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Yorodumi- PDB-1fpr: CRYSTAL STRUCTURE OF THE COMPLEX FORMED BETWEEN THE CATALYTIC DOM... -
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-Basic information
Entry | Database: PDB / ID: 1fpr | ||||||
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Title | CRYSTAL STRUCTURE OF THE COMPLEX FORMED BETWEEN THE CATALYTIC DOMAIN OF SHP-1 AND AN IN VITRO PEPTIDE SUBSTRATE PY469 DERIVED FROM SHPS-1. | ||||||
Components |
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Keywords | SIGNALING PROTEIN / protein tyrosine phosphatase / substrate specificity / residue shift | ||||||
Function / homology | Function and homology information negative regulation of humoral immune response mediated by circulating immunoglobulin / negative regulation of mast cell activation involved in immune response / negative regulation of B cell receptor signaling pathway / regulation of B cell differentiation / negative regulation of peptidyl-tyrosine phosphorylation / negative regulation of inflammatory response to wounding / epididymis development / transmembrane receptor protein tyrosine phosphatase activity / phosphorylation-dependent protein binding / alpha-beta T cell receptor complex ...negative regulation of humoral immune response mediated by circulating immunoglobulin / negative regulation of mast cell activation involved in immune response / negative regulation of B cell receptor signaling pathway / regulation of B cell differentiation / negative regulation of peptidyl-tyrosine phosphorylation / negative regulation of inflammatory response to wounding / epididymis development / transmembrane receptor protein tyrosine phosphatase activity / phosphorylation-dependent protein binding / alpha-beta T cell receptor complex / CD22 mediated BCR regulation / regulation of release of sequestered calcium ion into cytosol / Interleukin-37 signaling / positive regulation of cell adhesion mediated by integrin / Costimulation by the CD28 family / Signal regulatory protein family interactions / platelet formation / megakaryocyte development / natural killer cell mediated cytotoxicity / Regulation of KIT signaling / negative regulation of T cell receptor signaling pathway / Signaling by ALK / Platelet sensitization by LDL / regulation of G1/S transition of mitotic cell cycle / PECAM1 interactions / regulation of type I interferon-mediated signaling pathway / negative regulation of interleukin-6 production / non-membrane spanning protein tyrosine phosphatase activity / negative regulation of tumor necrosis factor production / peptidyl-tyrosine dephosphorylation / Interleukin-3, Interleukin-5 and GM-CSF signaling / Regulation of IFNA/IFNB signaling / PD-1 signaling / negative regulation of MAPK cascade / Interleukin receptor SHC signaling / hematopoietic progenitor cell differentiation / Regulation of IFNG signaling / negative regulation of T cell proliferation / Nuclear events stimulated by ALK signaling in cancer / Growth hormone receptor signaling / T cell proliferation / GPVI-mediated activation cascade / cell adhesion molecule binding / T cell costimulation / protein dephosphorylation / negative regulation of innate immune response / phosphotyrosine residue binding / SH2 domain binding / negative regulation of angiogenesis / protein-tyrosine-phosphatase / regulation of ERK1 and ERK2 cascade / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / protein tyrosine phosphatase activity / B cell receptor signaling pathway / platelet aggregation / cytokine-mediated signaling pathway / SH3 domain binding / peptidyl-tyrosine phosphorylation / specific granule lumen / Interferon gamma signaling / MAPK cascade / Interferon alpha/beta signaling / cell-cell junction / tertiary granule lumen / mitotic cell cycle / T cell receptor signaling pathway / regulation of apoptotic process / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell differentiation / intracellular signal transduction / G protein-coupled receptor signaling pathway / negative regulation of cell population proliferation / positive regulation of cell population proliferation / Neutrophil degranulation / nucleolus / protein kinase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / protein-containing complex / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.5 Å | ||||||
Authors | Yang, J. / Cheng, Z. / Niu, Z. / Zhao, Z.J. / Zhou, G.W. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2000 Title: Structural basis for substrate specificity of protein-tyrosine phosphatase SHP-1. Authors: Yang, J. / Cheng, Z. / Niu, T. / Liang, X. / Zhao, Z.J. / Zhou, G.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fpr.cif.gz | 71 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fpr.ent.gz | 52 KB | Display | PDB format |
PDBx/mmJSON format | 1fpr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1fpr_validation.pdf.gz | 376.5 KB | Display | wwPDB validaton report |
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Full document | 1fpr_full_validation.pdf.gz | 415.5 KB | Display | |
Data in XML | 1fpr_validation.xml.gz | 12.9 KB | Display | |
Data in CIF | 1fpr_validation.cif.gz | 18.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fp/1fpr ftp://data.pdbj.org/pub/pdb/validation_reports/fp/1fpr | HTTPS FTP |
-Related structure data
Similar structure data |
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-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: 32558.781 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN / Mutation: C455S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P29350, protein-tyrosine-phosphatase |
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#2: Protein/peptide | Mass: 1235.146 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: This peptide was chemically synthesized. The sequence of this peptide occurs naturally in humans (Homo sapiens) |
Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.4 % | ||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 8.5 Details: ammonium sulfate, pH 8.5, VAPOR DIFFUSION, temperature 277K | ||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 85 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 8, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Highest resolution: 2.5 Å / % possible obs: 85 % / Rmerge(I) obs: 0.097 |
Reflection | *PLUS Num. obs: 8998 / % possible obs: 85 % / Num. measured all: 27345 |
-Processing
Software |
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Refinement | Resolution: 2.5→6 Å / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 2.5→6 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 6 Å / σ(F): 2 / Rfactor all: 0.199 / Rfactor obs: 0.194 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_deg / Dev ideal: 1.4 |