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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: 6sod | ||||||
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タイトル | Fragment N14056a in complex with MAP kinase p38-alpha | ||||||
![]() | Mitogen-activated protein kinase 14 | ||||||
![]() | TRANSFERASE / FBDD / Fragment Based Drug Design / P38 / MAPK14 / Kinase / Transferase. | ||||||
機能・相同性 | ![]() p38MAPK events / Activation of the AP-1 family of transcription factors / Platelet sensitization by LDL / RHO GTPases Activate NADPH Oxidases / ERK/MAPK targets / activated TAK1 mediates p38 MAPK activation / NOD1/2 Signaling Pathway / ADP signalling through P2Y purinoceptor 1 / Oxidative Stress Induced Senescence / Regulation of TP53 Activity through Phosphorylation ...p38MAPK events / Activation of the AP-1 family of transcription factors / Platelet sensitization by LDL / RHO GTPases Activate NADPH Oxidases / ERK/MAPK targets / activated TAK1 mediates p38 MAPK activation / NOD1/2 Signaling Pathway / ADP signalling through P2Y purinoceptor 1 / Oxidative Stress Induced Senescence / Regulation of TP53 Activity through Phosphorylation / Myogenesis / VEGFA-VEGFR2 Pathway / regulation of synaptic membrane adhesion / stress-induced premature senescence / cell surface receptor protein serine/threonine kinase signaling pathway / cartilage condensation / positive regulation of myoblast fusion / cellular response to UV-B / mitogen-activated protein kinase p38 binding / positive regulation of myotube differentiation / NFAT protein binding / glucose import / negative regulation of hippo signaling / regulation of cytokine production involved in inflammatory response / p38MAPK cascade / fatty acid oxidation / cellular response to lipoteichoic acid / response to muramyl dipeptide / response to dietary excess / MAP kinase activity / regulation of ossification / cellular response to vascular endothelial growth factor stimulus / mitogen-activated protein kinase / positive regulation of myoblast differentiation / chondrocyte differentiation / vascular endothelial growth factor receptor signaling pathway / stress-activated MAPK cascade / skeletal muscle tissue development / positive regulation of cardiac muscle cell proliferation / lipopolysaccharide-mediated signaling pathway / striated muscle cell differentiation / response to muscle stretch / positive regulation of interleukin-12 production / positive regulation of brown fat cell differentiation / Neutrophil degranulation / osteoclast differentiation / positive regulation of erythrocyte differentiation / DNA damage checkpoint signaling / placenta development / positive regulation of glucose import / stem cell differentiation / cellular response to ionizing radiation / response to insulin / bone development / negative regulation of canonical Wnt signaling pathway / cell morphogenesis / cellular response to virus / spindle pole / positive regulation of protein import into nucleus / osteoblast differentiation / glucose metabolic process / positive regulation of reactive oxygen species metabolic process / MAPK cascade / cellular response to tumor necrosis factor / kinase activity / peptidyl-serine phosphorylation / protein phosphatase binding / cellular response to lipopolysaccharide / angiogenesis / transcription by RNA polymerase II / response to lipopolysaccharide / protein kinase activity / intracellular signal transduction / nuclear speck / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / glutamatergic synapse / regulation of transcription by RNA polymerase II / positive regulation of gene expression / regulation of DNA-templated transcription / apoptotic process / positive regulation of transcription by RNA polymerase II / mitochondrion / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol 類似検索 - 分子機能 | ||||||
生物種 | ![]() ![]() | ||||||
手法 | ![]() ![]() ![]() | ||||||
![]() | Nichols, C.E. / De Nicola, G.F. | ||||||
資金援助 | ![]()
