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Yorodumi- PDB-1ayd: CRYSTAL STRUCTURES OF PEPTIDE COMPLEXES OF THE AMINO-TERMINAL SH2... -
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-Basic information
Entry | Database: PDB / ID: 1ayd | ||||||
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Title | CRYSTAL STRUCTURES OF PEPTIDE COMPLEXES OF THE AMINO-TERMINAL SH2 DOMAIN OF THE SYP TYROSINE PHOSPHATASE | ||||||
Components | PROTEIN-TYROSINE PHOSPHATASE SYP (N-TERMINAL SH2 DOMAIN) | ||||||
Keywords | HYDROLASE(SH2 DOMAIN) | ||||||
Function / homology | Function and homology information PI-3K cascade:FGFR3 / PI-3K cascade:FGFR4 / PI-3K cascade:FGFR1 / PI-3K cascade:FGFR2 / FRS-mediated FGFR3 signaling / FRS-mediated FGFR4 signaling / MET activates PTPN11 / Regulation of IFNA/IFNB signaling / Costimulation by the CD28 family / FRS-mediated FGFR1 signaling ...PI-3K cascade:FGFR3 / PI-3K cascade:FGFR4 / PI-3K cascade:FGFR1 / PI-3K cascade:FGFR2 / FRS-mediated FGFR3 signaling / FRS-mediated FGFR4 signaling / MET activates PTPN11 / Regulation of IFNA/IFNB signaling / Costimulation by the CD28 family / FRS-mediated FGFR1 signaling / FRS-mediated FGFR2 signaling / Tie2 Signaling / PECAM1 interactions / Interleukin-20 family signaling / MAPK3 (ERK1) activation / MAPK1 (ERK2) activation / Signaling by CSF3 (G-CSF) / CTLA4 inhibitory signaling / GAB1 signalosome / PI3K Cascade / Regulation of RUNX1 Expression and Activity / Interleukin-6 signaling / GPVI-mediated activation cascade / Negative regulation of FGFR3 signaling / Negative regulation of FGFR4 signaling / Downstream signal transduction / Negative regulation of FGFR1 signaling / Negative regulation of FGFR2 signaling / Spry regulation of FGF signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / PD-1 signaling / Signaling by SCF-KIT / positive regulation of signal transduction / negative regulation of hormone secretion / negative regulation of cortisol secretion / intestinal epithelial cell migration / microvillus organization / negative regulation of growth hormone secretion / PIP3 activates AKT signaling / genitalia development / Platelet sensitization by LDL / atrioventricular canal development / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / negative regulation of cell adhesion mediated by integrin / Interleukin-3, Interleukin-5 and GM-CSF signaling / RET signaling / 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 / negative regulation of chondrocyte differentiation / face morphogenesis / peptide hormone receptor binding / negative regulation of type I interferon production / platelet formation / megakaryocyte development / organ growth / triglyceride metabolic process / plasma membrane raft / positive regulation of focal adhesion assembly / Bergmann glial cell differentiation / regulation of cell adhesion mediated by integrin / phospholipase binding / phosphoprotein phosphatase activity / regulation of MAPK cascade / inner ear development / neurotrophin TRK receptor signaling pathway / platelet-derived growth factor receptor signaling pathway / non-membrane spanning protein tyrosine phosphatase activity / peptidyl-tyrosine dephosphorylation / insulin receptor substrate binding / D1 dopamine receptor binding / regulation of protein-containing complex assembly / ephrin receptor signaling pathway / fibroblast growth factor receptor signaling pathway / negative regulation of insulin secretion / positive regulation of insulin receptor signaling pathway / homeostasis of number of cells within a tissue / cellular response to epidermal growth factor stimulus / cell adhesion molecule binding / positive regulation of interferon-beta production / hormone-mediated signaling pathway / phosphotyrosine residue binding / positive regulation of mitotic cell cycle / 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 / insulin receptor binding / epidermal growth factor receptor signaling pathway / multicellular organism growth / lipid metabolic process / receptor tyrosine kinase binding / cellular response to mechanical stimulus / positive regulation of interleukin-6 production Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.2 Å | ||||||
Authors | Lee, C.-H. / Kuriyan, J. | ||||||
Citation | Journal: Structure / Year: 1994 Title: Crystal structures of peptide complexes of the amino-terminal SH2 domain of the Syp tyrosine phosphatase. Authors: Lee, C.H. / Kominos, D. / Jacques, S. / Margolis, B. / Schlessinger, J. / Shoelson, S.E. / Kuriyan, J. #1: Journal: Cell(Cambridge,Mass.) / Year: 1993 Title: Binding of a High Affinity Phosphotyrosyl Peptide to the Src Sh2 Domain: Crystal Structures of the Complexed and Peptide-Free Forms Authors: Waksman, G. / Shoelson, S.E. / Pant, N. / Cowburn, D. / Kuriyan, J. #2: Journal: Curr.Opin.Struct.Biol. / Year: 1993 Title: Structures of Sh2 and SH3 Domains Authors: Kuriyan, J. / Cowburn, D. #3: Journal: Nature / Year: 1992 Title: Crystal Structure of the Phosphotyrosine Recognition Domain Sh2 of V-Src Complexed with Tyrosine-Phosphorylated Peptides Authors: Waksman, G. / Kominos, D. / Robertson, S.R. / Pant, N. / Baltimore, D. / Birge, R.B. / Cowburn, D. / Hanafusa, H. / Mayer, B.J. / Overduin, M. / Resh, M.D. / Rios, C.B. / Silverman, L. / Kuriyan, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ayd.cif.gz | 33.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ayd.ent.gz | 22.4 KB | Display | PDB format |
PDBx/mmJSON format | 1ayd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ayd_validation.pdf.gz | 410 KB | Display | wwPDB validaton report |
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Full document | 1ayd_full_validation.pdf.gz | 412.8 KB | Display | |
Data in XML | 1ayd_validation.xml.gz | 7.4 KB | Display | |
Data in CIF | 1ayd_validation.cif.gz | 9.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ay/1ayd ftp://data.pdbj.org/pub/pdb/validation_reports/ay/1ayd | HTTPS FTP |
-Related 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: 11528.979 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / References: UniProt: P35235, protein-tyrosine-phosphatase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.29 Å3/Da / Density % sol: 62.66 % | |||||||||||||||
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Crystal grow | *PLUS pH: 6 / Method: vapor diffusion, hanging drop | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 30 Å / Num. obs: 8075 / % possible obs: 97 % / Num. measured all: 63420 / Rmerge(I) obs: 0.053 |
Reflection shell | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 2.24 Å / % possible obs: 92.1 % |
-Processing
Software |
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Refinement | Resolution: 2.2→6 Å / σ(F): 2 /
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Refinement step | Cycle: LAST / Resolution: 2.2→6 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 3 |