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- PDB-29mp: Crystal structure of human CLK3 in complex with RNAZ88 -

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Basic information

Entry
Database: PDB / ID: 29mp
TitleCrystal structure of human CLK3 in complex with RNAZ88
ComponentsDual specificity protein kinase CLK3
KeywordsTRANSFERASE / CLK3 / Bosutinib / Macrocycle / Kinase / Inhibitor
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 / membrane / identical protein binding / nucleus
Similarity search - Function
: / 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
Similarity search - Domain/homology
: / Dual specificity protein kinase CLK3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsZerva, A. / Raig, N. / Hanke, T. / Knapp, S. / Kraemer, A. / Structural Genomics Consortium (SGC)
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Innovative Medicines Initiative875510 Switzerland
CitationJournal: To Be Published
Title: Crystal structure of human CLK3 in complex with RNAZ88
Authors: Zerva, A. / Raig, N.D. / Knapp, S. / Kraemer, A. / Structural Genomics Consortium (SGC)
History
DepositionMar 23, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dual specificity protein kinase CLK3
D: Dual specificity protein kinase CLK3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,4885
Polymers84,6372
Non-polymers8513
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area630 Å2
ΔGint-17 kcal/mol
Surface area30920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.933, 57.277, 73.783
Angle α, β, γ (deg.)93.81, 103.74, 110.64
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 42318.414 Da / Num. of mol.: 2
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-A1J3B / 1^{7}-methoxy-4,7,10-trioxa-2-aza-1(4,6)-quinolina-3(1,2)-benzenacyclodecaphane-1^{3}-carbonitrile


Mass: 377.393 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H19N3O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.01 Å3/Da / Density % sol: 38.85 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20% PEG3350 0.1M bis-tris propane 0.2 Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.95374 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Oct 7, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95374 Å / Relative weight: 1
ReflectionResolution: 2.5→52.92 Å / Num. obs: 22505 / % possible obs: 98.1 % / Redundancy: 3.6 % / CC1/2: 0.991 / Net I/σ(I): 7.2
Reflection shellResolution: 2.5→2.6 Å / Num. unique obs: 2503 / CC1/2: 0.688

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
Aimlessdata scaling
DIALSdata reduction
MOLREPphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→52.92 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.894 / SU B: 15.023 / SU ML: 0.318 / Cross valid method: THROUGHOUT / ESU R Free: 0.353 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27228 1090 4.9 %RANDOM
Rwork0.22158 ---
obs0.22414 21280 98.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48 Å2
Baniso -1Baniso -2Baniso -3
1--2.7 Å21.26 Å21.24 Å2
2--0.27 Å20.03 Å2
3---0.5 Å2
Refinement stepCycle: 1 / Resolution: 2.5→52.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5401 0 61 7 5469
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0125616
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165095
X-RAY DIFFRACTIONr_angle_refined_deg1.4371.837607
X-RAY DIFFRACTIONr_angle_other_deg0.4921.76511683
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9195671
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.553536
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.20210892
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0660.2814
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026741
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021359
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_it3.9225.0222699
X-RAY DIFFRACTIONr_mcbond_other3.9155.0212699
X-RAY DIFFRACTIONr_mcangle_it6.19.0153365
X-RAY DIFFRACTIONr_mcangle_other6.0999.0163366
X-RAY DIFFRACTIONr_scbond_it3.9745.1682917
X-RAY DIFFRACTIONr_scbond_other3.9735.1682918
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.2439.3814243
X-RAY DIFFRACTIONr_long_range_B_refined8.60154.186270
X-RAY DIFFRACTIONr_long_range_B_other8.654.176271
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 80 -
Rwork0.305 1534 -
obs--97.29 %

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