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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: 4o3t | |||||||||
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タイトル | Zymogen HGF-beta/MET with Zymogen Activator Peptide ZAP.14 | |||||||||
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![]() | transferase/growth factor / trypsin homology / receptor activation / transferase-growth factor complex | |||||||||
機能・相同性 | ![]() regulation of p38MAPK cascade / skeletal muscle cell proliferation / negative regulation of guanyl-nucleotide exchange factor activity / hepatocyte growth factor receptor activity / regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling / Drug-mediated inhibition of MET activation / MET activates STAT3 / negative regulation of hydrogen peroxide-mediated programmed cell death / MET Receptor Activation / MET interacts with TNS proteins ...regulation of p38MAPK cascade / skeletal muscle cell proliferation / negative regulation of guanyl-nucleotide exchange factor activity / hepatocyte growth factor receptor activity / regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling / Drug-mediated inhibition of MET activation / MET activates STAT3 / negative regulation of hydrogen peroxide-mediated programmed cell death / MET Receptor Activation / MET interacts with TNS proteins / endothelial cell morphogenesis / hepatocyte growth factor receptor signaling pathway / semaphorin receptor activity / MET receptor recycling / pancreas development / MET activates PTPN11 / MET activates RAP1 and RAC1 / Sema4D mediated inhibition of cell attachment and migration / MET activates PI3K/AKT signaling / positive regulation of endothelial cell chemotaxis / negative regulation of stress fiber assembly / MET activates PTK2 signaling / positive regulation of DNA biosynthetic process / cellular response to hepatocyte growth factor stimulus / branching morphogenesis of an epithelial tube / positive chemotaxis / negative regulation of Rho protein signal transduction / negative regulation of release of cytochrome c from mitochondria / chemoattractant activity / negative regulation of thrombin-activated receptor signaling pathway / negative regulation of interleukin-6 production / semaphorin-plexin signaling pathway / myoblast proliferation / positive regulation of interleukin-10 production / epithelial to mesenchymal transition / establishment of skin barrier / positive regulation of osteoblast differentiation / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / MET activates RAS signaling / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / MECP2 regulates neuronal receptors and channels / positive regulation of microtubule polymerization / Interleukin-7 signaling / negative regulation of autophagy / cell surface receptor protein tyrosine kinase signaling pathway / basal plasma membrane / platelet alpha granule lumen / molecular function activator activity / InlB-mediated entry of Listeria monocytogenes into host cell / epithelial cell proliferation / cell chemotaxis / excitatory postsynaptic potential / growth factor activity / liver development / Negative regulation of MET activity / receptor protein-tyrosine kinase / negative regulation of inflammatory response / cell morphogenesis / neuron differentiation / Constitutive Signaling by Aberrant PI3K in Cancer / Platelet degranulation / PIP3 activates AKT signaling / mitotic cell cycle / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / protein tyrosine kinase activity / protein phosphatase binding / Interleukin-4 and Interleukin-13 signaling / cell surface receptor signaling pathway / receptor complex / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / postsynapse / positive regulation of MAPK cascade / positive regulation of cell migration / signaling receptor binding / negative regulation of apoptotic process / cell surface / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / ATP binding / identical protein binding / membrane / plasma membrane 類似検索 - 分子機能 | |||||||||
生物種 | ![]() synthetic (人工物) | |||||||||
手法 | ![]() ![]() ![]() | |||||||||
![]() | Eigenbrot, C. / Landgraf, K.E. / Steffek, M. | |||||||||
![]() | ![]() タイトル: An allosteric switch for pro-HGF/Met signaling using zymogen activator peptides. 著者: Landgraf, K.E. / Steffek, M. / Quan, C. / Tom, J. / Yu, C. / Santell, L. / Maun, H.R. / Eigenbrot, C. / Lazarus, R.A. | |||||||||
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 | ![]() | 162.2 KB | 表示 | ![]() |
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PDB形式 | ![]() | 123.3 KB | 表示 | ![]() |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
その他 | ![]() |
-検証レポート
文書・要旨 | ![]() | 852.9 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 864 KB | 表示 | |
XML形式データ | ![]() | 26.6 KB | 表示 | |
CIF形式データ | ![]() | 35.7 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
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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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要素
#1: タンパク質 | 分子量: 26800.920 Da / 分子数: 1 / 断片: HGF-beta (UNP Residues 25-567) / 変異: V495G/C604S / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() 発現宿主: ![]() ![]() 参照: UniProt: P14210 |
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#2: タンパク質 | 分子量: 62714.141 Da / 分子数: 1 / 断片: Sema-PSI (UNP Residues 496-728) / 変異: L303K/V304R/P305K/R306K/G307R / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() 発現宿主: ![]() ![]() 参照: UniProt: P08581, receptor protein-tyrosine kinase |
#3: タンパク質・ペプチド | 分子量: 1322.530 Da / 分子数: 1 / 由来タイプ: 合成 詳細: derived from synthetic peptide library displayed on phage particles 由来: (合成) synthetic (人工物) |
#4: 多糖 | alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta- ...alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose |
#5: 化合物 | ChemComp-1PE / |
Has protein modification | 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: 2.75 Å3/Da / 溶媒含有率: 55.29 % |
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結晶化 | 温度: 293 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 8.5 詳細: PEG6000, 800 mM NaCl, 400 mM trimethylammonium oxide, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-データ収集
回折 | 平均測定温度: 110 K |
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放射光源 | 由来: ![]() ![]() ![]() |
検出器 | タイプ: RAYONIX MX-225 / 検出器: CCD / 日付: 2011年11月4日 |
放射 | モノクロメーター: diamond (111) / 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: 0.9787 Å / 相対比: 1 |
反射 | 解像度: 2.99→45.54 Å / Num. all: 20873 / Num. obs: 20853 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / 冗長度: 6.1 % / Biso Wilson estimate: 73.84 Å2 / Rsym value: 0.112 / Net I/σ(I): 15 |
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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: PDB ENTRY 1SHY 解像度: 2.99→45.54 Å / Cor.coef. Fo:Fc: 0.8641 / Cor.coef. Fo:Fc free: 0.8233 / Isotropic thermal model: individual atom isotropic / 交差検証法: THROUGHOUT / σ(F): 0 / 立体化学のターゲット値: Engh & Huber
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原子変位パラメータ | Biso mean: 66.81 Å2
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Refine analyze | Luzzati coordinate error obs: 0.442 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 2.99→45.54 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 2.99→3.15 Å / Total num. of bins used: 10
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