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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: 5trf | ||||||
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タイトル | MDM2 in complex with SAR405838 | ||||||
![]() | E3 ubiquitin-protein ligase Mdm2 | ||||||
![]() | LIGASE/LIGASE INHIBITOR / P53-BINDING PROTEIN / ONCOPROTEIN / DOUBLE MINUTE 2 PROTEIN / SMALL MOLECULE INHIBITOR / LIGASE-LIGASE INHIBITOR complex | ||||||
機能・相同性 | ![]() cellular response to vitamin B1 / response to formaldehyde / response to water-immersion restraint stress / traversing start control point of mitotic cell cycle / negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator / response to ether / negative regulation of signal transduction by p53 class mediator / fibroblast activation / atrial septum development / receptor serine/threonine kinase binding ...cellular response to vitamin B1 / response to formaldehyde / response to water-immersion restraint stress / traversing start control point of mitotic cell cycle / negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator / response to ether / negative regulation of signal transduction by p53 class mediator / fibroblast activation / atrial septum development / receptor serine/threonine kinase binding / Trafficking of AMPA receptors / positive regulation of vascular associated smooth muscle cell migration / peroxisome proliferator activated receptor binding / SUMO transferase activity / negative regulation of protein processing / response to steroid hormone / NEDD8 ligase activity / response to iron ion / AKT phosphorylates targets in the cytosol / cellular response to peptide hormone stimulus / atrioventricular valve morphogenesis / ventricular septum development / endocardial cushion morphogenesis / positive regulation of muscle cell differentiation / SUMOylation of ubiquitinylation proteins / cellular response to alkaloid / regulation of protein catabolic process / blood vessel development / cardiac septum morphogenesis / ligase activity / Constitutive Signaling by AKT1 E17K in Cancer / negative regulation of DNA damage response, signal transduction by p53 class mediator / response to magnesium ion / SUMOylation of transcription factors / protein sumoylation / protein localization to nucleus / cellular response to UV-C / blood vessel remodeling / cellular response to estrogen stimulus / protein autoubiquitination / cellular response to actinomycin D / ribonucleoprotein complex binding / positive regulation of vascular associated smooth muscle cell proliferation / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / NPAS4 regulates expression of target genes / transcription repressor complex / regulation of heart rate / positive regulation of mitotic cell cycle / positive regulation of protein export from nucleus / proteolysis involved in protein catabolic process / response to cocaine / ubiquitin binding / Stabilization of p53 / Regulation of RUNX3 expression and activity / protein destabilization / RING-type E3 ubiquitin transferase / establishment of protein localization / Oncogene Induced Senescence / Regulation of TP53 Activity through Methylation / response to toxic substance / cellular response to gamma radiation / cellular response to growth factor stimulus / cellular response to hydrogen peroxide / protein polyubiquitination / ubiquitin-protein transferase activity / disordered domain specific binding / endocytic vesicle membrane / ubiquitin protein ligase activity / Signaling by ALK fusions and activated point mutants / Regulation of TP53 Degradation / p53 binding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of neuron projection development / cellular response to hypoxia / 5S rRNA binding / ubiquitin-dependent protein catabolic process / regulation of gene expression / protein-containing complex assembly / proteasome-mediated ubiquitin-dependent protein catabolic process / Oxidative Stress Induced Senescence / Regulation of TP53 Activity through Phosphorylation / amyloid fibril formation / regulation of cell cycle / Ub-specific processing proteases / protein ubiquitination / response to xenobiotic stimulus / protein domain specific binding / response to antibiotic / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / positive regulation of cell population proliferation / positive regulation of gene expression / nucleolus / negative regulation of apoptotic process / apoptotic process / negative regulation of transcription by RNA polymerase II / enzyme binding / protein-containing complex / zinc ion binding / nucleoplasm 類似検索 - 分子機能 | ||||||
生物種 | ![]() | ||||||
手法 | ![]() ![]() ![]() | ||||||
![]() | Meagher, J.L. / Stuckey, J.A. | ||||||
![]() | ![]() タイトル: SAR405838: an optimized inhibitor of MDM2-p53 interaction that induces complete and durable tumor regression. 著者: Wang, S. / Sun, W. / Zhao, Y. / McEachern, D. / Meaux, I. / Barriere, C. / Stuckey, J.A. / Meagher, J.L. / Bai, L. / Liu, L. / Hoffman-Luca, C.G. / Lu, J. / Shangary, S. / Yu, S. / Bernard, D. ...著者: Wang, S. / Sun, W. / Zhao, Y. / McEachern, D. / Meaux, I. / Barriere, C. / Stuckey, J.A. / Meagher, J.L. / Bai, L. / Liu, L. / Hoffman-Luca, C.G. / Lu, J. / Shangary, S. / Yu, S. / Bernard, D. / Aguilar, A. / Dos-Santos, O. / Besret, L. / Guerif, S. / Pannier, P. / Gorge-Bernat, D. / Debussche, L. | ||||||
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 | ![]() | 219.1 KB | 表示 | ![]() |
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PDB形式 | ![]() | 176.6 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
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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: 12506.351 Da / 分子数: 5 / 断片: residues 10-118 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() 参照: UniProt: Q00987, 合成酵素; C-N結合を形成; 酸-D-アミノ酸リガーゼ(ペプチド合成) #2: 化合物 | ChemComp-7HC / ( #3: 化合物 | #4: 化合物 | ChemComp-GOL / #5: 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: 3.47 Å3/Da / 溶媒含有率: 64.52 % |
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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 / 詳細: 2m2M Ammonium Sulfate and 0.2M Lithium Nitrate |
-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: MARMOSAIC 225 mm CCD / 検出器: CCD / 日付: 2011年10月13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: 0.97872 Å / 相対比: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
反射 | 解像度: 2.1→50 Å / Num. obs: 48047 / % possible obs: 100 % / 冗長度: 13.6 % / Biso Wilson estimate: 26.15 Å2 / Rmerge(I) obs: 0.102 / Χ2: 1.017 / Net I/av σ(I): 30.429 / Net I/σ(I): 8.4 / Num. measured all: 651706 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
反射 シェル |
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-位相決定
位相決定 | 手法: ![]() |
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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: ![]()
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原子変位パラメータ | Biso max: 105.31 Å2 / Biso mean: 29.02 Å2 / Biso min: 8.07 Å2
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Refine analyze | Luzzati coordinate error obs: 0.236 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: final / 解像度: 2.1→49.09 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 2.1→2.15 Å / Total num. of bins used: 20
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精密化 TLS | 手法: refined / Refine-ID: X-RAY DIFFRACTION
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精密化 TLSグループ |
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