+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 2fgi | ||||||
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タイトル | CRYSTAL STRUCTURE OF THE TYROSINE KINASE DOMAIN OF FGF RECEPTOR 1 IN COMPLEX WITH INHIBITOR PD173074 | ||||||
要素 | PROTEIN (FIBROBLAST GROWTH FACTOR (FGF) RECEPTOR 1) | ||||||
キーワード | TRANSFERASE / PROTEIN KINASE / TYROSINE-PROTEIN KINASE / ATP-BINDING / PHOSPHORYLATION / INHIBITOR | ||||||
機能・相同性 | 機能・相同性情報 Signaling by FGFR1 amplification mutants / negative regulation of fibroblast growth factor production / positive regulation of mitotic cell cycle DNA replication / regulation of extrinsic apoptotic signaling pathway in absence of ligand / fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development / Signaling by plasma membrane FGFR1 fusions / ventricular zone neuroblast division / diphosphate metabolic process / vitamin D3 metabolic process / regulation of phosphate transport ...Signaling by FGFR1 amplification mutants / negative regulation of fibroblast growth factor production / positive regulation of mitotic cell cycle DNA replication / regulation of extrinsic apoptotic signaling pathway in absence of ligand / fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development / Signaling by plasma membrane FGFR1 fusions / ventricular zone neuroblast division / diphosphate metabolic process / vitamin D3 metabolic process / regulation of phosphate transport / regulation of lateral mesodermal cell fate specification / FGFR1c and Klotho ligand binding and activation / cementum mineralization / positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway / regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling / response to sodium phosphate / receptor-receptor interaction / auditory receptor cell development / Epithelial-Mesenchymal Transition (EMT) during gastrulation / chordate embryonic development / fibroblast growth factor receptor activity / positive regulation of parathyroid hormone secretion / branching involved in salivary gland morphogenesis / positive regulation of phospholipase activity / mesenchymal cell proliferation / paraxial mesoderm development / lung-associated mesenchyme development / FGFR1b ligand binding and activation / Signaling by activated point mutants of FGFR1 / FGFR1c ligand binding and activation / organ induction / Downstream signaling of activated FGFR1 / Phospholipase C-mediated cascade: FGFR1 / cell projection assembly / cellular response to fibroblast growth factor stimulus / skeletal system morphogenesis / outer ear morphogenesis / positive regulation of mesenchymal cell proliferation / ureteric bud development / middle ear morphogenesis / embryonic limb morphogenesis / inner ear morphogenesis / positive regulation of vascular endothelial cell proliferation / positive regulation of endothelial cell chemotaxis / midbrain development / cardiac muscle cell proliferation / fibroblast growth factor binding / regulation of cell differentiation / positive regulation of stem cell proliferation / PI-3K cascade:FGFR1 / Formation of paraxial mesoderm / phosphatidylinositol-mediated signaling / PI3K Cascade / epithelial to mesenchymal transition / fibroblast growth factor receptor signaling pathway / positive regulation of blood vessel endothelial cell migration / chondrocyte differentiation / calcium ion homeostasis / SHC-mediated cascade:FGFR1 / positive regulation of cardiac muscle cell proliferation / cell maturation / FRS-mediated FGFR1 signaling / positive regulation of neuron differentiation / Signaling by FGFR1 in disease / SH2 domain binding / NCAM signaling for neurite out-growth / stem cell proliferation / skeletal system development / Signal transduction by L1 / stem cell differentiation / positive regulation of cell differentiation / sensory perception of sound / Negative regulation of FGFR1 signaling / positive regulation of MAP kinase activity / neuron migration / receptor protein-tyrosine kinase / positive regulation of neuron projection development / peptidyl-tyrosine phosphorylation / Constitutive Signaling by Aberrant PI3K in Cancer / MAPK cascade / neuron projection development / cell migration / PIP3 activates AKT signaling / heparin binding / gene expression / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / cytoplasmic vesicle / protein tyrosine kinase activity / angiogenesis / in utero embryonic development / protein autophosphorylation / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / protein phosphorylation / positive regulation of cell population proliferation / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / extracellular region 類似検索 - 分子機能 | ||||||
