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- PDB-9ez3: Crystal structure of human CLK3 bound to RN129 -

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Basic information

Entry
Database: PDB / ID: 9ez3
TitleCrystal structure of human CLK3 bound to RN129
ComponentsDual specificity protein kinase CLK3
KeywordsTRANSFERASE / CLK3 / Kinase / Inhibitor / TYPII
Function / homology
Function and homology information


intermediate filament cytoskeleton / dual-specificity kinase / 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 ...intermediate filament cytoskeleton / dual-specificity kinase / 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 / nucleus / membrane
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: 2.7 Å
AuthorsKraemer, A. / Raig, N. / Knapp, S.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Innovative Medicines Initiative875510 Switzerland
CitationJournal: To Be Published
Title: Crystal structure of human CLK3 bound to RN129
Authors: Kraemer, A. / Raig, N. / Knapp, S.
History
DepositionApr 10, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2024Provider: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0984
Polymers42,3181
Non-polymers7803
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area350 Å2
ΔGint-26 kcal/mol
Surface area16020 Å2
Unit cell
Length a, b, c (Å)74.587, 74.587, 97.035
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

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


Mass: 42318.414 Da / Num. of mol.: 1
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.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-A1H74 / 1-(5-~{tert}-butyl-2-quinolin-6-yl-pyrazol-3-yl)-3-[3-(4-morpholin-4-yl-7~{H}-pyrrolo[2,3-d]pyrimidin-5-yl)phenyl]urea


Mass: 587.674 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H33N9O2 / Feature type: SUBJECT OF INVESTIGATION
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: 3.19 Å3/Da / Density % sol: 61.43 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 15% PEG 6k 0.1M bicine 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99999 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 3, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 2.7→48.52 Å / Num. obs: 14673 / % possible obs: 100 % / Redundancy: 14 % / CC1/2: 0.999 / Net I/σ(I): 17.4
Reflection shellResolution: 2.7→2.83 Å / Num. unique obs: 1953 / CC1/2: 0.76

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→46.38 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.893 / SU B: 25.856 / SU ML: 0.247 / Cross valid method: THROUGHOUT / ESU R: 0.489 / ESU R Free: 0.32 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26833 650 4.4 %RANDOM
Rwork0.20307 ---
obs0.20583 13999 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 76.141 Å2
Baniso -1Baniso -2Baniso -3
1--1.56 Å20 Å2-0 Å2
2---1.56 Å20 Å2
3---3.11 Å2
Refinement stepCycle: 1 / Resolution: 2.7→46.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2580 0 54 0 2634
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0122714
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162410
X-RAY DIFFRACTIONr_angle_refined_deg1.3521.6513693
X-RAY DIFFRACTIONr_angle_other_deg0.451.5955502
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2875333
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.72513
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.44410391
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0610.2400
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023401
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02649
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_it4.6555.8061338
X-RAY DIFFRACTIONr_mcbond_other4.655.8071338
X-RAY DIFFRACTIONr_mcangle_it7.00410.4321670
X-RAY DIFFRACTIONr_mcangle_other7.00210.4351670
X-RAY DIFFRACTIONr_scbond_it5.0815.8271376
X-RAY DIFFRACTIONr_scbond_other4.8225.8381369
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.4110.6112012
X-RAY DIFFRACTIONr_long_range_B_refined10.01253.993012
X-RAY DIFFRACTIONr_long_range_B_other10.01153.993013
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.425 56 -
Rwork0.319 1037 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -21.6739 Å / Origin y: 23.6109 Å / Origin z: 0.4503 Å
111213212223313233
T0.1106 Å20.0584 Å2-0.0349 Å2-0.0854 Å2-0.0521 Å2--0.0738 Å2
L1.7828 °20.3258 °2-0.4994 °2-3.1695 °2-0.7738 °2--3.8621 °2
S0.0306 Å °-0.0044 Å °-0.1461 Å °0.4323 Å °0.1414 Å °0.0824 Å °0.153 Å °-0.0983 Å °-0.1719 Å °

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