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

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Basic information

Entry
Database: PDB / ID: 6hmp
TitleCrystal structure of human Casein Kinase I delta in complex with a photoswitchable 2-Azoimidazole-based Inhibitor (compound 3)
ComponentsCasein kinase I isoform delta
KeywordsTRANSFERASE / Kinase / Photoswitchable Inhibitor / Complex
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-GEW / PHOSPHATE ION / Casein kinase I isoform delta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.039 Å
AuthorsPichlo, C. / Schehr, M. / Charl, J. / Brunstein, E. / Peifer, C. / Baumann, U.
CitationJournal: Photochem. Photobiol. Sci. / Year: 2019
Title: 2-Azo-, 2-diazocine-thiazols and 2-azo-imidazoles as photoswitchable kinase inhibitors: limitations and pitfalls of the photoswitchable inhibitor approach.
Authors: Schehr, M. / Ianes, C. / Weisner, J. / Heintze, L. / Muller, M.P. / Pichlo, C. / Charl, J. / Brunstein, E. / Ewert, J. / Lehr, M. / Baumann, U. / Rauh, D. / Knippschild, U. / Peifer, C. / Herges, R.
History
DepositionSep 12, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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)74,1116
Polymers72,7562
Non-polymers1,3554
Water4,125229
1
A: Casein kinase I isoform delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0553
Polymers36,3781
Non-polymers6782
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Casein kinase I isoform delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0553
Polymers36,3781
Non-polymers6782
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.819, 72.223, 89.161
Angle α, β, γ (deg.)90.00, 103.21, 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 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P48730, non-specific serine/threonine protein kinase, tau-protein kinase
#2: Chemical ChemComp-GEW / 3-(2,5-dimethoxyphenyl)-~{N}-[4-[5-(4-fluorophenyl)-2-[(~{E})-(4-fluorophenyl)diazenyl]-3-methyl-imidazol-4-yl]pyridin-2-yl]propanamide


Mass: 582.600 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C32H28F2N6O3
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 2.1 Å3/Da / Density % sol: 41.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium citrate tribasic pH 7.0 20 % w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.000021 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Mar 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000021 Å / Relative weight: 1
ReflectionResolution: 2.039→46.39 Å / Num. obs: 37921 / % possible obs: 98.29 % / Redundancy: 8.2 % / Net I/σ(I): 12.76
Reflection shellResolution: 2.039→2.112 Å

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDS20180126data reduction
XDS20180126data scaling
PHASER(1.12_2829: 000)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MQV

5mqv


Resolution: 2.039→47.527 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 23.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.219 1890 4.99 %
Rwork0.1853 --
obs0.1869 37898 98.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.039→47.527 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4563 0 96 229 4888
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054807
X-RAY DIFFRACTIONf_angle_d0.7346480
X-RAY DIFFRACTIONf_dihedral_angle_d13.0472825
X-RAY DIFFRACTIONf_chiral_restr0.045665
X-RAY DIFFRACTIONf_plane_restr0.004825
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0389-2.08990.35931180.32942068X-RAY DIFFRACTION81
2.0899-2.14640.32951160.29792477X-RAY DIFFRACTION95
2.1464-2.20950.28391440.25232636X-RAY DIFFRACTION100
2.2095-2.28090.28151270.23552581X-RAY DIFFRACTION100
2.2809-2.36240.26191520.21742587X-RAY DIFFRACTION100
2.3624-2.4570.24071330.20252615X-RAY DIFFRACTION100
2.457-2.56880.25041400.19632615X-RAY DIFFRACTION100
2.5688-2.70420.19981390.19482615X-RAY DIFFRACTION100
2.7042-2.87360.22481380.18612606X-RAY DIFFRACTION100
2.8736-3.09540.26161320.18592611X-RAY DIFFRACTION100
3.0954-3.40690.21321410.17752608X-RAY DIFFRACTION100
3.4069-3.89960.21171400.16252630X-RAY DIFFRACTION100
3.8996-4.91230.15051350.13552665X-RAY DIFFRACTION100
4.9123-47.54030.19431350.1752694X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.1452-0.00310.01450.07120.01430.07520.1690.40420.61520.07340.0495-0.0056-0.21170.5993-0.00040.508-0.02180.09930.64760.14690.6448.91857.670314.0159
20.5079-0.17620.15750.3824-0.36620.4751-0.2641-0.1692-0.01840.05520.2426-0.30330.19641.0836-0.00550.3420.06380.05061.1320.01260.541812.86420.183420.8507
31.01830.07760.05350.7398-0.24173.42650.03360.0761-0.01890.0553-0.0131-0.05760.13150.1136-0.00080.23280.0139-0.00270.25160.00570.289-4.63471.325733.6231
40.10670.00770.01090.17090.12060.34-0.2793-0.25110.0427-0.2362-0.23830.20790.6315-0.9108-0.00970.3683-0.1060.01960.622-0.02160.3536-19.9965-1.986419.5601
50.1644-0.00820.13220.21590.04040.13190.089-0.56360.38560.7715-0.10940.454-0.2861-0.2335-0.00130.62860.02810.05760.6376-0.05330.52345.9284-24.372-4.6987
60.3006-0.25110.19950.2404-0.1950.2061-0.0494-0.50410.17650.6843-0.3188-0.0421-0.19860.04890.00020.6834-0.10220.00090.6494-0.02470.44698.2655-26.8495-0.6781
71.46390.35550.69380.91080.29231.7356-0.05670.1470.0689-0.07470.0286-0.0215-0.18360.1096-0.00270.29280.0504-0.00810.2989-0.00050.2897-2.8167-35.693418.4512
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 28 )
2X-RAY DIFFRACTION2chain 'A' and (resid 29 through 59 )
3X-RAY DIFFRACTION3chain 'A' and (resid 60 through 279 )
4X-RAY DIFFRACTION4chain 'A' and (resid 280 through 294 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 21 )
6X-RAY DIFFRACTION6chain 'B' and (resid 22 through 48 )
7X-RAY DIFFRACTION7chain 'B' and (resid 49 through 293 )

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