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![]() | ![]() タイトル: Mining the PDB for Tractable Cases Where X-ray Crystallography Combined with Fragment Screens Can Be Used to Systematically Design Protein-Protein Inhibitors: Two Test Cases Illustrated ...タイトル: Mining the PDB for Tractable Cases Where X-ray Crystallography Combined with Fragment Screens Can Be Used to Systematically Design Protein-Protein Inhibitors: Two Test Cases Illustrated by IL1 beta-IL1R and p38 alpha-TAB1 Complexes. 著者: Nichols, C. / Ng, J. / Keshu, A. / Kelly, G. / Conte, M.R. / Marber, M.S. / Fraternali, F. / De Nicola, G.F. | ||||||
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 | ![]() | 109.1 KB | 表示 | ![]() |
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PDB形式 | ![]() | 65.8 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 | ![]() 5r85C ![]() 5r86C ![]() 5r87C ![]() 5r88C ![]() 5r89C ![]() 5r8aC ![]() 5r8bC ![]() 5r8cC ![]() 5r8dC ![]() 5r8eC ![]() 5r8fC ![]() 5r8gC ![]() 5r8hC ![]() 5r8iC ![]() 5r8jC ![]() 5r8kC ![]() 5r8lC ![]() 5r8mC ![]() 5r8nC ![]() 5r8oC ![]() 5r8pC ![]() 5r8qC ![]() 5r8uC ![]() 5r8vC ![]() 5r8wC ![]() 5r8xC ![]() 5r8yC ![]() 5r8zC ![]() 5r90C ![]() 5r91C ![]() 5r92C ![]() 5r93C ![]() 5r94C ![]() 5r95C ![]() 5r96C ![]() 5r97C ![]() 5r98C ![]() 5r99C ![]() 5r9aC ![]() 5r9bC ![]() 5r9cC ![]() 5r9dC ![]() 5r9eC ![]() 5r9fC ![]() 5r9gC ![]() 5r9hC ![]() 5r9iC ![]() 5r9jC ![]() 5r9kC ![]() 5r9lC ![]() 5r9mC ![]() 5r9nC ![]() 5r9oC ![]() 5r9pC ![]() 5r9qC ![]() 5r9rC ![]() 5r9sC ![]() 5r9tC ![]() 5r9uC ![]() 5r9vC ![]() 5r9wC ![]() 5r9xC ![]() 5r9yC ![]() 5r9zC ![]() 5ra0C ![]() 5ra1C ![]() 5ra2C ![]() 5ra3C ![]() 5ra4C ![]() 5ra5C ![]() 5ra6C ![]() 5ra7C ![]() 5ra8C ![]() 5ra9C ![]() 6so1SC ![]() 6so2C ![]() 6so4C ![]() 6soiC ![]() 6sotC ![]() 6souC ![]() 6sovC ![]() 6sp9C ![]() 6splC ![]() 6y7wC ![]() 6y7xC ![]() 6y7yC ![]() 6y80C ![]() 6y81C ![]() 6ycuC ![]() 6ycwC 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 |
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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
-タンパク質 , 1種, 1分子 A
#1: タンパク質 | 分子量: 43808.738 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() ![]() |
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-非ポリマー , 6種, 204分子 ![](data/chem/img/LOE.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/HOH.gif)
#2: 化合物 | ChemComp-LOE / | ||||||||
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#3: 化合物 | ChemComp-CL / #4: 化合物 | ChemComp-MG / | #5: 化合物 | #6: 化合物 | ChemComp-DMS / | #7: 水 | ChemComp-HOH / | |
-詳細
研究の焦点であるリガンドがあるか | Y |
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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: 3.12 Å3/Da / 溶媒含有率: 60.63 % |
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結晶化 | 温度: 291 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 6.9 詳細: 27.5% PEG3350, 0.1M magnesium chloride, 0.1M magnesium sulphate, 0.1M bis-tris propane, 10% glycerol |
-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 PILATUS 6M-F / 検出器: PIXEL / 日付: 2016年4月24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: 0.92 Å / 相対比: 1 |
反射 | 解像度: 1.87→63.17 Å / Num. obs: 41836 / % possible obs: 99.8 % / 冗長度: 6.5 % / Biso Wilson estimate: 32.46 Å2 / CC1/2: 0.999 / Net I/σ(I): 13.5 |
反射 シェル | 解像度: 1.87→1.92 Å / 冗長度: 6.8 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3064 / CC1/2: 0.551 / % possible all: 100 |
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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: 6SO1 解像度: 1.87→63.17 Å / SU ML: 0.2187 / 交差検証法: FREE R-VALUE / σ(F): 0.06 / 位相誤差: 22.3988
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溶媒の処理 | 減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 37.09 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 1.87→63.17 Å
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拘束条件 |
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LS精密化 シェル |
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