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- PDB-5mqv: Crystal structure of human Casein Kinase I delta in complex with ... -

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Basic information

Entry
Database: PDB / ID: 5mqv
TitleCrystal structure of human Casein Kinase I delta in complex with 4-(2,5-Dimethoxyphenyl)-N-(4-(5-(4-fluorphenyl)-2-(methylthio)-1H-imidazol-4-yl)-pyridin-2-yl)-1-methyl-1H-pyrrole-2-carboxamide
ComponentsCasein kinase I isoform delta
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-D5Q / PHOSPHATE ION / Casein kinase I isoform delta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.154 Å
AuthorsPichlo, C. / Brunstein, E. / Baumann, U.
CitationJournal: Molecules / Year: 2017
Title: Optimized 4,5-Diarylimidazoles as Potent/Selective Inhibitors of Protein Kinase CK1 delta and Their Structural Relation to p38 alpha MAPK.
Authors: Halekotte, J. / Witt, L. / Ianes, C. / Kruger, M. / Buhrmann, M. / Rauh, D. / Pichlo, C. / Brunstein, E. / Luxenburger, A. / Baumann, U. / Knippschild, U. / Bischof, J. / Peifer, C.
History
DepositionDec 20, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 5, 2017Provider: 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

Downloads & links

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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
E: Casein kinase I isoform delta
F: Casein kinase I isoform delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)223,52333
Polymers218,2676
Non-polymers5,25627
Water12,556697
1
A: Casein kinase I isoform delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2065
Polymers36,3781
Non-polymers8294
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Casein kinase I isoform delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3016
Polymers36,3781
Non-polymers9235
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Casein kinase I isoform delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3967
Polymers36,3781
Non-polymers1,0186
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Casein kinase I isoform delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3967
Polymers36,3781
Non-polymers1,0186
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Casein kinase I isoform delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1114
Polymers36,3781
Non-polymers7343
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Casein kinase I isoform delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1114
Polymers36,3781
Non-polymers7343
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)197.934, 127.276, 154.780
Angle α, β, γ (deg.)90.000, 113.630, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-427-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 9 or resseq 11:12 or (resid...
21(chain B and (resseq 9 or resseq 11:12 or (resid...
31(chain C and (resseq 9 or resseq 11:12 or (resid...
41(chain D and (resseq 9 or resseq 11:12 or (resid...
51(chain E and (resseq 9 or resseq 11:12 or (resid...
61(chain F and (resseq 9 or resseq 11:12 or (resid...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resseq 9 or resseq 11:12 or (resid...A0
211(chain B and (resseq 9 or resseq 11:12 or (resid...B0
311(chain C and (resseq 9 or resseq 11:12 or (resid...C0
411(chain D and (resseq 9 or resseq 11:12 or (resid...D0
511(chain E and (resseq 9 or resseq 11:12 or (resid...E0
611(chain F and (resseq 9 or resseq 11:12 or (resid...F0

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Components

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


Mass: 36377.887 Da / Num. of mol.: 6 / Fragment: kinase domain
Source method: isolated from a genetically manipulated source
Details: CSNK1D 1-294 with N-terminal thrombin cleavage site and polyHis-tag
Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK1D, HCKID / Plasmid: CK1D / 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-D5Q / 4-(2,5-Dimethoxyphenyl)-N-(4-(5-(4-fluorphenyl)-2-(methylthio)-1H-imidazol-4-yl)-pyridin-2-yl)-1-methyl-1H-pyrrole-2-carboxamide


Mass: 543.612 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C29H26FN5O3S
#3: Chemical...
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 697 / 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: 4.09 Å3/Da / Density % sol: 69.94 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Hepes pH 7.0, 0.7 M NaH2PO4, 0.7 M KH2PO4

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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 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.154→49.291 Å / Num. obs: 187597 / % possible obs: 99 % / Redundancy: 4.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Rrim(I) all: 0.068 / Net I/σ(I): 14.76
Reflection shellResolution: 2.154→2.231 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.49 / Num. unique all: 17796 / CC1/2: 0.828 / Rrim(I) all: 0.51 / % possible all: 94

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.22data extraction
XDSMay 1, 2016data scaling
PHASER1.10.1_2155phasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TWC

