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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: 8hv5 | ||||||
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タイトル | Crystal structure of EGFR_DMX in complex with compound 7 | ||||||
![]() | Epidermal growth factor receptor | ||||||
![]() | TRANSFERASE / Epidermal growth factor receptor kinase / covalent fragments / mutant EGFR / anti-cancer | ||||||
機能・相同性 | ![]() response to hydroxyisoflavone / multivesicular body, internal vesicle lumen / positive regulation of prolactin secretion / negative regulation of cardiocyte differentiation / positive regulation of protein kinase C activity / diterpenoid metabolic process / Shc-EGFR complex / ovulation cycle / Inhibition of Signaling by Overexpressed EGFR / epidermal growth factor receptor activity ...response to hydroxyisoflavone / multivesicular body, internal vesicle lumen / positive regulation of prolactin secretion / negative regulation of cardiocyte differentiation / positive regulation of protein kinase C activity / diterpenoid metabolic process / Shc-EGFR complex / ovulation cycle / Inhibition of Signaling by Overexpressed EGFR / epidermal growth factor receptor activity / EGFR interacts with phospholipase C-gamma / positive regulation of mucus secretion / response to UV-A / epidermal growth factor binding / PLCG1 events in ERBB2 signaling / tongue development / midgut development / ERBB2-EGFR signaling pathway / hydrogen peroxide metabolic process / PTK6 promotes HIF1A stabilization / digestive tract morphogenesis / morphogenesis of an epithelial fold / ERBB2 Activates PTK6 Signaling / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / intracellular vesicle / Signaling by EGFR / response to cobalamin / transmembrane receptor protein tyrosine kinase activator activity / protein tyrosine kinase activator activity / negative regulation of epidermal growth factor receptor signaling pathway / Signaling by ERBB4 / eyelid development in camera-type eye / protein insertion into membrane / cerebral cortex cell migration / ERBB2 Regulates Cell Motility / Respiratory syncytial virus (RSV) attachment and entry / regulation of JNK cascade / : / PI3K events in ERBB2 signaling / positive regulation of cyclin-dependent protein serine/threonine kinase activity / negative regulation of mitotic cell cycle / hair follicle development / MAP kinase kinase kinase activity / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / embryonic placenta development / positive regulation of bone resorption / GAB1 signalosome / positive regulation of G1/S transition of mitotic cell cycle / salivary gland morphogenesis / peptidyl-tyrosine autophosphorylation / regulation of peptidyl-tyrosine phosphorylation / positive regulation of phosphorylation / positive regulation of glial cell proliferation / positive regulation of vasoconstriction / Signaling by ERBB2 / cellular response to epidermal growth factor stimulus / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / EGFR Transactivation by Gastrin / cellular response to cadmium ion / GRB2 events in ERBB2 signaling / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / positive regulation of DNA repair / transmembrane receptor protein tyrosine kinase activity / SHC1 events in ERBB2 signaling / cellular response to dexamethasone stimulus / ossification / neurogenesis / positive regulation of synaptic transmission, glutamatergic / regulation of ERK1 and ERK2 cascade / neuron projection morphogenesis / basal plasma membrane / positive regulation of epithelial cell proliferation / positive regulation of superoxide anion generation / positive regulation of DNA replication / epithelial cell proliferation / Signal transduction by L1 / cellular response to estradiol stimulus / NOTCH3 Activation and Transmission of Signal to the Nucleus / astrocyte activation / liver regeneration / positive regulation of protein localization to plasma membrane / EGFR downregulation / positive regulation of smooth muscle cell proliferation / cellular response to amino acid stimulus / Signaling by ERBB2 TMD/JMD mutants / lung development / positive regulation of MAP kinase activity / clathrin-coated endocytic vesicle membrane / Constitutive Signaling by EGFRvIII / Signaling by ERBB2 ECD mutants / epidermal growth factor receptor signaling pathway / Signaling by ERBB2 KD Mutants / negative regulation of protein catabolic process / receptor protein-tyrosine kinase / Downregulation of ERBB2 signaling / kinase binding / cell-cell adhesion / ruffle membrane / positive regulation of miRNA transcription 類似検索 - 分子機能 | ||||||
