+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 7d25 | ||||||
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タイトル | Hsp90 alpha N-terminal domain in complex with a 14 compund | ||||||
要素 | Heat shock protein HSP 90-alphaHeat shock response | ||||||
キーワード | CHAPERONE/INHIBITOR / CHAPERONE-Inhibitor complex | ||||||
機能・相同性 | 機能・相同性情報 Drug-mediated inhibition of ERBB2 signaling / ESR-mediated signaling / DDX58/IFIH1-mediated induction of interferon-alpha/beta / HSF1-dependent transactivation / Signaling by ERBB2 / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / eNOS activation / HSF1 activation / RHOBTB2 GTPase cycle / Sema3A PAK dependent Axon repulsion ...Drug-mediated inhibition of ERBB2 signaling / ESR-mediated signaling / DDX58/IFIH1-mediated induction of interferon-alpha/beta / HSF1-dependent transactivation / Signaling by ERBB2 / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / eNOS activation / HSF1 activation / RHOBTB2 GTPase cycle / Sema3A PAK dependent Axon repulsion / Downregulation of ERBB2 signaling / Attenuation phase / Regulation of necroptotic cell death / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / VEGFR2 mediated vascular permeability / positive regulation of cytotoxic T cell differentiation / Extra-nuclear estrogen signaling / The role of GTSE1 in G2/M progression after G2 checkpoint / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Regulation of actin dynamics for phagocytic cup formation / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / Regulation of PLK1 Activity at G2/M Transition / Estrogen-dependent gene expression / VEGFA-VEGFR2 Pathway / sperm mitochondrial sheath / dATP binding / sulfonylurea receptor binding / CTP binding / positive regulation of protein polymerization / UTP binding / sperm plasma membrane / protein insertion into mitochondrial outer membrane / telomerase holoenzyme complex assembly / Rho GDP-dissociation inhibitor binding / TPR domain binding / non-chaperonin molecular chaperone ATPase / regulation of postsynaptic membrane neurotransmitter receptor levels / dendritic growth cone / regulation of protein ubiquitination / skeletal muscle contraction / positive regulation of cell size / telomere maintenance via telomerase / response to unfolded protein / chaperone-mediated protein complex assembly / sperm flagellum / positive regulation of lamellipodium assembly / axonal growth cone / DNA polymerase binding / protein folding chaperone / positive regulation of cardiac muscle contraction / cardiac muscle cell apoptotic process / positive regulation of defense response to virus by host / response to salt stress / nitric oxide biosynthetic process / activation of innate immune response / Neutrophil degranulation / nitric-oxide synthase regulator activity / response to cold / positive regulation of interferon-beta production / protein tyrosine kinase binding / response to cocaine / brush border membrane / ATP-dependent protein folding chaperone / neuron migration / tau protein binding / cellular response to virus / histone deacetylase binding / positive regulation of protein import into nucleus / response to estrogen / positive regulation of protein catabolic process / regulation of protein localization / positive regulation of nitric oxide biosynthetic process / disordered domain specific binding / unfolded protein binding / メラノソーム / フォールディング / GTPase binding / 髄鞘 / cellular response to heat / response to heat / protein refolding / scaffold protein binding / basolateral plasma membrane / regulation of apoptotic process / protein phosphatase binding / collagen-containing extracellular matrix / transmembrane transporter binding / protein stabilization / response to xenobiotic stimulus / apical plasma membrane / positive regulation of protein phosphorylation / response to antibiotic / mRNA binding / neuronal cell body / ubiquitin protein ligase binding / GTP binding 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: 1.65 Å | ||||||
データ登録者 | Shin, S.C. / Kim, E.E. | ||||||
資金援助 | 韓国, 1件
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引用 | ジャーナル: Int J Mol Sci / 年: 2020 タイトル: Structural Basis for Design of New Purine-Based Inhibitors Targeting the Hydrophobic Binding Pocket of Hsp90. 著者: Shin, S.C. / El-Damasy, A.K. / Lee, J.H. / Seo, S.H. / Kim, J.H. / Seo, Y.H. / Lee, Y. / Yu, J.H. / Bang, E.K. / Kim, E.E. / Keum, G. | ||||||
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 | 7d25.cif.gz | 65 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb7d25.ent.gz | 44.6 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 7d25.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
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/d2/7d25 ftp://data.pdbj.org/pub/pdb/validation_reports/d2/7d25 | HTTPS FTP |
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-関連構造データ
-リンク
-集合体
登録構造単位 |
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1 |
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単位格子 |
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-要素
#1: タンパク質 | 分子量: 24109.275 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: Hsp90aa1, Hsp86, Hsp86-1, Hspca / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P07901 | ||||
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#2: 化合物 | #3: 水 | ChemComp-HOH / | 研究の焦点であるリガンドがあるか | Y | |
-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: 3.19 Å3/Da / 溶媒含有率: 61.46 % |
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結晶化 | 温度: 295 K / 手法: 蒸気拡散法, シッティングドロップ法 / 詳細: 1.0M ammonium Sulfate, 0.1M Tris-HCl (pH8.5) |
-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: PAL/PLS / ビームライン: 5C (4A) / 波長: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
検出器 | タイプ: ADSC QUANTUM 315r / 検出器: CCD / 日付: 2011年2月20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 Å / 相対比: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
反射 | 解像度: 1.65→50 Å / Num. obs: 35747 / % possible obs: 98.5 % / 冗長度: 5.8 % / Rmerge(I) obs: 0.053 / Χ2: 1.073 / Net I/σ(I): 16.1 / Num. measured all: 207351 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
反射 シェル |
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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: 分子置換 開始モデル: 5h22 解像度: 1.65→34.961 Å / SU ML: 0.18 / 交差検証法: THROUGHOUT / σ(F): 1.5 / 位相誤差: 19.29 / 立体化学のターゲット値: ML
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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 / 溶媒モデル: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso max: 54.93 Å2 / Biso mean: 23.8834 Å2 / Biso min: 10.98 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: final / 解像度: 1.65→34.961 Å
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LS精密化 シェル | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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