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- PDB-6yty: CLK3 A319V mutant bound with benzothiazole Tg003 (Cpd 2) -

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Basic information

Entry
Database: PDB / ID: 6yty
TitleCLK3 A319V mutant bound with benzothiazole Tg003 (Cpd 2)
ComponentsDual specificity protein kinase CLK3
KeywordsTRANSFERASE / Inhibitor / Complex / CLK3 / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


dual-specificity kinase / intermediate filament cytoskeleton / regulation of RNA splicing / protein serine/threonine/tyrosine kinase activity / acrosomal vesicle / protein tyrosine kinase activity / protein phosphorylation / nuclear speck / protein serine kinase activity / protein serine/threonine kinase activity ...dual-specificity kinase / intermediate filament cytoskeleton / regulation of RNA splicing / protein serine/threonine/tyrosine kinase activity / acrosomal vesicle / protein tyrosine kinase activity / protein phosphorylation / nuclear speck / protein serine kinase activity / protein serine/threonine kinase activity / RNA binding / nucleoplasm / ATP binding / identical protein binding / nucleus / membrane
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-EAE / Dual specificity protein kinase CLK3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsSchroeder, M. / Chaikuad, A. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: J.Med.Chem. / Year: 2020
Title: DFG-1 Residue Controls Inhibitor Binding Mode and Affinity, Providing a Basis for Rational Design of Kinase Inhibitor Selectivity.
Authors: Schroder, M. / Bullock, A.N. / Fedorov, O. / Bracher, F. / Chaikuad, A. / Knapp, S.
History
DepositionApr 24, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 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 CLK3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6583
Polymers42,3461
Non-polymers3112
Water3,351186
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint4 kcal/mol
Surface area16650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.468, 44.949, 106.359
Angle α, β, γ (deg.)90.000, 110.540, 90.000
Int Tables number5
Space group name H-MI121

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Components

#1: Protein Dual specificity protein kinase CLK3 / CDC-like kinase 3


Mass: 42346.465 Da / Num. of mol.: 1 / Mutation: A319V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLK3 / Production host: Escherichia coli (E. coli) / References: UniProt: P49761, dual-specificity kinase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-EAE / (1~{Z})-1-(3-ethyl-5-methoxy-1,3-benzothiazol-2-ylidene)propan-2-one


Mass: 249.329 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H15NO2S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 2.21 Å3/Da / Density % sol: 44.24 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 17% PEG 3350, 0,2M NaBr, 10% Ethylene Glycol, 0.1M bis-tris propane

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Sep 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.76→53.1 Å / Num. obs: 36800 / % possible obs: 99.9 % / Redundancy: 5.2 % / CC1/2: 0.995 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.046 / Rrim(I) all: 0.107 / Net I/σ(I): 10.7
Reflection shell

Diffraction-ID: 1 / Redundancy: 5.3 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.76-1.80.5531122421040.7930.2580.6123.199.8
8.98-53.10.08616233050.9890.0410.09723.699.6

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2eu9

2eu9


Resolution: 1.76→53.1 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.924 / SU B: 5.237 / SU ML: 0.086 / SU R Cruickshank DPI: 0.1244 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.124 / ESU R Free: 0.12
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2235 1790 4.9 %RANDOM
Rwork0.1864 ---
obs0.1881 35007 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 55.8 Å2 / Biso mean: 15.915 Å2 / Biso min: 6.73 Å2
Baniso -1Baniso -2Baniso -3
1--0.44 Å20 Å2-0.7 Å2
2--0.19 Å20 Å2
3---0.61 Å2
Refinement stepCycle: final / Resolution: 1.76→53.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2869 0 21 186 3076
Biso mean--16.2 19.69 -
Num. residues----353
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0133019
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172712
X-RAY DIFFRACTIONr_angle_refined_deg1.6921.6434087
X-RAY DIFFRACTIONr_angle_other_deg1.4581.5786278
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6575363
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.92621.758182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.88415519
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7161523
X-RAY DIFFRACTIONr_chiral_restr0.090.2372
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023474
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02687
LS refinement shellResolution: 1.762→1.808 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 130 -
Rwork0.219 2601 -
all-2731 -
obs--99.64 %
Refinement TLS params.Method: refined / Origin x: -14.0257 Å / Origin y: 33.4355 Å / Origin z: 95.5061 Å
111213212223313233
T0.01 Å2-0.0002 Å2-0.0047 Å2-0.0032 Å20.002 Å2--0.0077 Å2
L1.3242 °20.0961 °2-0.3889 °2-0.8542 °2-0.039 °2--0.6194 °2
S0.0079 Å °0.0124 Å °0.0772 Å °0.0259 Å °-0.01 Å °-0.0031 Å °-0.021 Å °0.0337 Å °0.0021 Å °

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