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Open data
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Basic information
Entry | Database: PDB / ID: 1wbp | ||||||
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Title | SRPK1 bound to 9mer docking motif peptide | ||||||
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![]() | TRANSFERASE / SRPK / KINASE / SERINE/THREONINE-PROTEIN KINASE / ATP-BINDING / CHROMOSOME PARTITION / DIFFERENTIATION / MRNA PROCESSING / MRNA SPLICING / NUCLEAR PROTEIN / NUCLEOTIDE-BINDING / PHOSPHORYLATION | ||||||
Function / homology | ![]() protein serine/threonine kinase activity => GO:0004674 / sperm DNA condensation / positive regulation of cell-cell adhesion / regulation of mRNA processing / regulation of mRNA splicing, via spliceosome / Maturation of nucleoprotein / negative regulation of viral genome replication / spliceosomal complex assembly / alpha-actinin binding / MAP kinase activity ...protein serine/threonine kinase activity => GO:0004674 / sperm DNA condensation / positive regulation of cell-cell adhesion / regulation of mRNA processing / regulation of mRNA splicing, via spliceosome / Maturation of nucleoprotein / negative regulation of viral genome replication / spliceosomal complex assembly / alpha-actinin binding / MAP kinase activity / bicellular tight junction / positive regulation of viral genome replication / Replacement of protamines by nucleosomes in the male pronucleus / viral process / RNA splicing / cell projection / cell periphery / chromosome segregation / adherens junction / nuclear matrix / cell-cell junction / cell junction / regulation of gene expression / protein-containing complex assembly / cell surface receptor signaling pathway / non-specific serine/threonine protein kinase / cell adhesion / protein kinase activity / intracellular signal transduction / nuclear speck / protein phosphorylation / innate immune response / protein serine kinase activity / protein serine/threonine kinase activity / chromatin / nucleolus / magnesium ion binding / endoplasmic reticulum / signal transduction / RNA binding / nucleoplasm / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ngo, J.C. / Gullinsgrud, J. / Chakrabarti, S. / Nolen, B. / Aubol, B.E. / Fu, X.-D. / Adams, J.A. / McCammon, J.A. / Ghosh, G. | ||||||
![]() | ![]() Title: Interplay between Srpk and Clk/Sty Kinases in Phosphorylation of the Splicing Factor Asf/Sf2 is Regulated by a Docking Motif in Asf/Sf2 Authors: Ngo, J.C. / Chakrabarti, S. / Ding, J.-H. / Velazquez-Dones, A. / Nolen, B. / Aubol, B.E. / Adams, J.A. / Fu, X.-D. / Ghosh, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 89 KB | Display | ![]() |
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PDB format | ![]() | 66 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 466.7 KB | Display | ![]() |
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Full document | ![]() | 477.6 KB | Display | |
Data in XML | ![]() | 10.5 KB | Display | |
Data in CIF | ![]() | 15.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1wakS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Details | THE PROTEIN IS A MONOMER IN SOLUTION, BUT SINCEIN THIS ENTRY, IT IS COMPLEX WITH A PEPTIDE, THEENTRY IS BEING MARKED AS DIMERIC.FOR THE HETERO-ASSEMBLY DESCRIBED BY REMARK 350 |
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Components
#1: Protein | Mass: 45225.598 Da / Num. of mol.: 1 / Fragment: RESIDUES 42-256 AND 474-655 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q12890, UniProt: Q96SB4*PLUS, EC: 2.7.1.37 |
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#2: Protein/peptide | Mass: 1218.394 Da / Num. of mol.: 1 / Fragment: RESIDUES 1382-1390 / Source method: obtained synthetically Details: 9 MER PEPTIDE RRRERSPTR BOUND TO A GROOVE FORMED BY THE MAP KINASE INSERT, HELIX AF AND HELIX AG Source: (synth.) ![]() |
#3: Chemical | ChemComp-ACT / |
#4: Chemical | ChemComp-ADP / |
Compound details | INVOLVED IN THE REGULATORY NETWORK FOR SPLICING, CONTROLLING THE INTRANUCLEAR DISTRIBUTION OF ...INVOLVED IN THE REGULATORY |
Sequence details | PROTEIN SEQUENCE FROM NCBI (PROTEIN) ACCESSION NP_003128 |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.99 Å3/Da / Density % sol: 58.82 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7 Details: 100MM SODIUM CITRATE PH5.6, 200MM AMMONIUM ACETATE, 15%PEG3350, 5MM PEPTIDE, 5MM ADP, 10MM MGCL2, pH 7.00 | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / pH: 8.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 105 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 22, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→30 Å / Num. obs: 22765 / % possible obs: 97.8 % / Observed criterion σ(I): 1 / Redundancy: 11 % / Biso Wilson estimate: 10.9 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.9 / % possible all: 84 |
Reflection | *PLUS Num. measured all: 255743 / Rmerge(I) obs: 0.072 |
Reflection shell | *PLUS % possible obs: 84 % / Rmerge(I) obs: 0.565 / Mean I/σ(I) obs: 2.86 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1WAK Resolution: 2.4→28.26 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 384267.63 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 51.7232 Å2 / ksol: 0.319045 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 96.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→28.26 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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