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- PDB-7o9y: Crystal structure of di-phosphorylated human CLK1 in complex with... -

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Basic information

Entry
Database: PDB / ID: 7o9y
TitleCrystal structure of di-phosphorylated human CLK1 in complex with 4-(1H-indol-3-yl)pyrimidin-2-amine
ComponentsDual specificity protein kinase CLK1
KeywordsSIGNALING PROTEIN / CLK1 / splicing / kinase / viral infection
Function / homology
Function and homology information


dual-specificity kinase / regulation of RNA splicing / protein serine/threonine/tyrosine kinase activity / non-membrane spanning protein tyrosine kinase activity / protein tyrosine kinase activity / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / nucleus
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
4-(1~{H}-indol-3-yl)pyrimidin-2-amine / Dual specificity protein kinase CLK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsLivnah, O. / Domovich, Y. / Bracher, F. / Aiger, C.
Funding support Israel, 1items
OrganizationGrant numberCountry
German-Israeli Foundation for Research and Developmenti-1453-207.9/2018 Israel
CitationJournal: To Be Published
Title: Development of novel CLK1 inhibitors as potential drugs for treatment of Chikungunya virus infections
Authors: Livnah, O. / Domovich, Y. / Bracher, F. / Aiger, C.
History
DepositionApr 18, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dual specificity protein kinase CLK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6602
Polymers39,4491
Non-polymers2101
Water3,117173
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.430, 68.430, 284.450
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-753-

HOH

21A-759-

HOH

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Components

#1: Protein Dual specificity protein kinase CLK1 / CDC-like kinase 1


Mass: 39449.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLK1, CLK / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P49759, dual-specificity kinase
#2: Chemical ChemComp-V5T / 4-(1~{H}-indol-3-yl)pyrimidin-2-amine


Mass: 210.235 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H10N4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.45 Å3/Da / Density % sol: 49.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 24% PEG3350, 200mM MgCl2, 100mM BisTris (pH 6.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.969 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.969 Å / Relative weight: 1
ReflectionResolution: 1.66→54.76 Å / Num. obs: 47191 / % possible obs: 98.4 % / Redundancy: 13.6 % / CC1/2: 0.999 / Rrim(I) all: 0.076 / Net I/σ(I): 18.3
Reflection shellResolution: 1.66→1.72 Å / Mean I/σ(I) obs: 1.72 / Num. unique obs: 4294 / CC1/2: 0.599

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
MOSFLMdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6QTY

6qty


Resolution: 1.66→54.76 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.87 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24626 2391 5.1 %RANDOM
Rwork0.21709 ---
obs0.21859 44781 98.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.683 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å20.44 Å20 Å2
2--0.44 Å20 Å2
3----1.41 Å2
Refinement stepCycle: 1 / Resolution: 1.66→54.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2719 0 16 173 2908
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0192807
X-RAY DIFFRACTIONr_bond_other_d0.0010.022660
X-RAY DIFFRACTIONr_angle_refined_deg1.81.9533793
X-RAY DIFFRACTIONr_angle_other_deg0.8943.0016120
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4375329
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.99523.143140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.38915499
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6081521
X-RAY DIFFRACTIONr_chiral_restr0.1120.2406
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213120
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02687
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.9133.4031319
X-RAY DIFFRACTIONr_mcbond_other2.9123.41318
X-RAY DIFFRACTIONr_mcangle_it3.6715.0961647
X-RAY DIFFRACTIONr_mcangle_other3.675.0991648
X-RAY DIFFRACTIONr_scbond_it3.5133.8271488
X-RAY DIFFRACTIONr_scbond_other3.5123.8271489
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.35.5792147
X-RAY DIFFRACTIONr_long_range_B_refined6.60627.5933289
X-RAY DIFFRACTIONr_long_range_B_other6.58127.4473239
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.664→1.707 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 191 -
Rwork0.334 3117 -
obs--96.19 %

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