生物種 | ![]() | ||||||
手法 | ![]() ![]() ![]() | ||||||
![]() | Dokurno, P. | ||||||
資金援助 | 1件
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![]() | ![]() タイトル: A covalent fragment-based strategy targeting a novel cysteine to inhibit activity of mutant EGFR kinase. 著者: Kuki, N. / Walmsley, D.L. / Kanai, K. / Takechi, S. / Yoshida, M. / Murakami, R. / Takano, K. / Tominaga, Y. / Takahashi, M. / Ito, S. / Nakao, N. / Angove, H. / Baker, L.M. / Carter, E. / ...著者: Kuki, N. / Walmsley, D.L. / Kanai, K. / Takechi, S. / Yoshida, M. / Murakami, R. / Takano, K. / Tominaga, Y. / Takahashi, M. / Ito, S. / Nakao, N. / Angove, H. / Baker, L.M. / Carter, E. / Dokurno, P. / Le Strat, L. / Macias, A.T. / Molyneaux, C.A. / Murray, J.B. / Surgenor, A.E. / Hamada, T. / Hubbard, R.E. | ||||||
履歴 |
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構造の表示
構造ビューア | 分子: ![]() ![]() |
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ダウンロードとリンク
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ダウンロード
PDBx/mmCIF形式 | ![]() | 81.5 KB | 表示 | ![]() |
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PDB形式 | ![]() | 58.1 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 | ![]() 8hv1C ![]() 8hv2C ![]() 8hv3C ![]() 8hv4C ![]() 8hv6C ![]() 8hv7C ![]() 8hv8C ![]() 8hv9C ![]() 8hvaC ![]() 5edqS S: 精密化の開始モデル C: 同じ文献を引用 ( |
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類似構造データ | 類似検索 - 機能・相同性 ![]() |
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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: 37549.398 Da / 分子数: 1 / 変異: T790M, L858R, E865A, E866A, K867A / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() 発現宿主: ![]() ![]() 参照: UniProt: P00533, receptor protein-tyrosine kinase |
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#2: 化合物 | ChemComp-PE5 / |
#3: 化合物 | ChemComp-N7C / ~{ |
#4: 水 | ChemComp-HOH / |
研究の焦点であるリガンドがあるか | Y |
-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: 3.36 Å3/Da / 溶媒含有率: 63.4 % |
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結晶化 | 温度: 292 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 8.5 / 詳細: 0.1M TRIS pH 8.5, 0.15M Sodium citrate, 25%PEG400 |
-データ収集
回折 | 平均測定温度: 100 K / Serial crystal experiment: N |
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放射光源 | 由来: ![]() ![]() ![]() |
検出器 | タイプ: DECTRIS EIGER X 9M / 検出器: PIXEL / 日付: 2018年8月15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: 0.9786 Å / 相対比: 1 |
反射 | 解像度: 2.06→45.75 Å / Num. obs: 30952 / % possible obs: 99.5 % / 冗長度: 13.8 % / CC1/2: 1 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.016 / Rrim(I) all: 0.059 / Χ2: 0.92 / Net I/σ(I): 22.7 / Num. measured all: 427473 |
反射 シェル | 解像度: 2.06→2.12 Å / % possible obs: 98.3 % / 冗長度: 13.3 % / Rmerge(I) obs: 1.458 / Num. measured all: 29962 / Num. unique obs: 2257 / CC1/2: 0.72 / Rpim(I) all: 0.409 / Rrim(I) all: 1.515 / Χ2: 0.75 / Net I/σ(I) obs: 1.7 |
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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: 5EDQ 解像度: 2.2→20 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.949 / SU B: 4.383 / SU ML: 0.111 / 交差検証法: THROUGHOUT / ESU R: 0.177 / ESU R Free: 0.163 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD / 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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溶媒の処理 | イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.2 Å / 溶媒モデル: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 57.309 Å2
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精密化ステップ | サイクル: 1 / 解像度: 2.2→20 Å
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拘束条件 |
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