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- PDB-5xv7: SRPK1 in complex with Alectinib -

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Basic information

Entry
Database: PDB / ID: 5xv7
TitleSRPK1 in complex with Alectinib
Componentsserine-arginine (SR) protein kinase 1
KeywordsTRANSFERASE/INHIBITOR / SRPK1 / Alectinib / SRPKIN-1 / 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 / 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 / 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. ...: / 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 / Alpha Beta
Similarity search - Domain/homology
Chem-EMH / SRSF protein kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsZeng, C. / Ngo, J.C.K.
CitationJournal: Cell Chem Biol / Year: 2018
Title: SRPKIN-1: A Covalent SRPK1/2 Inhibitor that Potently Converts VEGF from Pro-angiogenic to Anti-angiogenic Isoform
Authors: Hatcher, J.M. / Wu, G. / Zeng, C. / Zhu, J. / Meng, F. / Patel, S. / Wang, W. / Ficarro, S.B. / Leggett, A.L. / Powell, C.E. / Marto, J.A. / Zhang, K. / Ki Ngo, J.C. / Fu, X.D. / Zhang, T. / Gray, N.S.
History
DepositionJun 26, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1May 2, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 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

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Assembly

Deposited unit
A: serine-arginine (SR) protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1586
Polymers42,4271
Non-polymers7315
Water59433
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area770 Å2
ΔGint11 kcal/mol
Surface area16990 Å2
Unit cell
Length a, b, c (Å)74.767, 74.767, 310.687
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 serine-arginine (SR) protein kinase 1


Mass: 42426.840 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q96SB4*PLUS
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-EMH / 9-ethyl-6,6-dimethyl-8-[4-(morpholin-4-yl)piperidin-1-yl]-11-oxo-6,11-dihydro-5H-benzo[b]carbazole-3-carbonitrile


Mass: 482.617 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H34N4O2 / Comment: medication, anticancer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.95 Å3/Da / Density % sol: 58.37 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 11% PEG 4000 100mM sodium citrate (pH 5.6) 200mM ammonium acetate

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 30, 2016
Details: Vertically Collimating Premirror, LN2-Cooled Fixed-Exit Double Crystal Si(111) Monochromator , Toroidal Focusing Mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.32→63.39 Å / Num. obs: 316057 / % possible obs: 99.1 % / Redundancy: 13.6 % / Net I/σ(I): 33.67

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
Blu-Icedata collection
HKL-2000data processing
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WAK

1wak


Resolution: 2.32→63.39 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.925 / SU B: 11.98 / SU ML: 0.147 / Cross valid method: THROUGHOUT / ESU R: 0.267 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23797 1195 5.1 %RANDOM
Rwork0.21211 ---
obs0.21345 22080 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.743 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20.01 Å20 Å2
2--0.03 Å20 Å2
3----0.09 Å2
Refinement stepCycle: 1 / Resolution: 2.32→63.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2849 0 52 33 2934
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192973
X-RAY DIFFRACTIONr_bond_other_d0.0070.022899
X-RAY DIFFRACTIONr_angle_refined_deg1.3951.9714024
X-RAY DIFFRACTIONr_angle_other_deg0.8983.0066676
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7595348
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.31924.135133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.6915529
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.911514
X-RAY DIFFRACTIONr_chiral_restr0.0750.2440
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213245
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02670
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_it1.9133.2831398
X-RAY DIFFRACTIONr_mcbond_other1.9113.2821397
X-RAY DIFFRACTIONr_mcangle_it3.0464.9091744
X-RAY DIFFRACTIONr_mcangle_other3.0454.911745
X-RAY DIFFRACTIONr_scbond_it2.6743.7081575
X-RAY DIFFRACTIONr_scbond_other2.6733.7081576
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4355.3872281
X-RAY DIFFRACTIONr_long_range_B_refined6.0926.6143369
X-RAY DIFFRACTIONr_long_range_B_other6.08926.6173370
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.321→2.381 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 82 -
Rwork0.238 1589 -
obs--99.94 %
Refinement TLS params.Method: refined / Origin x: 92.6736 Å / Origin y: 17.9198 Å / Origin z: 330.3957 Å
111213212223313233
T0.0649 Å2-0.0445 Å2-0.0116 Å2-0.0588 Å2-0.0005 Å2--0.0368 Å2
L0.0542 °2-0.1066 °20.0764 °2-0.3613 °2-0.2025 °2--0.6511 °2
S-0.0038 Å °0.0306 Å °0.0067 Å °0.0023 Å °-0.1017 Å °0.0174 Å °0.0547 Å °0.0065 Å °0.1055 Å °

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