+Open data
-Basic information
Entry | Database: PDB / ID: 5myv | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of SRPK2 in complex with compound 1 | ||||||
Components | SRSF protein kinase 2,SRSF protein kinase 2 | ||||||
Keywords | TRANSFERASE / kinase / splicing kinase / inhibitor / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information nuclear speck organization / R-loop processing / 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 cell cycle / positive regulation of viral genome replication / 14-3-3 protein binding ...nuclear speck organization / R-loop processing / 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 cell cycle / positive regulation of viral genome replication / 14-3-3 protein binding / RNA splicing / positive regulation of neuron apoptotic process / peptidyl-serine phosphorylation / angiogenesis / cell differentiation / non-specific serine/threonine protein kinase / intracellular signal transduction / nuclear speck / protein phosphorylation / innate immune response / protein serine kinase activity / protein serine/threonine kinase activity / positive regulation of cell population proliferation / positive regulation of gene expression / chromatin / nucleolus / magnesium ion binding / RNA binding / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Chaikuad, A. / Pike, A.C.W. / Savitsky, P. / von Delft, F. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5myv.cif.gz | 586.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5myv.ent.gz | 493 KB | Display | PDB format |
PDBx/mmJSON format | 5myv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5myv_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5myv_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 5myv_validation.xml.gz | 48.8 KB | Display | |
Data in CIF | 5myv_validation.cif.gz | 66.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/my/5myv ftp://data.pdbj.org/pub/pdb/validation_reports/my/5myv | HTTPS FTP |
-Related structure data
Related structure data | 5mxxC 5my8C 2x7gS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
2 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
4 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components on special symmetry positions |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: TYR / Beg label comp-ID: TYR / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _ / Auth seq-ID: 79 - 699 / Label seq-ID: 20 - 389
NCS ensembles :
|
-Components
#1: Protein | Mass: 44300.676 Da / Num. of mol.: 4 / Fragment: UNP Residues 51-256,UNP Residues 508-688 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SRPK2 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): R3-pRARE2 References: UniProt: P78362, non-specific serine/threonine protein kinase #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-W4A / #4: Chemical | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.87 Å3/Da / Density % sol: 74.72 % |
---|---|
Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 5.25 / Details: 1.0 M ammonium sulfate and 0.1 M acetate pH 5.25 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 18, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→29.87 Å / Num. obs: 75969 / % possible obs: 99.3 % / Redundancy: 5.8 % / Biso Wilson estimate: 63.7 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.138 / Net I/σ(I): 9.5 |
Reflection shell | Redundancy: 6.1 % / Rmerge(I) obs: 0.957 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 11061 / CC1/2: 0.84 / % possible all: 99.8 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb id 2X7G Resolution: 2.9→29.87 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.933 / SU B: 27.56 / SU ML: 0.231 / Cross valid method: THROUGHOUT / ESU R: 0.404 / ESU R Free: 0.259 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 79.094 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.9→29.87 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|