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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: 3lnz | ||||||
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タイトル | Crystal structure of human MDM2 with a 12-mer peptide inhibitor PMI (N8A mutant) | ||||||
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![]() | LIGASE/LIGASE INHIBITOR / P53-BINDING PROTEIN of MDM2 / ONCOPROTEIN MDM2 / HUMAN DOUBLE MINUTE 2 PROTEIN / HDM2 / MDM2-peptide inhibitor complex / p53 peptide activator N8A-PMI / Host-virus interaction / Ligase / Metal-binding / Nucleus / Phosphoprotein / Proto-oncogene / Ubl conjugation pathway / Zinc-finger / 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 iron ion / response to steroid hormone / NEDD8 ligase activity / AKT phosphorylates targets in the cytosol / atrioventricular valve morphogenesis / cellular response to peptide hormone stimulus / ventricular septum development / endocardial cushion morphogenesis / positive regulation of muscle cell differentiation / SUMOylation of ubiquitinylation proteins / cellular response to alkaloid / blood vessel development / regulation of protein catabolic process / cardiac septum morphogenesis / Constitutive Signaling by AKT1 E17K in Cancer / ligase activity / 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 / response to cocaine / proteolysis involved in protein catabolic process / 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 / endocytic vesicle membrane / ubiquitin protein ligase activity / disordered domain specific binding / 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 / Ub-specific processing proteases / regulation of cell cycle / protein ubiquitination / response to xenobiotic stimulus / protein domain specific binding / response to antibiotic / negative regulation of DNA-templated transcription / apoptotic process / ubiquitin protein ligase binding / positive regulation of cell population proliferation / positive regulation of gene expression / nucleolus / negative regulation of apoptotic process / enzyme binding / negative regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / nucleoplasm 類似検索 - 分子機能 | ||||||
手法 | ![]() ![]() | ||||||
![]() | Pazgier, M. / Lu, W. | ||||||
![]() | ![]() タイトル: Systematic mutational analysis of peptide inhibition of the p53-MDM2/MDMX interactions. 著者: Li, C. / Pazgier, M. / Li, C. / Yuan, W. / Liu, M. / Wei, G. / Lu, W.Y. / Lu, W. | ||||||
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 | ![]() | 178.6 KB | 表示 | ![]() |
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PDB形式 | ![]() | 143.7 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 | ![]() | 504.6 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 516.4 KB | 表示 | |
XML形式データ | ![]() | 37.7 KB | 表示 | |
CIF形式データ | ![]() | 55 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
関連構造データ | ![]() 3eqsS S: 精密化の開始モデル |
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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
#1: タンパク質 | 分子量: 10044.889 Da / 分子数: 8 / 断片: UNP residues 25-109, P53 BINDING DOMAIN / 由来タイプ: 合成 / 詳細: This sequence occurs naturally in humans. 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: タンパク質・ペプチド | 分子量: 1384.532 Da / 分子数: 8 / Mutation: N8A / 由来タイプ: 合成 / 詳細: Synthetic peptide found by phage dissplay #3: 化合物 | ChemComp-CL / #4: 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: 2.55 Å3/Da / 溶媒含有率: 51.78 % |
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結晶化 | 温度: 273 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 6.5 詳細: 0.2 M Mg acetate tetrahydrate sulfate, 0.1 M cacodylate trihydrate, 20% PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 273K |
-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: RIGAKU RAXIS IV++ / 検出器: IMAGE PLATE / 日付: 2010年1月6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: 1.54 Å / 相対比: 1 |
反射 | 解像度: 1.949→78.413 Å / Num. all: 67750 / Num. obs: 67730 / % possible obs: 99 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / 冗長度: 8.2 % / Rmerge(I) obs: 0.119 / Rsym value: 0.152 / Net I/σ(I): 23.1 |
反射 シェル | 解像度: 1.95→1.98 Å / 冗長度: 8.1 % / Rmerge(I) obs: 0.575 / Mean I/σ(I) obs: 4 / Rsym value: 0.556 / % 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: PDB ENTRY 3EQS 解像度: 1.95→20 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.916 / SU B: 7.873 / SU ML: 0.126 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / ESU R: 0.191 / ESU R Free: 0.175 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD
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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: 1.4 Å / 溶媒モデル: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 27.757 Å2
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精密化ステップ | サイクル: LAST / 解像度: 1.95→20 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 1.949→1.999 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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