+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1fpu | ||||||
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タイトル | CRYSTAL STRUCTURE OF ABL KINASE DOMAIN IN COMPLEX WITH A SMALL MOLECULE INHIBITOR | ||||||
要素 | PROTO-ONCOGENE TYROSINE-PROTEIN KINASE ABL | ||||||
キーワード | TRANSFERASE / kinase / kinase inhibitor / STI-571 / activation loop | ||||||
機能・相同性 | 機能・相同性情報 Role of ABL in ROBO-SLIT signaling / HDR through Single Strand Annealing (SSA) / RHO GTPases Activate WASPs and WAVEs / Cyclin D associated events in G1 / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / protein localization to cytoplasmic microtubule plus-end / DNA conformation change / circulatory system development / podocyte apoptotic process / DN4 thymocyte differentiation ...Role of ABL in ROBO-SLIT signaling / HDR through Single Strand Annealing (SSA) / RHO GTPases Activate WASPs and WAVEs / Cyclin D associated events in G1 / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / protein localization to cytoplasmic microtubule plus-end / DNA conformation change / circulatory system development / podocyte apoptotic process / DN4 thymocyte differentiation / response to epinephrine / regulation of cellular senescence / transitional one stage B cell differentiation / RUNX1 regulates transcription of genes involved in differentiation of HSCs / regulation of modification of synaptic structure / Regulation of actin dynamics for phagocytic cup formation / delta-catenin binding / B cell proliferation involved in immune response / positive regulation of extracellular matrix organization / neuroepithelial cell differentiation / microspike assembly / positive regulation of Wnt signaling pathway, planar cell polarity pathway / regulation of extracellular matrix organization / cerebellum morphogenesis / positive regulation of blood vessel branching / B-1 B cell homeostasis / neuropilin signaling pathway / neuropilin binding / Myogenesis / bubble DNA binding / activated T cell proliferation / regulation of Cdc42 protein signal transduction / proline-rich region binding / positive regulation of dendrite development / negative regulation of mitotic cell cycle / mitogen-activated protein kinase binding / myoblast proliferation / syntaxin binding / negative regulation of BMP signaling pathway / alpha-beta T cell differentiation / cardiac muscle cell proliferation / regulation of T cell differentiation / regulation of axon extension / positive regulation of cell migration involved in sprouting angiogenesis / negative regulation of cell-cell adhesion / BMP signaling pathway / B cell proliferation / cell leading edge / positive regulation of osteoblast proliferation / regulation of microtubule polymerization / platelet-derived growth factor receptor-beta signaling pathway / negative regulation of cellular senescence / positive regulation of focal adhesion assembly / associative learning / Bergmann glial cell differentiation / positive regulation of vasoconstriction / platelet-derived growth factor receptor signaling pathway / neuromuscular process controlling balance / negative regulation of long-term synaptic potentiation / endothelial cell migration / positive regulation of T cell migration / signal transduction in response to DNA damage / negative regulation of double-strand break repair via homologous recombination / negative regulation of endothelial cell apoptotic process / phagocytosis / canonical NF-kappaB signal transduction / four-way junction DNA binding / positive regulation of substrate adhesion-dependent cell spreading / spleen development / positive regulation of stress fiber assembly / cellular response to transforming growth factor beta stimulus / ruffle / positive regulation of establishment of T cell polarity / ERK1 and ERK2 cascade / positive regulation of interleukin-2 production / ephrin receptor binding / actin filament polymerization / phosphotyrosine residue binding / response to endoplasmic reticulum stress / positive regulation of mitotic cell cycle / substrate adhesion-dependent cell spreading / SH2 domain binding / positive regulation of release of sequestered calcium ion into cytosol / post-embryonic development / thymus development / neural tube closure / epidermal growth factor receptor signaling pathway / establishment of localization in cell / integrin-mediated signaling pathway / regulation of actin cytoskeleton organization / protein kinase C binding / cell-cell adhesion / B cell receptor signaling pathway / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / peptidyl-tyrosine phosphorylation / cellular senescence / neuron differentiation / negative regulation of ERK1 and ERK2 cascade / autophagy 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 / 解像度: 2.4 Å | ||||||
