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Yorodumi- PDB-5mxx: Crystal structure of human SR protein kinase 1 (SRPK1) in complex... -
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-Basic information
Entry | Database: PDB / ID: 5mxx | ||||||
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Title | Crystal structure of human SR protein kinase 1 (SRPK1) in complex with compound 1 | ||||||
Components | SRPK1 | ||||||
Keywords | SPLICING / phosphorylation / 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 / Replacement of protamines by nucleosomes in the male pronucleus / positive regulation of viral genome replication / 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 / Replacement of protamines by nucleosomes in the male pronucleus / positive regulation of viral genome replication / RNA splicing / chromosome segregation / nuclear matrix / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / nuclear speck / protein phosphorylation / protein serine kinase activity / innate immune response / protein serine/threonine kinase activity / chromatin / magnesium ion binding / endoplasmic reticulum / RNA binding / nucleoplasm / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Tallant, C. / Redondo, C. / Batson, J. / Toop, H.D. / Babaebi-Jadidib, R. / Savitsky, P. / Elkins, J.M. / Newman, J.A. / Burgess-Brown, N. / von Delft, F. ...Tallant, C. / Redondo, C. / Batson, J. / Toop, H.D. / Babaebi-Jadidib, R. / Savitsky, P. / Elkins, J.M. / Newman, J.A. / Burgess-Brown, N. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Bates, D.O. / Morris, J.C. / Knapp, S. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5mxx.cif.gz | 99.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mxx.ent.gz | 72.5 KB | Display | PDB format |
PDBx/mmJSON format | 5mxx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mx/5mxx ftp://data.pdbj.org/pub/pdb/validation_reports/mx/5mxx | HTTPS FTP |
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-Related structure data
Related structure data | 5my8C 5myvC 1wakS 1wbpS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 45431.816 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96SB4*PLUS |
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-Non-polymers , 5 types, 234 molecules
#2: Chemical | ChemComp-W4A / | ||||||
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#3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-CA / #5: Chemical | ChemComp-TRS / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 51.11 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M tris pH 7.5, 0.1 M CaCl2, 20% PEG6K, 11% ethylene glycol PH range: 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 12, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→29.29 Å / Num. obs: 47639 / % possible obs: 99.8 % / Redundancy: 14.2 % / Biso Wilson estimate: 21.5 Å2 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.023 / Net I/σ(I): 28.4 |
Reflection shell | Resolution: 1.75→1.78 Å / Redundancy: 13.8 % / Rmerge(I) obs: 0.826 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 2468 / Rpim(I) all: 0.323 / % possible all: 96 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1wak, 1wbp Resolution: 1.75→29.29 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.912 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.098 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.591 Å2
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Refinement step | Cycle: 1 / Resolution: 1.75→29.29 Å
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Refine LS restraints |
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