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Yorodumi- PDB-5ax3: Crystal structure of ERK2 complexed with allosteric and ATP-compe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ax3 | ||||||
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Title | Crystal structure of ERK2 complexed with allosteric and ATP-competitive inhibitors. | ||||||
Components |
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Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / ternary complex / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information RNA sequestering activity / positive regulation of metalloendopeptidase activity / PTK6 Activates STAT3 / eye photoreceptor cell differentiation / retinal rod cell differentiation / radial glial cell differentiation / cell surface receptor signaling pathway via STAT / negative regulation of primary miRNA processing / leptin-mediated signaling pathway / negative regulation of neuron migration ...RNA sequestering activity / positive regulation of metalloendopeptidase activity / PTK6 Activates STAT3 / eye photoreceptor cell differentiation / retinal rod cell differentiation / radial glial cell differentiation / cell surface receptor signaling pathway via STAT / negative regulation of primary miRNA processing / leptin-mediated signaling pathway / negative regulation of neuron migration / T-helper 17 type immune response / Signalling to STAT3 / negative regulation of inflammatory response to wounding / primary miRNA binding / POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation / response to leptin / sexual reproduction / interleukin-11-mediated signaling pathway / regulation of feeding behavior / T-helper 17 cell lineage commitment / cellular response to interleukin-17 / Transcriptional regulation of pluripotent stem cells / Interleukin-9 signaling / Interleukin-21 signaling / interleukin-9-mediated signaling pathway / MET activates STAT3 / phospho-PLA2 pathway / interleukin-2-mediated signaling pathway / Signaling by MAPK mutants / RAF-independent MAPK1/3 activation / Suppression of apoptosis / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / intracellular receptor signaling pathway / Signaling by Activin / Gastrin-CREB signalling pathway via PKC and MAPK / cardiac neural crest cell development involved in heart development / caveolin-mediated endocytosis / negative regulation of stem cell differentiation / ERKs are inactivated / cytosine metabolic process / response to epidermal growth factor / interleukin-15-mediated signaling pathway / cellular response to leptin stimulus / Signaling by MAP2K mutants / Signaling by NODAL / STAT3 nuclear events downstream of ALK signaling / astrocyte differentiation / Interleukin-23 signaling / RSK activation / positive regulation of cytokine production involved in inflammatory response / Signaling by cytosolic FGFR1 fusion mutants / Golgi Cisternae Pericentriolar Stack Reorganization / Interleukin-37 signaling / Interleukin-15 signaling / positive regulation of macrophage proliferation / Signaling by Leptin / Regulation of the apoptosome activity / outer ear morphogenesis / Interleukin-27 signaling / Interleukin-35 Signalling / negative regulation of glycolytic process / regulation of cellular pH / regulation of Golgi inheritance / ERBB signaling pathway / labyrinthine layer blood vessel development / growth hormone receptor signaling pathway / positive regulation of vascular endothelial cell proliferation / mammary gland epithelial cell proliferation / trachea formation / Negative feedback regulation of MAPK pathway / regulation of early endosome to late endosome transport / temperature homeostasis / eating behavior / Signaling by ALK / regulation of stress-activated MAPK cascade / IFNG signaling activates MAPKs / Frs2-mediated activation / Interleukin-20 family signaling / interleukin-6-mediated signaling pathway / Interleukin-6 signaling / positive regulation of macrophage chemotaxis / positive regulation of Notch signaling pathway / lung morphogenesis / ERBB2-ERBB3 signaling pathway / response to exogenous dsRNA / regulation of cytoskeleton organization / face development / Activation of the AP-1 family of transcription factors / ERK/MAPK targets / progesterone receptor signaling pathway / androgen receptor signaling pathway / RUNX2 regulates osteoblast differentiation / pseudopodium / Association of TriC/CCT with target proteins during biosynthesis / Recycling pathway of L1 / Interleukin-10 signaling / somatic stem cell population maintenance / MAPK1 (ERK2) activation / cell surface receptor signaling pathway via JAK-STAT / Bergmann glial cell differentiation Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.984 Å | ||||||
Authors | Kinoshita, T. / Sugiyama, H. / Mori, Y. / Takahashi, N. / Tomonaga, A. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2016 Title: Identification of allosteric ERK2 inhibitors through in silico biased screening and competitive binding assay Authors: Kinoshita, T. / Sugiyama, H. / Mori, Y. / Takahashi, N. / Tomonaga, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ax3.cif.gz | 87 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ax3.ent.gz | 62.6 KB | Display | PDB format |
PDBx/mmJSON format | 5ax3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ax3_validation.pdf.gz | 773.1 KB | Display | wwPDB validaton report |
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Full document | 5ax3_full_validation.pdf.gz | 780.9 KB | Display | |
Data in XML | 5ax3_validation.xml.gz | 14.6 KB | Display | |
Data in CIF | 5ax3_validation.cif.gz | 18.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ax/5ax3 ftp://data.pdbj.org/pub/pdb/validation_reports/ax/5ax3 | HTTPS FTP |
-Related structure data
Related structure data | 2fysS S: Starting model for refinement |
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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: 42231.438 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MAPK1, ERK2, PRKM1, PRKM2 / Plasmid: pGEX 6p-1 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 References: UniProt: P28482, mitogen-activated protein kinase |
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#2: Protein/peptide | Mass: 1491.815 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P40763*PLUS |
#3: Chemical | ChemComp-5ID / ( |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 36.82 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: PEG3350, Sodium chloride |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 14, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.98→43.89 Å / Num. obs: 13356 / % possible obs: 99.5 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 2.98→3.16 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.693 / Mean I/σ(I) obs: 2.25 / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2FYS Resolution: 2.984→43.886 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 32.85 / 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: 2.984→43.886 Å
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Refine LS restraints |
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LS refinement shell |
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