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- PDB-5my8: Crystal structure of SRPK1 in complex with SPHINX31 -

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Basic information

Entry
Database: PDB / ID: 5my8
TitleCrystal structure of SRPK1 in complex with SPHINX31
ComponentsSRSF protein kinase 1,SRSF protein kinase 1
KeywordsTRANSFERASE / splicing kinase / inhibitor / Structural Genomics / Structural Genomics Consortium / SGC
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 / 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
: / 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
CITRIC ACID / SPHINX31 / SRSF protein kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsChaikuad, A. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: ACS Chem. Biol. / Year: 2017
Title: Development of Potent, Selective SRPK1 Inhibitors as Potential Topical Therapeutics for Neovascular Eye Disease.
Authors: Batson, J. / Toop, H.D. / Redondo, C. / Babaei-Jadidi, R. / Chaikuad, A. / Wearmouth, S.F. / Gibbons, B. / Allen, C. / Tallant, C. / Zhang, J. / Du, C. / Hancox, J.C. / Hawtrey, T. / Da ...Authors: Batson, J. / Toop, H.D. / Redondo, C. / Babaei-Jadidi, R. / Chaikuad, A. / Wearmouth, S.F. / Gibbons, B. / Allen, C. / Tallant, C. / Zhang, J. / Du, C. / Hancox, J.C. / Hawtrey, T. / Da Rocha, J. / Griffith, R. / Knapp, S. / Bates, D.O. / Morris, J.C.
History
DepositionJan 25, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 10, 2017Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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,SRSF protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,71125
Polymers43,6001
Non-polymers2,11124
Water7,134396
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint53 kcal/mol
Surface area17690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.883, 74.883, 310.129
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-701-

CIT

21A-1188-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 43600.113 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SRPK1 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): R3-pRARE2
References: UniProt: Q96SB4, non-specific serine/threonine protein kinase

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Non-polymers , 6 types, 420 molecules

#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / 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.: 20 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-RXZ / SPHINX31


Mass: 507.507 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H24F3N5O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 396 / 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: 2.88 Å3/Da / Density % sol: 57.27 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 22% broad-molecular-weight PEG smears (BMW PEG smears) and 0.1 M citrate, pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.7→28.74 Å / Num. obs: 57614 / % possible obs: 99.2 % / Redundancy: 7.6 % / Biso Wilson estimate: 20.9 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 14.2
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.799 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 8123 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→28.74 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.958 / SU B: 3.621 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.084 / ESU R Free: 0.088 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2002 2893 5 %RANDOM
Rwork0.16414 ---
obs0.16585 54679 99.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 32.393 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20.12 Å20 Å2
2--0.25 Å20 Å2
3----0.8 Å2
Refine analyzeLuzzati coordinate error obs: 0.213 Å
Refinement stepCycle: 1 / Resolution: 1.7→28.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2874 0 140 396 3410
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0193181
X-RAY DIFFRACTIONr_bond_other_d0.0020.023112
X-RAY DIFFRACTIONr_angle_refined_deg1.6481.9634287
X-RAY DIFFRACTIONr_angle_other_deg0.93537168
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8935381
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.91824.113141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.35515555
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.3841516
X-RAY DIFFRACTIONr_chiral_restr0.1090.2465
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023604
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02722
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_it1.5512.0321459
X-RAY DIFFRACTIONr_mcbond_other1.5512.0321460
X-RAY DIFFRACTIONr_mcangle_it2.4573.0321829
X-RAY DIFFRACTIONr_mcangle_other2.4583.0321829
X-RAY DIFFRACTIONr_scbond_it2.3152.4861722
X-RAY DIFFRACTIONr_scbond_other2.3142.4871723
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.683.5072447
X-RAY DIFFRACTIONr_long_range_B_refined8.18319.1793934
X-RAY DIFFRACTIONr_long_range_B_other8.18619.173932
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 218 -
Rwork0.251 3892 -
obs--98.56 %
Refinement TLS params.Method: refined / Origin x: 19.678 Å / Origin y: 46.597 Å / Origin z: 19.865 Å
111213212223313233
T0.094 Å2-0.0679 Å20.0139 Å2-0.0629 Å2-0.0064 Å2--0.014 Å2
L0.2655 °2-0.2062 °2-0.1204 °2-0.6193 °20.2749 °2--0.8355 °2
S0.0182 Å °0.0332 Å °0.0007 Å °0.0219 Å °-0.0974 Å °0.0038 Å °-0.065 Å °0.0365 Å °0.0792 Å °

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