+Open data
-Basic information
Entry | Database: PDB / ID: 6qa1 | ||||||
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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: 1.58 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 | 6qa1.cif.gz | 158.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qa1.ent.gz | 128.4 KB | Display | PDB format |
PDBx/mmJSON format | 6qa1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6qa1_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 6qa1_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 6qa1_validation.xml.gz | 17.1 KB | Display | |
Data in CIF | 6qa1_validation.cif.gz | 25.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qa/6qa1 ftp://data.pdbj.org/pub/pdb/validation_reports/qa/6qa1 | HTTPS FTP |
-Related structure data
Related structure data | 6q7kC 6q7sC 6q7tC 6qa3C 6qa4C 6qagC 6qahC 6qalC 6qaqC 6qawC 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: 42551.922 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-HVK / #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: 2.28 Å3/Da / Density % sol: 45.98 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2 Details: 0.2M (NH4)2SO4 33% 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: May 2, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.58→48.65 Å / Num. obs: 38645 / % possible obs: 73.6 % / Redundancy: 2.9 % / Biso Wilson estimate: 16.95 Å2 / Rrim(I) all: 0.048 / Net I/σ(I): 13 |
Reflection shell | Resolution: 1.58→1.62 Å / Num. unique obs: 159 / Rrim(I) all: 0.203 / % possible all: 4.1 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.58→26.5 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.931 / SU R Cruickshank DPI: 0.136 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.105 / SU Rfree Blow DPI: 0.104 / SU Rfree Cruickshank DPI: 0.102
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Displacement parameters | Biso mean: 22.681 Å2
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Refine analyze | Luzzati coordinate error obs: 0.19 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.58→26.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.58→1.68 Å / Total num. of bins used: 50
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Refinement TLS params. | Method: refined / Origin x: -0.5379 Å / Origin y: 3.4659 Å / Origin z: 38.1561 Å
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Refinement TLS group | Selection details: { A|11 - A|365 } |