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- PDB-6khe: Crystal structure of CLK2 in complex with CX-4945 -

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Basic information

Entry
Database: PDB / ID: 6khe
TitleCrystal structure of CLK2 in complex with CX-4945
ComponentsDual specificity protein kinase CLK2
KeywordsTRANSFERASE / Cdc2-like kinase / Casein kinase / CX-4945 / Alternative splicing / SPLICING
Function / homology
Function and homology information


dual-specificity kinase / response to ionizing radiation / regulation of RNA splicing / negative regulation of gluconeogenesis / protein serine/threonine/tyrosine kinase activity / protein tyrosine kinase activity / protein autophosphorylation / nuclear body / nuclear speck / protein phosphorylation ...dual-specificity kinase / response to ionizing radiation / regulation of RNA splicing / negative regulation of gluconeogenesis / protein serine/threonine/tyrosine kinase activity / protein tyrosine kinase activity / protein autophosphorylation / nuclear body / nuclear speck / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / nucleoplasm / ATP binding / identical protein 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. / Protein kinase domain ...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 CLK2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsLee, J.Y. / Yun, J.S. / Jin, H. / Chang, J.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (Korea) Korea, Republic Of
CitationJournal: Biomed Res Int / Year: 2019
Title: Structural Basis for the Selective Inhibition of Cdc2-Like Kinases by CX-4945.
Authors: Lee, J.Y. / Yun, J.S. / Kim, W.K. / Chun, H.S. / Jin, H. / Cho, S. / Chang, J.H.
History
DepositionJul 15, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 2, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 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 CLK2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,5622
Polymers60,2121
Non-polymers3501
Water61334
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area16950 Å2
Unit cell
Length a, b, c (Å)75.627, 75.627, 161.825
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 CLK2 / CDC-like kinase 2


Mass: 60212.391 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLK2 / Production host: Escherichia coli (E. coli) / References: UniProt: P49760, 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 / Feature type: SUBJECT OF INVESTIGATION / Comment: chemotherapy, inhibitor*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 1.92 Å3/Da / Density % sol: 35.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1M Bis-Tris pH 5.5, 0.2M MgCl2, 25% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 12244 / % possible obs: 100 % / Redundancy: 18.5 % / Biso Wilson estimate: 57.61 Å2 / Rmerge(I) obs: 0.189 / Rpim(I) all: 0.045 / Rrim(I) all: 0.195 / Χ2: 0.598 / Net I/σ(I): 3 / Num. measured all: 226791
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.8-2.918.61.36711900.8370.3231.4050.432100
2.9-3.0219.71.06111850.8860.2431.0890.431100
3.02-3.1519.40.68612030.9610.1580.7040.449100
3.15-3.3219.30.49611930.9710.1150.5090.474100
3.32-3.5318.80.31711870.9850.0740.3260.484100
3.53-3.817.60.2112170.9930.0510.2160.566100
3.8-4.1819.60.14912120.9970.0350.1530.628100
4.18-4.7918.90.10912300.9960.0260.1120.83299.9
4.79-6.0317.30.10512570.9960.0260.1080.752100
6.03-5016.40.07313700.9980.0180.0750.938100

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.13_2998: ???refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→40.456 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.64
RfactorNum. reflection% reflection
Rfree0.2606 1216 10 %
Rwork0.1961 --
obs0.2025 12156 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 110.37 Å2 / Biso mean: 53.4125 Å2 / Biso min: 29.62 Å2
Refinement stepCycle: final / Resolution: 2.8→40.456 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2848 0 25 34 2907
Biso mean--54.88 47.15 -
Num. residues----342
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.8001-2.91220.42441310.31611181100
2.9122-3.04470.34711320.27931189100
3.0447-3.20520.34591310.2521182100
3.2052-3.40590.27771330.23391198100
3.4059-3.66870.25911340.18561204100
3.6687-4.03760.25841350.1711210100
4.0376-4.62110.20331360.15391221100
4.6211-5.81930.22991380.1781246100
5.8193-40.4560.2421460.1888130998

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