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- PDB-6fyv: X-RAY STRUCTURE OF CLK4-KD(146-480)/CX-4945 AT 2.46A -

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Basic information

Entry
Database: PDB / ID: 6fyv
TitleX-RAY STRUCTURE OF CLK4-KD(146-480)/CX-4945 AT 2.46A
ComponentsDual specificity protein kinase CLK4
KeywordsTRANSFERASE / SPLICING / KINASE / PHOSPHOTRANSFERASE
Function / homology
Function and homology information


dual-specificity kinase / regulation of RNA splicing / protein serine/threonine/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
Chem-3NG / Dual specificity protein kinase CLK4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.46 Å
AuthorsKallen, J.
CitationJournal: ChemMedChem / Year: 2018
Title: X-ray Structures and Feasibility Assessment of CLK2 Inhibitors for Phelan-McDermid Syndrome.
Authors: Kallen, J. / Bergsdorf, C. / Arnaud, B. / Bernhard, M. / Brichet, M. / Cobos-Correa, A. / Elhajouji, A. / Freuler, F. / Galimberti, I. / Guibourdenche, C. / Haenni, S. / Holzinger, S. / ...Authors: Kallen, J. / Bergsdorf, C. / Arnaud, B. / Bernhard, M. / Brichet, M. / Cobos-Correa, A. / Elhajouji, A. / Freuler, F. / Galimberti, I. / Guibourdenche, C. / Haenni, S. / Holzinger, S. / Hunziker, J. / Izaac, A. / Kaufmann, M. / Leder, L. / Martus, H.J. / von Matt, P. / Polyakov, V. / Roethlisberger, P. / Roma, G. / Stiefl, N. / Uteng, M. / Lerchner, A.
History
DepositionMar 12, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 18, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 12, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Sep 26, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 3, 2018Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_CC_half / _reflns.pdbx_Rpim_I_all ..._reflns.pdbx_CC_half / _reflns.pdbx_Rpim_I_all / _reflns_shell.pdbx_CC_half / _reflns_shell.pdbx_Rpim_I_all
Revision 1.4Jan 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

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Assembly

Deposited unit
A: Dual specificity protein kinase CLK4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3295
Polymers39,6911
Non-polymers6384
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area450 Å2
ΔGint-30 kcal/mol
Surface area16100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.335, 66.335, 190.684
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Dual specificity protein kinase CLK4 / CDC-like kinase 4


Mass: 39691.496 Da / Num. of mol.: 1 / Fragment: kinase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLK4 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q9HAZ1, dual-specificity kinase
#2: Chemical ChemComp-3NG / 5-[(3-chlorophenyl)amino]benzo[c][2,6]naphthyridine-8-carboxylic acid


Mass: 349.770 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H12ClN3O2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 2.64 Å3/Da / Density % sol: 53.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 30% Pentaerythritol ethoxylate (15/4 EO/OH),0.05M Ammonium Sulfate, 0.05M TRIS

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 5, 2016
RadiationMonochromator: SI 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.46→19.36 Å / Num. obs: 16267 / % possible obs: 99.6 % / Redundancy: 12.9 % / Biso Wilson estimate: 55.7 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.084 / Rrim(I) all: 0.087 / Net I/σ(I): 23.9
Reflection shellResolution: 2.46→2.52 Å / Redundancy: 13.3 % / Rmerge(I) obs: 0.889 / Mean I/σ(I) obs: 3.4 / CC1/2: 0.895 / Rrim(I) all: 0.924 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FYL

6fyl


Resolution: 2.46→19.36 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.952 / SU B: 7.581 / SU ML: 0.171 / SU R Cruickshank DPI: 0.4361 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.436 / ESU R Free: 0.242
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2234 811 5 %RANDOM
Rwork0.203 ---
obs0.2041 15395 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 144.38 Å2 / Biso mean: 59.556 Å2 / Biso min: 29.36 Å2
Baniso -1Baniso -2Baniso -3
1-1.46 Å20 Å20 Å2
2--1.46 Å20 Å2
3----2.92 Å2
Refinement stepCycle: final / Resolution: 2.46→19.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2727 0 40 92 2859
Biso mean--61.73 54.66 -
Num. residues----329
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0212851
X-RAY DIFFRACTIONr_angle_refined_deg0.951.953859
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2535333
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.02523.467150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.65115501
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3371521
X-RAY DIFFRACTIONr_chiral_restr0.0690.2408
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212180
LS refinement shellResolution: 2.46→2.523 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 57 -
Rwork0.277 1086 -
all-1143 -
obs--100 %

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