+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 2axi | ||||||
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タイトル | HDM2 in complex with a beta-hairpin | ||||||
要素 |
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キーワード | LIGASE/LIGASE INHIBITOR / P53 / DRUG DESIGN / PROTEIN-PROTEIN INTERACTIONS / LIGASE / LIGASE-LIGASE INHIBITOR complex | ||||||
機能・相同性 | 機能・相同性情報 cellular response to vitamin B1 / response to formaldehyde / response to water-immersion restraint stress / traversing start control point of mitotic cell cycle / response to ether / negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator / 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 / response to ether / negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator / 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 / response to iron ion / NEDD8 ligase activity / cellular response to peptide hormone stimulus / atrioventricular valve morphogenesis / AKT phosphorylates targets in the cytosol / ventricular septum development / endocardial cushion morphogenesis / positive regulation of muscle cell differentiation / cellular response to alkaloid / SUMOylation of ubiquitinylation proteins / regulation of protein catabolic process / blood vessel development / cardiac septum morphogenesis / ligase activity / Constitutive Signaling by AKT1 E17K in Cancer / response to magnesium ion / negative regulation of DNA damage response, signal transduction by p53 class mediator / SUMOylation of transcription factors / protein sumoylation / protein localization to nucleus / blood vessel remodeling / cellular response to UV-C / 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 / transcription repressor complex / NPAS4 regulates expression of target genes / regulation of heart rate / positive regulation of mitotic cell cycle / positive regulation of protein export from nucleus / ubiquitin binding / proteolysis involved in protein catabolic process / response to cocaine / Stabilization of p53 / protein destabilization / Regulation of RUNX3 expression and activity / establishment of protein localization / RING-type E3 ubiquitin transferase / cellular response to growth factor stimulus / Oncogene Induced Senescence / Regulation of TP53 Activity through Methylation / cellular response to gamma radiation / response to toxic substance / cellular response to hydrogen peroxide / protein polyubiquitination / ubiquitin-protein transferase activity / disordered domain specific binding / endocytic vesicle membrane / ubiquitin protein ligase activity / p53 binding / Signaling by ALK fusions and activated point mutants / Regulation of TP53 Degradation / negative regulation of neuron projection development / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / 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 / negative regulation of apoptotic process / nucleolus / 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 | Homo sapiens (ヒト) | ||||||
手法 | X線回折 / 分子置換 / 解像度: 1.4 Å | ||||||
データ登録者 | Mittl, P.R.E. / Fasan, R. / Robinson, J. / Gruetter, M.G. | ||||||
引用 | ジャーナル: Chembiochem / 年: 2006 タイトル: Structure-Activity Studies in a Family of beta-Hairpin Protein Epitope Mimetic Inhibitors of the p53-HDM2 Protein-Protein Interaction. 著者: Fasan, R. / Dias, R.L. / Moehle, K. / Zerbe, O. / Obrecht, D. / Mittl, P.R. / Robinson, J.A. | ||||||
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 | 2axi.cif.gz | 41.7 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb2axi.ent.gz | 26.9 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 2axi.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 | 2axi_validation.pdf.gz | 446.1 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 2axi_full_validation.pdf.gz | 449.4 KB | 表示 | |
XML形式データ | 2axi_validation.xml.gz | 5.9 KB | 表示 | |
CIF形式データ | 2axi_validation.cif.gz | 7.7 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/ax/2axi ftp://data.pdbj.org/pub/pdb/validation_reports/ax/2axi | HTTPS FTP |
-関連構造データ
関連構造データ | 1ycrS S: 精密化の開始モデル |
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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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Components on special symmetry positions |
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-要素
#1: タンパク質 | 分子量: 13364.231 Da / 分子数: 1 / 断片: HDM2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: MDM2 / プラスミド: pET14b / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3)pLysS 参照: UniProt: Q9UMT8, UniProt: Q00987*PLUS, 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) | ||||
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#2: タンパク質・ペプチド | | ||||
#3: 化合物 | #4: 化合物 | ChemComp-MPO / | #5: 水 | ChemComp-HOH / | |
-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: 1.82115 Å3/Da / 溶媒含有率: 32.460266 % / 解説: Data was collected in-house and at the synchrotron |
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結晶化 | 温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 5.5 詳細: MES, ammonium sulfate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-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: 回転陽極 / タイプ: ENRAF-NONIUS FR571 / 波長: 1.54 Å |
検出器 | タイプ: MARRESEARCH / 検出器: IMAGE PLATE / 日付: 2003年10月1日 / 詳細: Osmic Mirrors |
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: 1.4→50 Å / Num. obs: 21288 / % possible obs: 98.4 % / Observed criterion σ(I): 0 / 冗長度: 4.18 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 15.19 |
反射 シェル | 解像度: 1.4→1.41 Å / 冗長度: 3.9 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.91 / % possible all: 90.8 |
-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: 1YCR 解像度: 1.4→10 Å / σ(F): 4 / 立体化学のターゲット値: ENGH & HUBER
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精密化ステップ | サイクル: LAST / 解像度: 1.4→10 Å
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