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- PDB-2wu7: Crystal Structure of the Human CLK3 in complex with V25 -

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Basic information

Entry
Database: PDB / ID: 2wu7
TitleCrystal Structure of the Human CLK3 in complex with V25
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 / Protein kinases ATP-binding region signature. ...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-V25 / Dual specificity protein kinase CLK3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsMuniz, J.R.C. / Fedorov, O. / King, O. / Filippakopoulos, P. / Bullock, A.N. / Phillips, C. / Heightman, T. / Ugochukwu, E. / von Delft, F. / Arrowsmith, C.H. ...Muniz, J.R.C. / Fedorov, O. / King, O. / Filippakopoulos, P. / Bullock, A.N. / Phillips, C. / Heightman, T. / Ugochukwu, E. / von Delft, F. / Arrowsmith, C.H. / Bracher, F. / Huber, K. / 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 1.1Dec 7, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Other / Refinement description / Structure summary / Version format compliance
Revision 1.2May 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)45,6799
Polymers44,7901
Non-polymers8898
Water2,936163
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)87.870, 62.200, 75.370
Angle α, β, γ (deg.)90.00, 97.97, 90.00
Int Tables number5
Space group name H-MC121

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Components

#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
#2: Chemical ChemComp-V25 / ethyl 3-[(E)-2-amino-1-cyanoethenyl]-6,7-dichloro-1-methyl-1H-indole-2-carboxylate


Mass: 338.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H13Cl2N3O2
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 2.28 Å3/Da / Density % sol: 46.17 % / 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: ROTATING ANODE / Wavelength: 1.5418
DetectorType: BRUKER / Detector: IMAGE PLATE / Date: Mar 16, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.24→37.32 Å / Num. obs: 19231 / % possible obs: 99.8 % / Observed criterion σ(I): 2.12 / Redundancy: 6.59 % / Biso Wilson estimate: 18.07 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 7.26
Reflection shellResolution: 2.24→2.29 Å / Redundancy: 4.42 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.12 / % possible all: 96.2

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Processing

Software
NameVersionClassification
BUSTER-TNT2.8.0refinement
SADABSdata reduction
SAINTdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→28.94 Å / Cor.coef. Fo:Fc: 0.9183 / Cor.coef. Fo:Fc free: 0.8632 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2456 1034 5.38 %RANDOM
Rwork0.1904 ---
obs0.1934 19231 99.8 %-
Displacement parametersBiso mean: 18.65 Å2
Baniso -1Baniso -2Baniso -3
1--1.1476 Å20 Å2-4.1909 Å2
2--1.9276 Å20 Å2
3----0.78 Å2
Refine analyzeLuzzati coordinate error obs: 0.272 Å
Refinement stepCycle: LAST / Resolution: 2.25→28.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2816 0 49 163 3028
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012953HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.074001HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1011SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes79HARMONIC2
X-RAY DIFFRACTIONt_gen_planes435HARMONIC5
X-RAY DIFFRACTIONt_it2953HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.96
X-RAY DIFFRACTIONt_other_torsion16.21
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion363SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3596SEMIHARMONIC4
LS refinement shellResolution: 2.25→2.37 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2799 133 4.77 %
Rwork0.2103 2655 -
all0.2135 2788 -
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)
11.5377-0.45940.68520.30060.30892.65120.0163-0.0522-0.03350.14830.0562-0.0425-0.23250.1244-0.07260.1014-0.0136-0.0023-0.0130.0077-0.015247.047816.203216.9894
20.52510.2714-0.466800.20310.14210.01620.113-0.0123-0.032-0.0423-0.02570.0209-0.03480.0262-0.00350.006-0.0055-0.04210.0186-0.073526.161710.390718.0682
30.5337-0.1251-0.59320.90050.20550.2578-0.0070.1019-0.01010.031-0.04490.15570.1396-0.20140.0519-0.0276-0.0197-0.0014-0.0618-0.0074-0.083310.61658.250528.6172
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESSEQ 135-196
2X-RAY DIFFRACTION2CHAIN A AND RESSEQ 197-378
3X-RAY DIFFRACTION3CHAIN A AND RESSEQ 379-482

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