+Open data
-Basic information
Entry | Database: PDB / ID: 4ual | ||||||
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Title | MRCK beta in complex with BDP00005290 | ||||||
Components | Serine/threonine-protein kinase MRCK beta | ||||||
Keywords | TRANSFERASE / myotonic dystrophy kinase-related CDC42-binding kinase / metastasis / cell invasion | ||||||
Function / homology | Function and homology information actomyosin / actomyosin structure organization / establishment or maintenance of cell polarity / cell leading edge / RHOJ GTPase cycle / RHOQ GTPase cycle / CDC42 GTPase cycle / cytoskeleton organization / small GTPase binding / cell-cell junction ...actomyosin / actomyosin structure organization / establishment or maintenance of cell polarity / cell leading edge / RHOJ GTPase cycle / RHOQ GTPase cycle / CDC42 GTPase cycle / cytoskeleton organization / small GTPase binding / cell-cell junction / cell migration / lamellipodium / actin cytoskeleton organization / cytoskeleton / non-specific serine/threonine protein kinase / protein kinase activity / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / protein-containing complex binding / magnesium ion binding / signal transduction / extracellular exosome / ATP binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å | ||||||
Authors | Schuettelkopf, A.W. | ||||||
Citation | Journal: Cell Commun. Signal / Year: 2014 Title: A novel small-molecule MRCK inhibitor blocks cancer cell invasion. Authors: Unbekandt, M. / Croft, D.R. / Crighton, D. / Mezna, M. / McArthur, D. / McConnell, P. / Schuttelkopf, A.W. / Belshaw, S. / Pannifer, A. / Sime, M. / Bower, J. / Drysdale, M. / Olson, M.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ual.cif.gz | 182.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ual.ent.gz | 143.2 KB | Display | PDB format |
PDBx/mmJSON format | 4ual.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ual_validation.pdf.gz | 813.2 KB | Display | wwPDB validaton report |
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Full document | 4ual_full_validation.pdf.gz | 818.9 KB | Display | |
Data in XML | 4ual_validation.xml.gz | 19.4 KB | Display | |
Data in CIF | 4ual_validation.cif.gz | 27.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ua/4ual ftp://data.pdbj.org/pub/pdb/validation_reports/ua/4ual | HTTPS FTP |
-Related structure data
Related structure data | 4uakC 3tkuS 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
#1: Protein | Mass: 48023.367 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CDC42BPB, KIAA1124 / Production host: Escherichia coli (E. coli) References: UniProt: Q9Y5S2, non-specific serine/threonine protein kinase | ||||
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#2: Chemical | ChemComp-3FV / | ||||
#3: Chemical | #4: Chemical | ChemComp-EDO / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 12-18% PEG 3350, 100mM ammonium sulphate, 100mM sodium potassium tartrate, 100mM bis-tris pH 5.6 PH range: 5.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.969 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 16, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.969 Å / Relative weight: 1 |
Reflection | Resolution: 1.71→43.51 Å / Num. all: 46470 / Num. obs: 46470 / % possible obs: 98 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 1.71→1.75 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.571 / Mean I/σ(I) obs: 2.1 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3TKU Resolution: 1.71→43.51 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.47 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.71→43.51 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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