+Open data
-Basic information
Entry | Database: PDB / ID: 3zm3 | ||||||
---|---|---|---|---|---|---|---|
Title | Catalytic domain of human SHP2 | ||||||
Components | TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE 11 | ||||||
Keywords | HYDROLASE / PTP1B | ||||||
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 / multicellular organismal reproductive process / atrioventricular canal development / negative regulation of cell adhesion mediated by integrin / STAT5 Activation / Netrin mediated repulsion signals ...negative regulation of cortisol secretion / intestinal epithelial cell migration / microvillus organization / negative regulation of growth hormone secretion / genitalia development / multicellular organismal reproductive process / atrioventricular canal development / negative regulation of cell adhesion mediated by integrin / STAT5 Activation / Netrin mediated repulsion signals / cerebellar cortex formation / positive regulation of hormone secretion / Interleukin-37 signaling / regulation of protein export from nucleus / positive regulation of ossification / hormone metabolic process / Signaling by Leptin / MET activates PTPN11 / negative regulation of chondrocyte differentiation / Regulation of RUNX1 Expression and Activity / face morphogenesis / Costimulation by the CD28 family / triglyceride metabolic process / ERBB signaling pathway / Signal regulatory protein family interactions / organ growth / platelet formation / megakaryocyte development / negative regulation of type I interferon production / peptide hormone receptor binding / Platelet sensitization by LDL / CTLA4 inhibitory signaling / PI-3K cascade:FGFR2 / Interleukin-20 family signaling / PI-3K cascade:FGFR3 / Interleukin-6 signaling / STAT5 activation downstream of FLT3 ITD mutants / PI-3K cascade:FGFR4 / Prolactin receptor signaling / MAPK3 (ERK1) activation / PI-3K cascade:FGFR1 / PECAM1 interactions / regulation of cell adhesion mediated by integrin / MAPK1 (ERK2) activation / regulation of type I interferon-mediated signaling pathway / Bergmann glial cell differentiation / neurotrophin TRK receptor signaling pathway / inner ear development / phosphoprotein phosphatase activity / platelet-derived growth factor receptor signaling pathway / non-membrane spanning protein tyrosine phosphatase activity / PI3K Cascade / RET signaling / peptidyl-tyrosine dephosphorylation / Interleukin-3, Interleukin-5 and GM-CSF signaling / Regulation of IFNA/IFNB signaling / fibroblast growth factor receptor signaling pathway / regulation of protein-containing complex assembly / ephrin receptor signaling pathway / PD-1 signaling / GAB1 signalosome / Activated NTRK2 signals through FRS2 and FRS3 / negative regulation of insulin secretion / Regulation of IFNG signaling / Signaling by CSF3 (G-CSF) / positive regulation of insulin receptor signaling pathway / cell adhesion molecule binding / FRS-mediated FGFR2 signaling / FRS-mediated FGFR3 signaling / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR4 signaling / homeostasis of number of cells within a tissue / GPVI-mediated activation cascade / Tie2 Signaling / FRS-mediated FGFR1 signaling / FLT3 Signaling / T cell costimulation / cellular response to epidermal growth factor stimulus / phosphotyrosine residue binding / protein dephosphorylation / positive regulation of interferon-beta production / hormone-mediated signaling pathway / protein tyrosine kinase binding / Downstream signal transduction / positive regulation of mitotic cell cycle / axonogenesis / protein-tyrosine-phosphatase / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / protein tyrosine phosphatase activity / DNA damage checkpoint signaling / integrin-mediated signaling pathway / positive regulation of D-glucose import / Negative regulation of FGFR2 signaling / Negative regulation of FGFR3 signaling / Negative regulation of FGFR4 signaling / insulin receptor binding / Negative regulation of FGFR1 signaling / Spry regulation of FGF signaling / brain development / epidermal growth factor receptor signaling pathway Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Bohm, K. / Schuetz, A. / Roske, Y. / Heinemann, U. | ||||||
Citation | Journal: Chemmedchem / Year: 2015 Title: Selective Inhibitors of the Protein Tyrosine Phosphatase Shp2 Block Cellular Motility and Growth of Cancer Cells in Vitro and in Vivo. Authors: Grosskopf, S. / Eckert, C. / Arkona, C. / Radetzki, S. / Bohm, K. / Heinemann, U. / Wolber, G. / Von Kries, J. / Birchmeier, W. / Rademann, J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3zm3.cif.gz | 127.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3zm3.ent.gz | 100.2 KB | Display | PDB format |
PDBx/mmJSON format | 3zm3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3zm3_validation.pdf.gz | 426.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3zm3_full_validation.pdf.gz | 432.4 KB | Display | |
Data in XML | 3zm3_validation.xml.gz | 14.6 KB | Display | |
Data in CIF | 3zm3_validation.cif.gz | 21.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zm/3zm3 ftp://data.pdbj.org/pub/pdb/validation_reports/zm/3zm3 | HTTPS FTP |
-Related structure data
Related structure data | 3zm0C 3zm1C 3zm2C 3b7oS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 33163.660 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 248-527 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PT7HT (MODIFIED PET) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): SCS1 ROSETTA T1R / References: UniProt: Q06124, protein-tyrosine-phosphatase |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.84 % / Description: NONE |
---|---|
Crystal grow | Details: 16-22% (W/V) PEG3350, 0.1-0.2 M SODIUM CITRATE |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 26, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→20 Å / Num. obs: 39749 / % possible obs: 83 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 1.5→1.59 Å / Rmerge(I) obs: 0.04 / Mean I/σ(I) obs: 3.4 / % possible all: 50.7 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3B7O Resolution: 1.5→19.53 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.932 / SU B: 2.755 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.087 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 255-262 AND 314-321 ARE DISORDERED.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.745 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→19.53 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|