4twc


Resolution: 2.154→49.291 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1917 3864 1.06 %
Rwork0.1731 359219 -
obs0.1733 363083 97.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 282.11 Å2 / Biso mean: 57.0082 Å2 / Biso min: 19.85 Å2
Refinement stepCycle: final / Resolution: 2.154→49.291 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13805 0 495 697 14997
Biso mean--68.33 46.49 -
Num. residues----1721
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00314508
X-RAY DIFFRACTIONf_angle_d0.64619584
X-RAY DIFFRACTIONf_chiral_restr0.0422014
X-RAY DIFFRACTIONf_plane_restr0.0032477
X-RAY DIFFRACTIONf_dihedral_angle_d13.6358467
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A9346X-RAY DIFFRACTION5.693TORSIONAL
12B9346X-RAY DIFFRACTION5.693TORSIONAL
13C9346X-RAY DIFFRACTION5.693TORSIONAL
14D9346X-RAY DIFFRACTION5.693TORSIONAL
15E9346X-RAY DIFFRACTION5.693TORSIONAL
16F9346X-RAY DIFFRACTION5.693TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1544-2.18070.26571170.2589107391085681
2.1807-2.20830.23881430.2379130111315499
2.2083-2.23740.24671370.2287129001303798
2.2374-2.2680.23781410.2189131261326799
2.268-2.30040.25261420.21431316313305100
2.3004-2.33480.25951410.21531316113302100
2.3348-2.37130.23261400.20671313113271100
2.3713-2.41010.25851420.20241322113363100
2.4101-2.45170.2021440.19751322213366100
2.4517-2.49630.16741420.1852131861332899
2.4963-2.54430.19761400.1808130241316499
2.5443-2.59620.24951430.1791318113324100
2.5962-2.65270.19921410.179131361327799
2.6527-2.71440.21321430.1827131411328499
2.7144-2.78220.23181420.1778131141325699
2.7822-2.85750.20261410.1829130641320599
2.8575-2.94150.20811330.1803129671310098
2.9415-3.03650.22211370.1872126471278496
3.0365-3.1450.20251350.1913125671270296
3.145-3.27090.20551380.1777126861282495
3.2709-3.41970.19541330.1774126461277996
3.4197-3.59990.18091390.1697127021284196
3.5999-3.82540.15631380.1656126791281796
3.8254-4.12060.14291360.1464125611269795
4.1206-4.5350.16271300.1306125221265295
4.535-5.19060.14931300.1307124641259495
5.1906-6.53730.17551400.1794123921253294
6.5373-49.30350.20371360.179128661300297
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)
11.0470.17080.15611.50810.59451.6773-0.0284-0.00230.2381-0.11010.1311-0.1022-0.28410.1867-0.09680.2818-0.02270.04030.2346-0.03010.292336.640114.127850.9023
21.1466-0.0554-0.2241.0284-0.15641.9350.03370.0062-0.09290.16310.02880.3174-0.0222-0.35-0.05820.2154-0.01240.05640.27610.03240.32618.7823-17.679657.9504
31.06010.3110.57521.14170.1481.61880.1984-0.0577-0.12020.0849-0.06040.22510.2873-0.1923-0.1410.3174-0.0225-0.05360.2740.01540.32879.3801-29.998620.1638
41.32320.0410.35261.555-0.25911.90250.1276-0.1065-0.24610.0288-0.0735-0.17510.2810.2755-0.05910.22020.0645-0.05250.31180.02350.254250.6827-25.516157.5264
50.8899-0.140.11461.3811-0.15491.9703-0.05360.16780.2575-0.1540.05140.0474-0.3382-0.071-0.01860.3378-0.0044-0.01280.25290.07660.269728.67547.512112.3142
61.1637-0.1619-0.20581.17150.31981.76960.05710.0489-0.078-0.23610.0578-0.28970.15290.4606-0.10940.3210.09750.04590.3784-0.06160.295652.1242-27.453117.1795
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 8 through 293)A8 - 293
2X-RAY DIFFRACTION2(chain 'B' and resid 8 through 294)B8 - 294
3X-RAY DIFFRACTION3(chain 'C' and resid 6 through 293)C6 - 293
4X-RAY DIFFRACTION4(chain 'D' and resid 8 through 294)D8 - 294
5X-RAY DIFFRACTION5(chain 'E' and resid 8 through 294)E8 - 294
6X-RAY DIFFRACTION6(chain 'F' and resid 7 through 294)F7 - 294

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