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Yorodumi- PDB-6yky: Biochemical, Cellular and Structural Characterization of Novel ER... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6yky | ||||||
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Title | Biochemical, Cellular and Structural Characterization of Novel ERK3 Inhibitors | ||||||
Components | Mitogen-activated protein kinase 6 | ||||||
Keywords | TRANSFERASE / Mitogen-activated protein kinase 6 | ||||||
Function / homology | Function and homology information septin cytoskeleton / positive regulation of dendritic spine development / MAP kinase activity / mitogen-activated protein kinase / MAPK6/MAPK4 signaling / intracellular signal transduction / cell cycle / protein heterodimerization activity / protein phosphorylation / protein serine kinase activity ...septin cytoskeleton / positive regulation of dendritic spine development / MAP kinase activity / mitogen-activated protein kinase / MAPK6/MAPK4 signaling / intracellular signal transduction / cell cycle / protein heterodimerization activity / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / protein kinase binding / signal transduction / protein-containing complex / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 Å | ||||||
Authors | Graedler, U. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2020 Title: Biochemical, cellular and structural characterization of novel and selective ERK3 inhibitors. Authors: Gradler, U. / Busch, M. / Leuthner, B. / Raba, M. / Burgdorf, L. / Lehmann, M. / Linde, N. / Esdar, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6yky.cif.gz | 476.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6yky.ent.gz | 395.3 KB | Display | PDB format |
PDBx/mmJSON format | 6yky.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yk/6yky ftp://data.pdbj.org/pub/pdb/validation_reports/yk/6yky | HTTPS FTP |
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-Related structure data
Related structure data | 6ylcC 6yllC 2i6l 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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Unit cell |
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-Components
#1: Protein | Mass: 36193.672 Da / Num. of mol.: 4 / Mutation: L290V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MAPK6, ERK3, PRKM6 / Production host: Escherichia coli (E. coli) References: UniProt: Q16659, mitogen-activated protein kinase #2: Chemical | ChemComp-OWQ / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.67 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 100 mM Bis-Tris (pH 6), 100 mM Lithium acetate, 18%v/v Sokalan CP42, 3%vv Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.966 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 25, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.966 Å / Relative weight: 1 |
Reflection | Resolution: 2.52→65.9 Å / Num. obs: 36937 / % possible obs: 92.8 % / Redundancy: 4.1 % / Biso Wilson estimate: 74.12 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.051 / Rrim(I) all: 0.109 / Rsym value: 0.088 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 2.52→2.56 Å / Redundancy: 3.6 % / Rmerge(I) obs: 1.056 / Mean I/σ(I) obs: 2 / Num. unique obs: 103 / CC1/2: 0.53 / Rpim(I) all: 0.646 / Rrim(I) all: 1.243 / % possible all: 4.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2I6L 2i6l Resolution: 2.52→48.08 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.903 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.336
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Displacement parameters | Biso max: 174.05 Å2 / Biso mean: 70 Å2 / Biso min: 24.28 Å2
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Refine analyze | Luzzati coordinate error obs: 0.34 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.52→48.08 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.52→2.63 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
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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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