+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1ayd | ||||||
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タイトル | CRYSTAL STRUCTURES OF PEPTIDE COMPLEXES OF THE AMINO-TERMINAL SH2 DOMAIN OF THE SYP TYROSINE PHOSPHATASE | ||||||
要素 | PROTEIN-TYROSINE PHOSPHATASE SYP (N-TERMINAL SH2 DOMAIN) | ||||||
キーワード | HYDROLASE(SH2 DOMAIN) | ||||||
機能・相同性 | 機能・相同性情報 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 / Negative regulation of FGFR3 signaling / Negative regulation of FGFR4 signaling / Downstream signal transduction / Negative regulation of FGFR1 signaling / Negative regulation of FGFR2 signaling / GPVI-mediated activation cascade / 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 / regulation of cell adhesion mediated by integrin / Bergmann glial cell differentiation / phosphoprotein phosphatase activity / phospholipase binding / 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 類似検索 - 分子機能 | ||||||
生物種 | Mus musculus (ハツカネズミ) | ||||||
手法 | X線回折 / 解像度: 2.2 Å | ||||||
データ登録者 | Lee, C.-H. / Kuriyan, J. | ||||||
引用 | ジャーナル: Structure / 年: 1994 タイトル: Crystal structures of peptide complexes of the amino-terminal SH2 domain of the Syp tyrosine phosphatase. 著者: Lee, C.H. / Kominos, D. / Jacques, S. / Margolis, B. / Schlessinger, J. / Shoelson, S.E. / Kuriyan, J. #1: ジャーナル: Cell(Cambridge,Mass.) / 年: 1993 タイトル: Binding of a High Affinity Phosphotyrosyl Peptide to the Src Sh2 Domain: Crystal Structures of the Complexed and Peptide-Free Forms 著者: Waksman, G. / Shoelson, S.E. / Pant, N. / Cowburn, D. / Kuriyan, J. #2: ジャーナル: Curr.Opin.Struct.Biol. / 年: 1993 タイトル: Structures of Sh2 and SH3 Domains 著者: Kuriyan, J. / Cowburn, D. #3: ジャーナル: Nature / 年: 1992 タイトル: Crystal Structure of the Phosphotyrosine Recognition Domain Sh2 of V-Src Complexed with Tyrosine-Phosphorylated Peptides 著者: 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. | ||||||
履歴 |
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-構造の表示
構造ビューア | 分子: MolmilJmol/JSmol |
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-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 1ayd.cif.gz | 33.4 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb1ayd.ent.gz | 22.4 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1ayd.json.gz | ツリー表示 | PDBx/mmJSON形式 | |
その他 | その他のダウンロード |
-検証レポート
文書・要旨 | 1ayd_validation.pdf.gz | 410 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 1ayd_full_validation.pdf.gz | 412.8 KB | 表示 | |
XML形式データ | 1ayd_validation.xml.gz | 7.4 KB | 表示 | |
CIF形式データ | 1ayd_validation.cif.gz | 9.5 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/ay/1ayd ftp://data.pdbj.org/pub/pdb/validation_reports/ay/1ayd | HTTPS FTP |
-関連構造データ
-リンク
-集合体
登録構造単位 |
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単位格子 |
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-要素
#1: タンパク質 | 分子量: 11528.979 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / 参照: UniProt: P35235, protein-tyrosine-phosphatase |
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#2: 水 | ChemComp-HOH / |
-実験情報
-実験
実験 | 手法: X線回折 |
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-試料調製
結晶 | マシュー密度: 3.29 Å3/Da / 溶媒含有率: 62.66 % | |||||||||||||||
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結晶化 | *PLUS pH: 6 / 手法: 蒸気拡散法, ハンギングドロップ法 | |||||||||||||||
溶液の組成 | *PLUS
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-データ収集
放射 | 散乱光タイプ: x-ray |
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放射波長 | 相対比: 1 |
反射 | *PLUS 最高解像度: 2.2 Å / 最低解像度: 30 Å / Num. obs: 8075 / % possible obs: 97 % / Num. measured all: 63420 / Rmerge(I) obs: 0.053 |
反射 シェル | *PLUS 最高解像度: 2.2 Å / 最低解像度: 2.24 Å / % possible obs: 92.1 % |
-解析
ソフトウェア |
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精密化 | 解像度: 2.2→6 Å / σ(F): 2 /
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精密化ステップ | サイクル: LAST / 解像度: 2.2→6 Å
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拘束条件 |
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ソフトウェア | *PLUS 名称: X-PLOR / 分類: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化 | *PLUS Rfactor obs: 0.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
溶媒の処理 | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
拘束条件 | *PLUS タイプ: x_angle_d / Dev ideal: 3 |