+Open data
-Basic information
Entry | Database: PDB / ID: 6qaw | ||||||
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Title | ERK2 mini-fragment binding | ||||||
Components | Mitogen-activated protein kinase 1 | ||||||
Keywords | SIGNALING PROTEIN / Ser/Thr kinase / signal transduction / ATP binding | ||||||
Function / homology | Function and homology information phospho-PLA2 pathway / Suppression of apoptosis / Signaling by MAPK mutants / RAF-independent MAPK1/3 activation / Signaling by Activin / Gastrin-CREB signalling pathway via PKC and MAPK / caveolin-mediated endocytosis / cardiac neural crest cell development involved in heart development / cytosine metabolic process / response to epidermal growth factor ...phospho-PLA2 pathway / Suppression of apoptosis / Signaling by MAPK mutants / RAF-independent MAPK1/3 activation / Signaling by Activin / Gastrin-CREB signalling pathway via PKC and MAPK / caveolin-mediated endocytosis / cardiac neural crest cell development involved in heart development / cytosine metabolic process / response to epidermal growth factor / ERKs are inactivated / Signaling by MAP2K mutants / Signaling by NODAL / RSK activation / Golgi Cisternae Pericentriolar Stack Reorganization / positive regulation of macrophage proliferation / Regulation of the apoptosome activity / regulation of cellular pH / outer ear morphogenesis / regulation of Golgi inheritance / Signaling by LTK in cancer / ERBB signaling pathway / labyrinthine layer blood vessel development / mammary gland epithelial cell proliferation / trachea formation / Negative feedback regulation of MAPK pathway / regulation of early endosome to late endosome transport / regulation of stress-activated MAPK cascade / IFNG signaling activates MAPKs / Frs2-mediated activation / positive regulation of macrophage chemotaxis / ERBB2-ERBB3 signaling pathway / lung morphogenesis / response to exogenous dsRNA / pseudopodium / Activation of the AP-1 family of transcription factors / ERK/MAPK targets / androgen receptor signaling pathway / regulation of cytoskeleton organization / face development / : / RUNX2 regulates osteoblast differentiation / positive regulation of telomere capping / Recycling pathway of L1 / MAPK1 (ERK2) activation / Bergmann glial cell differentiation / thyroid gland development / negative regulation of cell differentiation / Advanced glycosylation endproduct receptor signaling / steroid hormone receptor signaling pathway / RHO GTPases Activate NADPH Oxidases / MAP kinase activity / regulation of ossification / Regulation of HSF1-mediated heat shock response / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / Transcriptional and post-translational regulation of MITF-M expression and activity / mitogen-activated protein kinase / RHO GTPases Activate WASPs and WAVEs / phosphatase binding / Signal attenuation / Estrogen-stimulated signaling through PRKCZ / progesterone receptor signaling pathway / Schwann cell development / Nuclear events stimulated by ALK signaling in cancer / Growth hormone receptor signaling / lipopolysaccharide-mediated signaling pathway / stress-activated MAPK cascade / positive regulation of telomere maintenance via telomerase / phosphotyrosine residue binding / cellular response to cadmium ion / NPAS4 regulates expression of target genes / myelination / cellular response to amino acid starvation / ERK1 and ERK2 cascade / NCAM signaling for neurite out-growth / ESR-mediated signaling / RNA polymerase II CTD heptapeptide repeat kinase activity / insulin-like growth factor receptor signaling pathway / thymus development / positive regulation of peptidyl-threonine phosphorylation / Signal transduction by L1 / Regulation of PTEN gene transcription / long-term synaptic potentiation / response to nicotine / peptidyl-threonine phosphorylation / Negative regulation of FGFR2 signaling / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / Negative regulation of FGFR3 signaling / B cell receptor signaling pathway / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Negative regulation of FGFR4 signaling / Negative regulation of FGFR1 signaling / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Signaling by high-kinase activity BRAF mutants / Spry regulation of FGF signaling / MAP2K and MAPK activation / regulation of protein stability / caveola / Oncogene Induced Senescence Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.84 Å | ||||||
Authors | O'Reilly, M. / Cleasby, A. / Davies, T.G. / Hall, R. / Ludlow, F. / Murray, C.W. / Tisi, D. / Jhoti, H. | ||||||
Citation | Journal: Drug Discov Today / Year: 2019 Title: Crystallographic screening using ultra-low-molecular-weight ligands to guide drug design. Authors: O'Reilly, M. / Cleasby, A. / Davies, T.G. / Hall, R.J. / Ludlow, R.F. / Murray, C.W. / Tisi, D. / Jhoti, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6qaw.cif.gz | 157.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qaw.ent.gz | 127.4 KB | Display | PDB format |
PDBx/mmJSON format | 6qaw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6qaw_validation.pdf.gz | 743.3 KB | Display | wwPDB validaton report |
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Full document | 6qaw_full_validation.pdf.gz | 744.7 KB | Display | |
Data in XML | 6qaw_validation.xml.gz | 17.7 KB | Display | |
Data in CIF | 6qaw_validation.cif.gz | 26.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qa/6qaw ftp://data.pdbj.org/pub/pdb/validation_reports/qa/6qaw | HTTPS FTP |
-Related structure data
Related structure data | 6q7kC 6q7sC 6q7tC 6qa1C 6qa3C 6qa4C 6qagC 6qahC 6qalC 6qaqC 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: 42628.039 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MAPK1, ERK2, PRKM1, PRKM2 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P28482, mitogen-activated protein kinase |
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#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-HVE / [ |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.56 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2 Details: 0.2M (NH4)2SO4 34% MPEG 2000 0.02M Mercaptoethanol 0.1M pH=7.2 HEPES/NaOH |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.54178 Å |
Detector | Type: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Nov 1, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.84→48.87 Å / Num. obs: 30456 / % possible obs: 90.7 % / Redundancy: 1.9 % / Biso Wilson estimate: 23.96 Å2 / Rmerge(I) obs: 0.032 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 1.84→1.89 Å / Rmerge(I) obs: 0.239 / Num. unique obs: 1467 / % possible all: 53 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.84→29.97 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.919 / SU R Cruickshank DPI: 0.224 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.145 / SU Rfree Blow DPI: 0.137 / SU Rfree Cruickshank DPI: 0.134
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Displacement parameters | Biso mean: 30.412 Å2
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Refine analyze | Luzzati coordinate error obs: 0.21 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.84→29.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.84→1.86 Å / Total num. of bins used: 50
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Refinement TLS params. | Method: refined / Origin x: -0.8379 Å / Origin y: 3.5132 Å / Origin z: 37.8911 Å
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Refinement TLS group | Selection details: { A|11 - A|365 } |