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- PDB-2wu6: Crystal Structure of the Human CLK3 in complex with DKI -

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Basic information

Entry
Database: PDB / ID: 2wu6
TitleCrystal Structure of the Human CLK3 in complex with DKI
ComponentsDUAL SPECIFICITY PROTEIN KINASE CLK3
KeywordsTRANSFERASE / KINASE / TYROSINE-PROTEIN KINASE / SERINE/THREONINE-PROTEIN KINASE / NUCLEOTIDE-BINDING
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 / nuclear speck / protein phosphorylation / 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 / nuclear speck / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / RNA binding / nucleoplasm / ATP binding / identical protein binding / membrane / nucleus
Similarity search - Function
: / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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 ...: / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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 / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-DKI / Dual specificity protein kinase CLK3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsMuniz, J.R.C. / Fedorov, O. / King, O. / Filippakopoulos, P. / Bullock, A.N. / Philips, C. / Heightman, T. / Ugochukwu, E. / von Delft, F. / Arrowsmith, C.H. ...Muniz, J.R.C. / Fedorov, O. / King, O. / Filippakopoulos, P. / Bullock, A.N. / Philips, C. / Heightman, T. / Ugochukwu, E. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. / Knapp, S.
CitationJournal: Chem.Biol / Year: 2011
Title: Specific Clk Inhibitors from a Novel Chemotype for Regulation of Alternative Splicing.
Authors: Fedorov, O. / Huber, K. / Eisenreich, A. / Filippakopoulos, P. / King, O. / Bullock, A.N. / Szklarczyk, D. / Jensen, L.J. / Fabbro, D. / Trappe, J. / Rauch, U. / Bracher, F. / Knapp, S.
History
DepositionSep 30, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 7, 2011Group: Database references / Structure summary
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)46,09315
Polymers44,7901
Non-polymers1,30314
Water5,531307
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.150, 62.330, 74.150
Angle α, β, γ (deg.)90.00, 96.04, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DUAL SPECIFICITY PROTEIN KINASE CLK3 / CDC-LIKE KINASE 3 / CDC-LIKE KINASE 3 ISOFORM HCLK3


Mass: 44790.062 Da / Num. of mol.: 1 / Fragment: RESIDUES 127-484
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: MUSCLE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)-R3 / References: UniProt: P49761, dual-specificity kinase

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Non-polymers , 6 types, 321 molecules

#2: Chemical ChemComp-DKI / 5-AMINO-3-{[4-(AMINOSULFONYL)PHENYL]AMINO}-N-(2,6-DIFLUOROPHENYL)-1H-1,2,4-TRIAZOLE-1-CARBOTHIOAMIDE / CDK 1/2 INHIBITOR


Mass: 425.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H13F2N7O2S2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 307 / 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: 2.53 Å3/Da / Density % sol: 51.4 % / Description: NONE
Crystal growDetails: 0.2M (NH4)2SO4, 0.1M BIS-TRIS PH 5.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.905
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 6, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.905 Å / Relative weight: 1
ReflectionResolution: 1.92→44.32 Å / Num. obs: 31032 / % possible obs: 97.1 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 7.3
Reflection shellResolution: 1.92→2.02 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 2 / % possible all: 96.2

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Processing

Software
NameVersionClassification
REFMAC5.5.0089refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.92→73.74 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.938 / SU B: 7.153 / SU ML: 0.095 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES RESIDUAL ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.21137 1512 5 %RANDOM
Rwork0.17 ---
obs0.17215 28646 97.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.837 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å2-0.62 Å2
2---0.06 Å20 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.92→73.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2859 0 74 307 3240
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0213060
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4491.9514135
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4965355
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.11123.333156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.93815524
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.131521
X-RAY DIFFRACTIONr_chiral_restr0.110.2435
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212336
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.8641.51770
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.5722869
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.731290
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.2494.51266
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.92→1.97 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 109 -
Rwork0.275 2071 -
obs--96.08 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.71170.19850.47460.05450.22462.086-0.07280.0613-0.06330.0134-0.03410.0006-0.21480.10210.10680.1143-0.0671-0.01470.08130.0190.035247.70254.08916.934
20.8936-0.1114-0.32630.1431-0.08230.29370.01090.150.03270.0164-0.035-0.0352-0.0243-0.01150.02420.0962-0.0112-0.0070.05970.0190.051226.59752.34417.874
30.4739-0.283-0.39570.66850.26411.1949-0.06050.0892-0.00640.0571-0.03460.17540.0611-0.15510.0950.0606-0.0194-0.00430.0535-0.01120.073712.21349.45227.906
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A134 - 210
2X-RAY DIFFRACTION2A211 - 378
3X-RAY DIFFRACTION3A379 - 483

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