データ登録者 | Schindler, T. / Bornmann, W. / Pellicena, P. / Miller, W.T. / Clarkson, B. / Kuriyan, J. | ||||||
引用 | ジャーナル: Science / 年: 2000 タイトル: Structural mechanism for STI-571 inhibition of abelson tyrosine kinase. 著者: Schindler, T. / Bornmann, W. / Pellicena, P. / Miller, W.T. / Clarkson, B. / Kuriyan, J. | ||||||
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 | 1fpu.cif.gz | 122.8 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb1fpu.ent.gz | 95.2 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1fpu.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 | 1fpu_validation.pdf.gz | 530.7 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 1fpu_full_validation.pdf.gz | 549 KB | 表示 | |
XML形式データ | 1fpu_validation.xml.gz | 15.3 KB | 表示 | |
CIF形式データ | 1fpu_validation.cif.gz | 22 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/fp/1fpu ftp://data.pdbj.org/pub/pdb/validation_reports/fp/1fpu | HTTPS FTP |
-関連構造データ
-リンク
-集合体
登録構造単位 |
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2 |
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単位格子 |
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詳細 | There are two kinase molecules in the asymmetric unit. The biological assembly is a monomer. |
-要素
#1: タンパク質 | 分子量: 33743.523 Da / 分子数: 2 / 断片: KINASE DOMAIN / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / プラスミド: PFASTBAC / 細胞株 (発現宿主): SF9 発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ) 参照: UniProt: P00520, EC: 2.7.1.112 #2: 化合物 | #3: 水 | ChemComp-HOH / | |
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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: 2.29 Å3/Da / 溶媒含有率: 46.24 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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結晶化 | 温度: 277 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 6.2 詳細: PEG 4000, magnesium chloride, mes, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||||||||
結晶化 | *PLUS 温度: 4 ℃ / pH: 8 | ||||||||||||||||||||||||||||||||||||||||||||||||
溶液の組成 | *PLUS
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-データ収集
回折 | 平均測定温度: 103 K |
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放射光源 | 由来: シンクロトロン / サイト: NSLS / ビームライン: X25 / 波長: 0.9393 |
検出器 | タイプ: BRANDEIS - B4 / 検出器: CCD / 日付: 1999年9月5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: 0.9393 Å / 相対比: 1 |
反射 | 解像度: 2.4→99 Å / Num. obs: 221636 / % possible obs: 98.7 % / 冗長度: 9.3 % / Biso Wilson estimate: 61 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 30.9 |
反射 シェル | 解像度: 2.4→2.49 Å / 冗長度: 5.7 % / Rmerge(I) obs: 0.216 / Num. unique all: 2190 / % possible all: 90.6 |
反射 | *PLUS Num. obs: 24122 / Num. measured all: 221636 |
反射 シェル | *PLUS % possible obs: 90.6 % |
-解析
ソフトウェア |
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精密化 | 解像度: 2.4→99 Å / 立体化学のターゲット値: Engh & Huber 詳細: Tight, noncrystallographic restraints were utilized throughout the refinement so that the final r.m.s. deviation between the two molecules is 0.05 and 0.04 Angstrom for the N-terminal and the ...詳細: Tight, noncrystallographic restraints were utilized throughout the refinement so that the final r.m.s. deviation between the two molecules is 0.05 and 0.04 Angstrom for the N-terminal and the C-terminal lobes, respectively (excluding residues 229 to 337, 252, 262, 271, 294, 306, 404, 447, 450, 466, and 491, which were built in different conformations in the two molecules). The electron density map was significantly weaker for one of the two molecules in the asymmetric unit (chain ID B), and all the analysis (cf. primary citation) relied on the better-ordered one (chain ID A).
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精密化ステップ | サイクル: LAST / 解像度: 2.4→99 Å
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拘束条件 |
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ソフトウェア | *PLUS 名称: CNS / 分類: refinement | |||||||||||||||||||||||||
精密化 | *PLUS 最高解像度: 2.4 Å / 最低解像度: 99 Å / Rfactor obs: 0.239 | |||||||||||||||||||||||||
溶媒の処理 | *PLUS | |||||||||||||||||||||||||
原子変位パラメータ | *PLUS | |||||||||||||||||||||||||
拘束条件 | *PLUS タイプ: c_angle_deg / Dev ideal: 1.4 |