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- PDB-4wua: Crystal structure of human SRPK1 complexed to an inhibitor SRPIN340 -

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Basic information

Entry
Database: PDB / ID: 4wua
TitleCrystal structure of human SRPK1 complexed to an inhibitor SRPIN340
ComponentsSRSF protein kinase 1, linker, SRSF protein kinase 1
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / protein kinase / kinase-inhibitor complex / pre-mRNA splicing / ATP-binding / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


sperm DNA condensation / regulation of mRNA processing / regulation of mRNA splicing, via spliceosome / Maturation of nucleoprotein / negative regulation of viral genome replication / spliceosomal complex assembly / positive regulation of viral genome replication / Replacement of protamines by nucleosomes in the male pronucleus / RNA splicing / chromosome segregation ...sperm DNA condensation / regulation of mRNA processing / regulation of mRNA splicing, via spliceosome / Maturation of nucleoprotein / negative regulation of viral genome replication / spliceosomal complex assembly / positive regulation of viral genome replication / Replacement of protamines by nucleosomes in the male pronucleus / RNA splicing / chromosome segregation / nuclear matrix / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / nuclear speck / protein phosphorylation / innate immune response / protein serine kinase activity / protein serine/threonine kinase activity / chromatin / magnesium ion binding / endoplasmic reticulum / RNA binding / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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 ...: / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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-3UL / CITRIC ACID / SRSF protein kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsHoshina, M. / Ikura, T. / Hosoya, T. / Hagiwara, M. / Ito, N.
CitationJournal: Mol.Pharmacol. / Year: 2015
Title: Identification of a Dual Inhibitor of SRPK1 and CK2 That Attenuates Pathological Angiogenesis of Macular Degeneration in Mice
Authors: Morooka, S. / Hoshina, M. / Kii, I. / Okabe, T. / Kojima, H. / Inoue, N. / Okuno, Y. / Denawa, M. / Yoshida, S. / Fukuhara, J. / Ninomiya, K. / Ikura, T. / Furuya, T. / Nagano, T. / Noda, K. ...Authors: Morooka, S. / Hoshina, M. / Kii, I. / Okabe, T. / Kojima, H. / Inoue, N. / Okuno, Y. / Denawa, M. / Yoshida, S. / Fukuhara, J. / Ninomiya, K. / Ikura, T. / Furuya, T. / Nagano, T. / Noda, K. / Ishida, S. / Hosoya, T. / Ito, N. / Yoshimura, N. / Hagiwara, M.
History
DepositionOct 31, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 16, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source ...citation / diffrn_source / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: SRSF protein kinase 1, linker, SRSF protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1813
Polymers45,6391
Non-polymers5412
Water2,036113
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area180 Å2
ΔGint1 kcal/mol
Surface area16450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.132, 75.132, 310.623
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein SRSF protein kinase 1, linker, SRSF protein kinase 1 / SFRS protein kinase 1 / Serine/arginine-rich protein-specific kinase 1 / SR-protein-specific kinase 1


Mass: 45639.066 Da / Num. of mol.: 1 / Fragment: UNP residues 213-426, UNP residues 465-826
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SRPK1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21(DE3)
References: UniProt: Q96SB4, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-3UL / N-[2-(1-piperidinyl)-5-(trifluoromethyl)phenyl]-4-pyridinecarboxamide


Mass: 349.350 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H18F3N3O
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 55.64 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1M sodium citrate, 0.2M ammonium acetate, 5%PEG6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 36614 / % possible obs: 99.5 % / Redundancy: 20.9 % / Rsym value: 0.056 / Net I/σ(I): 71.03
Reflection shellResolution: 2→2.03 Å / Redundancy: 21.5 % / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data processing
SCALEPACKdata scaling
PHASERphasing
RefinementStarting model: 1WAK

1wak


Resolution: 2→49.87 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.937 / SU B: 3.374 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.145 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23634 1840 5.1 %RANDOM
Rwork0.19661 ---
obs0.19861 34331 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.412 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å20.25 Å20 Å2
2--0.5 Å20 Å2
3----1.63 Å2
Refinement stepCycle: 1 / Resolution: 2→49.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2791 0 38 113 2942
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0192902
X-RAY DIFFRACTIONr_bond_other_d0.0010.022816
X-RAY DIFFRACTIONr_angle_refined_deg1.8481.9713933
X-RAY DIFFRACTIONr_angle_other_deg0.87236492
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8495344
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.48924.141128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.87515522
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7061514
X-RAY DIFFRACTIONr_chiral_restr0.1170.2433
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213195
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02660
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_it3.1553.3031377
X-RAY DIFFRACTIONr_mcbond_other3.1553.3031375
X-RAY DIFFRACTIONr_mcangle_it4.0774.9271717
X-RAY DIFFRACTIONr_mcangle_other4.0764.9281718
X-RAY DIFFRACTIONr_scbond_it4.1343.7941525
X-RAY DIFFRACTIONr_scbond_other4.1293.7951523
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.1285.4782215
X-RAY DIFFRACTIONr_long_range_B_refined7.58726.9023357
X-RAY DIFFRACTIONr_long_range_B_other7.57826.8393321
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.001→2.053 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 148 -
Rwork0.234 2426 -
obs--98.92 %

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