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データを開く
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基本情報
登録情報 | データベース: PDB / ID: 1lqf | ||||||
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タイトル | Structure of PTP1b in Complex with a Peptidic Bisphosphonate Inhibitor | ||||||
![]() | protein-tyrosine phosphatase, non-receptor type 1 | ||||||
![]() | HYDROLASE / Phosphatase / phosphonates / diabetes / inhibitor | ||||||
機能・相同性 | ![]() regulation of hepatocyte growth factor receptor signaling pathway / PTK6 Down-Regulation / positive regulation of receptor catabolic process / insulin receptor recycling / peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity / negative regulation of vascular endothelial growth factor receptor signaling pathway / negative regulation of PERK-mediated unfolded protein response / regulation of intracellular protein transport / IRE1-mediated unfolded protein response / cytoplasmic side of endoplasmic reticulum membrane ...regulation of hepatocyte growth factor receptor signaling pathway / PTK6 Down-Regulation / positive regulation of receptor catabolic process / insulin receptor recycling / peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity / negative regulation of vascular endothelial growth factor receptor signaling pathway / negative regulation of PERK-mediated unfolded protein response / regulation of intracellular protein transport / IRE1-mediated unfolded protein response / cytoplasmic side of endoplasmic reticulum membrane / platelet-derived growth factor receptor-beta signaling pathway / sorting endosome / mitochondrial crista / positive regulation of IRE1-mediated unfolded protein response / regulation of type I interferon-mediated signaling pathway / regulation of endocytosis / non-membrane spanning protein tyrosine phosphatase activity / positive regulation of protein tyrosine kinase activity / peptidyl-tyrosine dephosphorylation / Regulation of IFNA/IFNB signaling / regulation of signal transduction / cellular response to unfolded protein / growth hormone receptor signaling pathway via JAK-STAT / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / negative regulation of signal transduction / Regulation of IFNG signaling / MECP2 regulates neuronal receptors and channels / Growth hormone receptor signaling / endoplasmic reticulum unfolded protein response / positive regulation of JUN kinase activity / negative regulation of insulin receptor signaling pathway / Insulin receptor recycling / ephrin receptor binding / Integrin signaling / protein dephosphorylation / protein-tyrosine-phosphatase / negative regulation of MAP kinase activity / protein phosphatase 2A binding / protein tyrosine phosphatase activity / endosome lumen / insulin receptor binding / Negative regulation of MET activity / negative regulation of ERK1 and ERK2 cascade / receptor tyrosine kinase binding / insulin receptor signaling pathway / actin cytoskeleton organization / early endosome / mitochondrial matrix / cadherin binding / protein kinase binding / enzyme binding / endoplasmic reticulum / protein-containing complex / RNA binding / zinc ion binding / cytosol / cytoplasm 類似検索 - 分子機能 | ||||||
生物種 | ![]() | ||||||
手法 | ![]() ![]() ![]() | ||||||
![]() | Asante-Appiah, E. / Patel, S. / Dufresne, C. / Scapin, G. | ||||||
![]() | ![]() タイトル: The structure of PTP-1B in complex with a peptide inhibitor reveals an alternative binding mode for bisphosphonates. 著者: Asante-Appiah, E. / Patel, S. / Dufresne, C. / Roy, P. / Wang, Q. / Patel, V. / Friesen, R.W. / Ramachandran, C. / Becker, J.W. / Leblanc, Y. / Kennedy, B.P. / Scapin, G. #1: ![]() タイトル: The YRD motif is a major determinant of substrate and inhibitor specificity in T-cell protein-tyrosine phosphatase 著者: Asante-Appiah, E. / Ball, K. / Bateman, K. / Skorey, K. / Friesen, R. / Desponts, C. / Payette, P. / Bayly, C. / Zamboni, R. / Scapin, G. / Ramachandran, C. / Kennedy, B.P. | ||||||
履歴 |
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構造の表示
構造ビューア | 分子: ![]() ![]() |
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PDBx/mmCIF形式 | ![]() | 255.2 KB | 表示 | ![]() |
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PDB形式 | ![]() | 206.6 KB | 表示 | ![]() |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
その他 | ![]() |
-検証レポート
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
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-関連構造データ
関連構造データ | ![]() 1ptyS S: 精密化の開始モデル |
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類似構造データ |
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リンク
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集合体
登録構造単位 | ![]()
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単位格子 |
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Components on special symmetry positions |
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要素
#1: タンパク質 | 分子量: 34451.367 Da / 分子数: 4 / 断片: catalytic domain (residues 1-283) / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() #2: 化合物 | ChemComp-BGD / #3: 水 | ChemComp-HOH / | |
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-実験情報
-実験
実験 | 手法: ![]() |
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試料調製
結晶 | マシュー密度: 3.7 Å3/Da / 溶媒含有率: 73 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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結晶化 | 温度: 284 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 5.9 詳細: Peg 4000, propanol, citrate, pH 5.9, VAPOR DIFFUSION, SITTING DROP, temperature 284K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
結晶化 | *PLUS 温度: 4 ℃ / pH: 7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
溶液の組成 | *PLUS
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-データ収集
回折 | 平均測定温度: 100 K |
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放射光源 | 由来: ![]() ![]() ![]() |
検出器 | タイプ: MARRESEARCH / 検出器: CCD / 日付: 1998年12月9日 |
放射 | プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray |
放射波長 | 波長: 1 Å / 相対比: 1 |
反射 | 解像度: 2.5→29 Å / Num. all: 63052 / Num. obs: 61097 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / 冗長度: 2.8 % / Biso Wilson estimate: 38.9 Å2 / Rsym value: 0.121 / Net I/σ(I): 6 |
反射 シェル | 解像度: 2.5→2.65 Å / 冗長度: 1.9 % / Mean I/σ(I) obs: 1.5 / Num. unique all: 9039 / Rsym value: 0.38 / % possible all: 86.4 |
反射 | *PLUS 最低解像度: 30 Å / Num. measured all: 176274 / Rmerge(I) obs: 0.121 |
反射 シェル | *PLUS % possible obs: 86.4 % / Num. unique obs: 9039 / Num. measured obs: 17193 / Rmerge(I) obs: 0.38 |
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解析
ソフトウェア |
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精密化 | 構造決定の手法: ![]() 開始モデル: 1PTY 解像度: 2.5→29 Å / Isotropic thermal model: Anisotropic / 交差検証法: THROUGHOUT / σ(F): 0 / 立体化学のターゲット値: Engh & Huber 詳細: A 4% twinning was detected using both Truncate and CNS and the refinement was carried out using the CNS twinning procedures, with twinning operator h, -k, -l.
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原子変位パラメータ | Biso mean: 42.1 Å2
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精密化ステップ | サイクル: LAST / 解像度: 2.5→29 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 2.5→2.68 Å / Total num. of bins used: 10
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精密化 | *PLUS 最低解像度: 30 Å / Num. reflection obs: 61052 / % reflection Rfree: 5 % / Rfactor obs: 0.231 / Rfactor Rfree: 0.286 / Rfactor Rwork: 0.228 | |||||||||||||||||||||||||
溶媒の処理 | *PLUS | |||||||||||||||||||||||||
原子変位パラメータ | *PLUS | |||||||||||||||||||||||||
拘束条件 | *PLUS
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LS精密化 シェル | *PLUS Rfactor Rfree: 0.438 / Rfactor Rwork: 0.366 |