+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 6so1 | ||||||
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タイトル | Fragment N13569a in complex with MAP kinase p38-alpha | ||||||
要素 | Mitogen-activated protein kinase 14 | ||||||
キーワード | TRANSFERASE / FBDD / Fragment Based Drug Design / P38 / MAPK14 / Kinase / Transferase. | ||||||
機能・相同性 | 機能・相同性情報 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 | Mus musculus (ハツカネズミ) | ||||||
手法 | X線回折 / シンクロトロン / 分子置換 / 解像度: 1.66 Å | ||||||
データ登録者 | Nichols, C.E. / De Nicola, G.F. | ||||||
資金援助 | 英国, 1件
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引用 | ジャーナル: J.Med.Chem. / 年: 2020 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: 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 | 6so1.cif.gz | 111.1 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb6so1.ent.gz | 67.3 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 6so1.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 | 6so1_validation.pdf.gz | 819.1 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 6so1_full_validation.pdf.gz | 821.4 KB | 表示 | |
XML形式データ | 6so1_validation.xml.gz | 17 KB | 表示 | |
CIF形式データ | 6so1_validation.cif.gz | 25.3 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/so/6so1 ftp://data.pdbj.org/pub/pdb/validation_reports/so/6so1 | HTTPS FTP |
-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 6so2C 6so4C 6sodC 6soiC 6sotC 6souC 6sovC 6sp9C 6splC 6y7wC 6y7xC 6y7yC 6y80C 6y81C 6ycuC 6ycwC 4looS S: 精密化の開始モデル C: 同じ文献を引用 (文献) |
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類似構造データ |
-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
-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) Mus musculus (ハツカネズミ) / 遺伝子: Mapk14, Crk1, Csbp1, Csbp2 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P47811, mitogen-activated protein kinase |
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-非ポリマー , 5種, 281分子
#2: 化合物 | ChemComp-LO5 / | ||||||
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#3: 化合物 | ChemComp-CL / #4: 化合物 | ChemComp-MG / | #5: 化合物 | #6: 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: X線回折 / 使用した結晶の数: 1 |
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-試料調製
結晶 | マシュー密度: 3.14 Å3/Da / 溶媒含有率: 60.77 % |
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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 acetate, 0.1M bis-tris propane pH6.9 |
-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: シンクロトロン / サイト: Diamond / ビームライン: I04-1 / 波長: 0.92 Å |
検出器 | タイプ: DECTRIS PILATUS 6M-F / 検出器: PIXEL / 日付: 2016年2月11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: 1.66→29.18 Å / Num. obs: 59026 / % possible obs: 98.71 % / 冗長度: 6.7 % / Biso Wilson estimate: 25.88 Å2 / CC1/2: 0.999 / Net I/σ(I): 16.85 |
反射 シェル | 解像度: 1.66→1.72 Å / 冗長度: 6.5 % / Mean I/σ(I) obs: 1.96 / Num. unique obs: 5728 / CC1/2: 0.752 / % possible all: 97.04 |
-解析
ソフトウェア |
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精密化 | 構造決定の手法: 分子置換 開始モデル: 4LOO 解像度: 1.66→29.18 Å / SU ML: 0.2132 / 交差検証法: THROUGHOUT / σ(F): 1.37 / 位相誤差: 19.5065
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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: 29.77 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 1.66→29.18 Å
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拘束条件 |
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LS精密化 シェル |
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