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- PDB-6r8j: Crystal structure of di-phosphorylated human CLK1 in complex with... -

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Basic information

Entry
Database: PDB / ID: 6r8j
TitleCrystal structure of di-phosphorylated human CLK1 in complex with 4-(1-methyl-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
: / 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. ...: / 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 / Alpha Beta
Similarity search - Domain/homology
4-(1-methylindol-3-yl)pyrimidin-2-amine / Dual specificity protein kinase CLK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsLivnah, O. / Domovich, Y.
CitationJournal: To Be Published
Title: Non-phosphorylated human CLK1 in complex with an indole inhibitor to 1.65 Ang
Authors: Livnah, O. / Domovich, Y.
History
DepositionApr 2, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Dual specificity protein kinase CLK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8983
Polymers39,4491
Non-polymers4492
Water2,828157
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 area15880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.543, 68.543, 285.080
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-745-

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 (E. coli) / References: UniProt: P49759, dual-specificity kinase
#2: Chemical ChemComp-JUW / 4-(1-methylindol-3-yl)pyrimidin-2-amine


Mass: 224.261 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H12N4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 2.45 Å3/Da / Density % sol: 49.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 24% PEG 3350, 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: ID23-1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→59.36 Å / Num. obs: 41291 / % possible obs: 99.8 % / Redundancy: 6.2 % / Net I/σ(I): 19.5
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.644 / Num. unique obs: 2193 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
MOSFLMdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→59.36 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.696 / SU ML: 0.112 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.128 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26331 2097 5.1 %RANDOM
Rwork0.21575 ---
obs0.21815 39074 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 41.867 Å2
Baniso -1Baniso -2Baniso -3
1-0.76 Å20.38 Å20 Å2
2--0.76 Å2-0 Å2
3----2.48 Å2
Refinement stepCycle: LAST / Resolution: 1.75→59.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2719 0 34 157 2910
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0192827
X-RAY DIFFRACTIONr_bond_other_d0.0020.022674
X-RAY DIFFRACTIONr_angle_refined_deg1.7971.9633822
X-RAY DIFFRACTIONr_angle_other_deg1.0533.0036147
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6945329
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.82123.143140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.72515499
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9311521
X-RAY DIFFRACTIONr_chiral_restr0.1180.2406
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213142
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02695
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_it3.3123.8551319
X-RAY DIFFRACTIONr_mcbond_other3.3123.8531318
X-RAY DIFFRACTIONr_mcangle_it4.2075.7731647
X-RAY DIFFRACTIONr_mcangle_other4.2075.7771648
X-RAY DIFFRACTIONr_scbond_it4.1644.3711508
X-RAY DIFFRACTIONr_scbond_other4.1634.371509
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.2416.3472176
X-RAY DIFFRACTIONr_long_range_B_refined7.57244.4663244
X-RAY DIFFRACTIONr_long_range_B_other7.5744.3323218
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 145 -
Rwork0.335 2816 -
obs--99.87 %

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