097, 74.264, 86.332
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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


Mass: 36457.867 Da / Num. of mol.: 4
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) / Strain (production host): TAKARA 2
References: UniProt: P48730, non-specific serine/threonine protein kinase, tau-protein kinase
#2: Chemical
ChemComp-UX2 / 9-chloranyl-2-(furan-2-yl)-[1,2,4]triazolo[1,5-c]quinazolin-5-amine


Mass: 285.689 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C13H8ClN5O / Feature type: SUBJECT OF INVESTIGATION / Comment: antagonist*YM
#3: Chemical
ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H2O4
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 663 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.37 Å3/Da / Density % sol: 48.06 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 0.2 M sodium malonate pH = 5.0, 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.85→47.04 Å / Num. obs: 110137 / % possible obs: 96.27 % / Redundancy: 3.6 % / Biso Wilson estimate: 28.9 Å2 / CC1/2: 0.997 / Net I/σ(I): 9.96
Reflection shellResolution: 1.85→1.916 Å / Num. unique obs: 10873 / CC1/2: 0.797

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
PHENIX1.19.1_4122refinement
XDS20180126data reduction
XDS20180126data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TWC

4twc


Resolution: 1.85→47.04 Å / SU ML: 0.2443 / Cross valid method: FREE R-VALUE / σ(F): 2.03 / Phase error: 30.9771
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2289 1765 1.6 %
Rwork0.2049 108218 -
obs0.2053 109983 96.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.93 Å2
Refinement stepCycle: LAST / Resolution: 1.85→47.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9218 0 128 663 10009
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00749743
X-RAY DIFFRACTIONf_angle_d0.783313145
X-RAY DIFFRACTIONf_chiral_restr0.05041351
X-RAY DIFFRACTIONf_plane_restr0.00531681
X-RAY DIFFRACTIONf_dihedral_angle_d13.14443620
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.90.41641350.38738208X-RAY DIFFRACTION95.02
1.9-1.960.35551360.34188277X-RAY DIFFRACTION95.33
1.96-2.020.39251450.29628209X-RAY DIFFRACTION95.41
2.02-2.090.30091150.2798265X-RAY DIFFRACTION95.38
2.09-2.170.27221390.25348259X-RAY DIFFRACTION95.83
2.17-2.270.26291370.21978369X-RAY DIFFRACTION96.47
2.27-2.390.21591240.2018308X-RAY DIFFRACTION96.38
2.39-2.540.24461420.20428345X-RAY DIFFRACTION96.22
2.54-2.740.24371450.20898371X-RAY DIFFRACTION96.95
2.74-3.020.23731320.20838362X-RAY DIFFRACTION97.04
3.02-3.450.23321370.19728401X-RAY DIFFRACTION96.76
3.45-4.350.20531380.16558448X-RAY DIFFRACTION97.77
4.35-47.040.16121400.17448396X-RAY DIFFRACTION97.14

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