生物種 | Homo sapiens (ヒト) | ||||||
手法 | X線回折 / 解像度: 2.5 Å | ||||||
データ登録者 | Mohammadi, M. / Froum, S. / Hamby, J.M. / Schroeder, M. / Panek, R.L. / Lu, G.H. / Eliseenkova, A.V. / Green, D. / Schlessinger, J. / Hubbard, S.R. | ||||||
引用 | ジャーナル: EMBO J. / 年: 1998 タイトル: Crystal structure of an angiogenesis inhibitor bound to the FGF receptor tyrosine kinase domain. 著者: Mohammadi, M. / Froum, S. / Hamby, J.M. / Schroeder, M.C. / Panek, R.L. / Lu, G.H. / Eliseenkova, A.V. / Green, D. / Schlessinger, J. / Hubbard, S.R. | ||||||
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 | 2fgi.cif.gz | 124.6 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb2fgi.ent.gz | 96.3 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 2fgi.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 | 2fgi_validation.pdf.gz | 854 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 2fgi_full_validation.pdf.gz | 868.1 KB | 表示 | |
XML形式データ | 2fgi_validation.xml.gz | 25.4 KB | 表示 | |
CIF形式データ | 2fgi_validation.cif.gz | 34.7 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/fg/2fgi ftp://data.pdbj.org/pub/pdb/validation_reports/fg/2fgi | HTTPS FTP |
-関連構造データ
類似構造データ |
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-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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非結晶学的対称性 (NCS) | NCS oper: (Code: given Matrix: (-0.9944, -0.09773, 0.04029), ベクター: |
-要素
#1: タンパク質 | 分子量: 35308.613 Da / 分子数: 2 / 断片: TYROSINE KINASE DOMAIN / 変異: L457V, C488A, C584S / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 細胞株: SF9 / 細胞内の位置: CYTOPLASM / 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: P11362, 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: 2.68 Å3/Da / 溶媒含有率: 54 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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結晶化 | pH: 6.5 詳細: 16% PEG 10000, 0.3 M (NH4)2SO4, 100 MM BIS-TRIS, PH 6.5, 5% ETHYLENE GLYCOL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
結晶 | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
結晶化 | *PLUS 温度: 4 ℃ / pH: 8 / 手法: 蒸気拡散法, ハンギングドロップ法 / 詳細: Mohammadi, M., (1996) Cell, 86, 577. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
溶液の組成 | *PLUS
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-データ収集
回折 | 平均測定温度: 110 K |
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放射光源 | 由来: 回転陽極 / タイプ: RIGAKU RU200 / 波長: 1.5418 |
検出器 | タイプ: RIGAKU RAXIS IIC / 検出器: IMAGE PLATE / 日付: 1997年8月27日 / 詳細: YALE 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: 1.5418 Å / 相対比: 1 |
反射 | 解像度: 2.5→30 Å / Num. obs: 24664 / % possible obs: 94.5 % / Observed criterion σ(I): 0 / 冗長度: 3.7 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 12.4 |
反射 | *PLUS Num. measured all: 93535 |
反射 シェル | *PLUS % possible obs: 95.5 % / Rmerge(I) obs: 0.252 |
-解析
ソフトウェア |
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精密化 | 解像度: 2.5→6 Å / Rfactor Rfree error: 0.0081 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / 交差検証法: THROUGHOUT / σ(F): 2
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原子変位パラメータ | Biso mean: 45.9 Å2
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精密化ステップ | サイクル: LAST / 解像度: 2.5→6 Å
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拘束条件 |
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Refine LS restraints NCS | NCS model details: UNRESTRAINED | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
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ソフトウェア | *PLUS 名称: X-PLOR / バージョン: 3.816 / 分類: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化 | *PLUS 最高解像度: 2.5 Å / σ(F): 2 / % reflection Rfree: 4.3 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
溶媒の処理 | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | *PLUS Biso mean: 45.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
拘束条件 | *PLUS
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