+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 2f4j | ||||||
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タイトル | Structure of the Kinase Domain of an Imatinib-Resistant Abl Mutant in Complex with the Aurora Kinase Inhibitor VX-680 | ||||||
要素 | Proto-oncogene tyrosine-protein kinase ABL1 | ||||||
キーワード | TRANSFERASE (転移酵素) / kinase (キナーゼ) / kinase inhibitor / abl | ||||||
機能・相同性 | 機能・相同性情報 negative regulation of phospholipase C activity / positive regulation of actin filament binding / positive regulation of oxidoreductase activity / transitional one stage B cell differentiation / protein localization to cytoplasmic microtubule plus-end / DNA conformation change / podocyte apoptotic process / DN4 thymocyte differentiation / Role of ABL in ROBO-SLIT signaling / response to epinephrine ...negative regulation of phospholipase C activity / positive regulation of actin filament binding / positive regulation of oxidoreductase activity / transitional one stage B cell differentiation / protein localization to cytoplasmic microtubule plus-end / DNA conformation change / podocyte apoptotic process / DN4 thymocyte differentiation / Role of ABL in ROBO-SLIT signaling / response to epinephrine / activation of protein kinase C activity / nicotinate-nucleotide adenylyltransferase activity / regulation of modification of synaptic structure / positive regulation of extracellular matrix organization / positive regulation of microtubule binding / delta-catenin binding / B cell proliferation involved in immune response / neuroepithelial cell differentiation / microspike assembly / positive regulation of Wnt signaling pathway, planar cell polarity pathway / cerebellum morphogenesis / positive regulation of blood vessel branching / B-1 B cell homeostasis / mitochondrial depolarization / negative regulation of ubiquitin-protein transferase activity / neuropilin signaling pathway / neuropilin binding / bubble DNA binding / regulation of Cdc42 protein signal transduction / negative regulation of protein serine/threonine kinase activity / activated T cell proliferation / cellular response to dopamine / regulation of cell motility / regulation of axon extension / proline-rich region binding / positive regulation of dendrite development / mitogen-activated protein kinase binding / myoblast proliferation / alpha-beta T cell differentiation / regulation of hematopoietic stem cell differentiation / syntaxin binding / cardiac muscle cell proliferation / HDR through Single Strand Annealing (SSA) / regulation of T cell differentiation / negative regulation of double-strand break repair via homologous recombination / positive regulation of cell migration involved in sprouting angiogenesis / Fc-gamma receptor signaling pathway involved in phagocytosis / negative regulation of cell-cell adhesion / Myogenesis / regulation of microtubule polymerization / positive regulation of osteoblast proliferation / RUNX2 regulates osteoblast differentiation / platelet-derived growth factor receptor-beta signaling pathway / positive regulation of focal adhesion assembly / negative regulation of cellular senescence / negative regulation of long-term synaptic potentiation / Bergmann glial cell differentiation / 学習 / neuromuscular process controlling balance / regulation of endocytosis / actin monomer binding / negative regulation of BMP signaling pathway / negative regulation of mitotic cell cycle / DNAミスマッチ修復 / endothelial cell migration / RHO GTPases Activate WASPs and WAVEs / positive regulation of T cell migration / canonical NF-kappaB signal transduction / BMP signaling pathway / negative regulation of endothelial cell apoptotic process / regulation of cell adhesion / positive regulation of substrate adhesion-dependent cell spreading / four-way junction DNA binding / signal transduction in response to DNA damage / peptidyl-tyrosine autophosphorylation / positive regulation of vasoconstriction / spleen development / positive regulation of stress fiber assembly / ruffle / ERK1 and ERK2 cascade / cellular response to transforming growth factor beta stimulus / positive regulation of establishment of T cell polarity / positive regulation of interleukin-2 production / actin filament polymerization / SH2 domain binding / response to endoplasmic reticulum stress / phosphotyrosine residue binding / ephrin receptor binding / positive regulation of mitotic cell cycle / substrate adhesion-dependent cell spreading / post-embryonic development / protein kinase C binding / positive regulation of release of sequestered calcium ion into cytosol / positive regulation of endothelial cell migration / thymus development / regulation of autophagy / neural tube closure / integrin-mediated signaling pathway / establishment of localization in cell / regulation of actin cytoskeleton organization 類似検索 - 分子機能 | ||||||
生物種 | Homo sapiens (ヒト) | ||||||
手法 | X線回折 / シンクロトロン / 分子置換 / 解像度: 1.91 Å | ||||||
データ登録者 | Young, M.A. / Shah, N.P. / Chao, L.H. / Zarrinkar, P. / Sawyers, P. / Kuriyan, J. | ||||||
引用 | ジャーナル: Cancer Res. / 年: 2006 タイトル: Structure of the kinase domain of an imatinib-resistant Abl mutant in complex with the Aurora kinase inhibitor VX-680. 著者: Young, M.A. / Shah, N.P. / Chao, L.H. / Seeliger, M. / Milanov, Z.V. / Biggs, W.H. / Treiber, D.K. / Patel, H.K. / Zarrinkar, P.P. / Lockhart, D.J. / Sawyers, C.L. / 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 | 2f4j.cif.gz | 78.5 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb2f4j.ent.gz | 56.3 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 2f4j.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/f4/2f4j ftp://data.pdbj.org/pub/pdb/validation_reports/f4/2f4j | HTTPS FTP |
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-関連構造データ
関連構造データ | 1m52S 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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-要素
#1: タンパク質 | 分子量: 33171.938 Da / 分子数: 1 / 断片: Kinase domain, residues 227-513 / 変異: H396P / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: ABL1, ABL, JTK7 / プラスミド: pET28a-TEV / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3)-star 参照: GenBank: 62362414, UniProt: P00519*PLUS, EC: 2.7.1.112 |
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#2: 化合物 | ChemComp-VX6 / |
#3: 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: 2.65 Å3/Da / 溶媒含有率: 53.67 % |
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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 / pH: 3.5 詳細: 25% w/v PEG1500, 0.1M citric acid, pH 3.5, VAPOR DIFFUSION, SITTING 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: シンクロトロン / サイト: ALS / ビームライン: 8.2.1 / 波長: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
検出器 | タイプ: ADSC QUANTUM 210 / 検出器: CCD / 日付: 2004年10月26日 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
放射 | モノクロメーター: Double crystal Si(111) / 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: 1.9→50 Å / Num. obs: 24731 / % possible obs: 90.4 % / Rmerge(I) obs: 0.121 / Χ2: 1.036 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: PDB ENTRY 1M52 解像度: 1.91→44.29 Å / Rfactor Rfree error: 0.006 / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0 / 立体化学のターゲット値: Engh & Huber 詳細: Cross-validation method: -> "throughout" Free R value test set selection criteria: -> "random"
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溶媒の処理 | 溶媒モデル: CNS bulk solvent model used / Bsol: 47.7103 Å2 / ksol: 0.391374 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso max: 77.63 Å2 / Biso mean: 25.8 Å2 / Biso min: 10.41 Å2
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Refine analyze |
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精密化ステップ | サイクル: LAST / 解像度: 1.91→44.29 Å
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拘束条件 |
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LS精密化 シェル | Refine-ID: X-RAY DIFFRACTION
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Xplor file |
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