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Yorodumi- PDB-6bmv: Non-receptor Protein Tyrosine Phosphatase SHP2 in Complex with Al... -
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-Basic information
Entry | Database: PDB / ID: 6bmv | ||||||
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Title | Non-receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitor SHP504 | ||||||
Components | Tyrosine-protein phosphatase non-receptor type 11 | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / SHP2 / PTPN11 / protein tyrosine phosphatase / phosphatase / allosteric inhibitor / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information negative regulation of cortisol secretion / intestinal epithelial cell migration / microvillus organization / negative regulation of growth hormone secretion / genitalia development / atrioventricular canal development / negative regulation of cell adhesion mediated by integrin / STAT5 Activation / Netrin mediated repulsion signals / positive regulation of hormone secretion ...negative regulation of cortisol secretion / intestinal epithelial cell migration / microvillus organization / negative regulation of growth hormone secretion / genitalia development / atrioventricular canal development / negative regulation of cell adhesion mediated by integrin / STAT5 Activation / Netrin mediated repulsion signals / positive regulation of hormone secretion / cerebellar cortex formation / multicellular organismal reproductive process / regulation of protein export from nucleus / positive regulation of ossification / hormone metabolic process / Interleukin-37 signaling / Signaling by Leptin / negative regulation of chondrocyte differentiation / MET activates PTPN11 / Regulation of RUNX1 Expression and Activity / face morphogenesis / ERBB signaling pathway / Costimulation by the CD28 family / Signal regulatory protein family interactions / peptide hormone receptor binding / negative regulation of type I interferon production / platelet formation / megakaryocyte development / organ growth / CTLA4 inhibitory signaling / triglyceride metabolic process / Platelet sensitization by LDL / Interleukin-20 family signaling / PI-3K cascade:FGFR3 / Interleukin-6 signaling / STAT5 activation downstream of FLT3 ITD mutants / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR4 / Prolactin receptor signaling / PI-3K cascade:FGFR1 / MAPK3 (ERK1) activation / PECAM1 interactions / MAPK1 (ERK2) activation / regulation of cell adhesion mediated by integrin / regulation of type I interferon-mediated signaling pathway / Bergmann glial cell differentiation / phosphoprotein phosphatase activity / inner ear development / neurotrophin TRK receptor signaling pathway / platelet-derived growth factor receptor signaling pathway / non-membrane spanning protein tyrosine phosphatase activity / RET signaling / peptidyl-tyrosine dephosphorylation / Interleukin-3, Interleukin-5 and GM-CSF signaling / Regulation of IFNA/IFNB signaling / PI3K Cascade / PD-1 signaling / regulation of protein-containing complex assembly / ephrin receptor signaling pathway / fibroblast growth factor receptor signaling pathway / GAB1 signalosome / Activated NTRK2 signals through FRS2 and FRS3 / negative regulation of insulin secretion / Regulation of IFNG signaling / positive regulation of insulin receptor signaling pathway / FRS-mediated FGFR3 signaling / Signaling by CSF3 (G-CSF) / Signaling by FLT3 ITD and TKD mutants / homeostasis of number of cells within a tissue / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Tie2 Signaling / FRS-mediated FGFR1 signaling / cellular response to epidermal growth factor stimulus / cell adhesion molecule binding / GPVI-mediated activation cascade / T cell costimulation / FLT3 Signaling / positive regulation of interferon-beta production / hormone-mediated signaling pathway / phosphotyrosine residue binding / positive regulation of mitotic cell cycle / Downstream signal transduction / protein dephosphorylation / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / protein-tyrosine-phosphatase / axonogenesis / protein tyrosine kinase binding / DNA damage checkpoint signaling / protein tyrosine phosphatase activity / integrin-mediated signaling pathway / positive regulation of glucose import / Negative regulation of FGFR3 signaling / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / Negative regulation of FGFR1 signaling / Spry regulation of FGF signaling / insulin receptor binding / epidermal growth factor receptor signaling pathway / multicellular organism growth Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.053 Å | ||||||
Authors | Stams, T. / Fodor, M. | ||||||
Citation | Journal: ACS Chem. Biol. / Year: 2018 Title: Dual Allosteric Inhibition of SHP2 Phosphatase. Authors: Fodor, M. / Price, E. / Wang, P. / Lu, H. / Argintaru, A. / Chen, Z. / Glick, M. / Hao, H.X. / Kato, M. / Koenig, R. / LaRochelle, J.R. / Liu, G. / McNeill, E. / Majumdar, D. / Nishiguchi, G. ...Authors: Fodor, M. / Price, E. / Wang, P. / Lu, H. / Argintaru, A. / Chen, Z. / Glick, M. / Hao, H.X. / Kato, M. / Koenig, R. / LaRochelle, J.R. / Liu, G. / McNeill, E. / Majumdar, D. / Nishiguchi, G.A. / Perez, L.B. / Paris, G. / Quinn, C.M. / Ramsey, T. / Sendzik, M. / Shultz, M.D. / Williams, S.L. / Stams, T. / Blacklow, S.C. / Acker, M.G. / LaMarche, M.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6bmv.cif.gz | 223.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6bmv.ent.gz | 176.2 KB | Display | PDB format |
PDBx/mmJSON format | 6bmv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6bmv_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6bmv_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6bmv_validation.xml.gz | 41.3 KB | Display | |
Data in CIF | 6bmv_validation.cif.gz | 61.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bm/6bmv ftp://data.pdbj.org/pub/pdb/validation_reports/bm/6bmv | HTTPS FTP |
-Related structure data
Related structure data | 6bmrSC 6bmuC 6bmwC 6bmxC 6bmyC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 60335.035 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN11, PTP2C, SHPTP2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q06124, protein-tyrosine-phosphatase #2: Chemical | #3: Chemical | ChemComp-PO4 / #4: Water | ChemComp-HOH / | |
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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: 2.31 Å3/Da / Density % sol: 46.78 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 17% PEG3350, 200MM AMMONIUM PHOSPHATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 8, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.053→216.879 Å / Num. obs: 66612 / % possible obs: 97.9 % / Redundancy: 3.4 % / Biso Wilson estimate: 36.93 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.075 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 2.053→2.06 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.752 / Num. unique obs: 708 / CC1/2: 0.683 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 6BMR Resolution: 2.053→108.44 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.911 / SU R Cruickshank DPI: 0.185 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.188 / SU Rfree Blow DPI: 0.165 / SU Rfree Cruickshank DPI: 0.165
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Displacement parameters | Biso mean: 44.79 Å2
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Refine analyze | Luzzati coordinate error obs: 0.25 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.053→108.44 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.053→2.1 Å / Total num. of bins used: 20
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