+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 3srv | ||||||
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タイトル | Crystal structure of spleen tyrosine kinase (SYK) in complex with a diaminopyrimidine carboxamide inhibitor | ||||||
要素 | (Tyrosine-protein kinase SYK) x 2 | ||||||
キーワード | TRANSFERASE/TRANSFERASE INHIBITOR / SK363 / SYK / non-receptor tyrosine kinase / spleen tyrosine kinase / TRANSFERASE / PHOSPHORYLATION / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
機能・相同性 | 機能・相同性情報 interleukin-15 receptor binding / regulation of superoxide anion generation / regulation of neutrophil degranulation / regulation of arachidonate secretion / cellular response to lectin / gamma-delta T cell differentiation / positive regulation of interleukin-3 production / positive regulation of gamma-delta T cell differentiation / B cell receptor complex / positive regulation of mast cell cytokine production ...interleukin-15 receptor binding / regulation of superoxide anion generation / regulation of neutrophil degranulation / regulation of arachidonate secretion / cellular response to lectin / gamma-delta T cell differentiation / positive regulation of interleukin-3 production / positive regulation of gamma-delta T cell differentiation / B cell receptor complex / positive regulation of mast cell cytokine production / serotonin secretion by platelet / Toll-like receptor binding / regulation of platelet aggregation / positive regulation of alpha-beta T cell proliferation / leukocyte activation involved in immune response / neutrophil activation involved in immune response / positive regulation of mast cell degranulation / lymph vessel development / regulation of platelet activation / collagen-activated tyrosine kinase receptor signaling pathway / cell activation / positive regulation of killing of cells of another organism / macrophage activation involved in immune response / beta selection / regulation of phagocytosis / cellular response to molecule of fungal origin / early phagosome / FLT3 signaling through SRC family kinases / regulation of tumor necrosis factor-mediated signaling pathway / leukotriene biosynthetic process / positive regulation of monocyte chemotactic protein-1 production / interleukin-3-mediated signaling pathway / cellular response to lipid / regulation of DNA-binding transcription factor activity / positive regulation of cell adhesion mediated by integrin / positive regulation of granulocyte macrophage colony-stimulating factor production / Interleukin-2 signaling / positive regulation of alpha-beta T cell differentiation / blood vessel morphogenesis / Fc epsilon receptor (FCERI) signaling / T cell receptor complex / mast cell degranulation / positive regulation of B cell differentiation / leukocyte cell-cell adhesion / Fc-gamma receptor signaling pathway involved in phagocytosis / positive regulation of interleukin-4 production / Dectin-2 family / stimulatory C-type lectin receptor signaling pathway / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / Fc-epsilon receptor signaling pathway / positive regulation of receptor internalization / phospholipase binding / amyloid-beta clearance / positive regulation of interleukin-10 production / cellular response to low-density lipoprotein particle stimulus / FCGR activation / positive regulation of type I interferon production / positive regulation of bone resorption / phosphatase binding / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Signaling by CSF3 (G-CSF) / negative regulation of inflammatory response to antigenic stimulus / cell surface receptor protein tyrosine kinase signaling pathway / GPVI-mediated activation cascade / positive regulation of interleukin-12 production / positive regulation of TORC1 signaling / neutrophil chemotaxis / positive regulation of calcium-mediated signaling / phosphotyrosine residue binding / SH2 domain binding / Integrin signaling / B cell differentiation / FCERI mediated Ca+2 mobilization / regulation of ERK1 and ERK2 cascade / FCGR3A-mediated IL10 synthesis / positive regulation of superoxide anion generation / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / positive regulation of interleukin-8 production / integrin-mediated signaling pathway / Regulation of signaling by CBL / FCERI mediated MAPK activation / animal organ morphogenesis / FCGR3A-mediated phagocytosis / B cell receptor signaling pathway / non-specific protein-tyrosine kinase / calcium-mediated signaling / non-membrane spanning protein tyrosine kinase activity / positive regulation of protein-containing complex assembly / Inactivation of CSF3 (G-CSF) signaling / receptor internalization / platelet activation / CLEC7A (Dectin-1) signaling / Regulation of actin dynamics for phagocytic cup formation / positive regulation of interleukin-6 production / peptidyl-tyrosine phosphorylation / protein import into nucleus / positive regulation of peptidyl-tyrosine phosphorylation / cellular response to amyloid-beta / positive regulation of tumor necrosis factor production 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 / フーリエ合成 / 解像度: 1.95 Å | ||||||
データ登録者 | Somers, D.O. / Neu, M. | ||||||
引用 | ジャーナル: Bioorg.Med.Chem.Lett. / 年: 2011 タイトル: Discovery of GSK143, a highly potent, selective and orally efficacious spleen tyrosine kinase inhibitor. 著者: Liddle, J. / Atkinson, F.L. / Barker, M.D. / Carter, P.S. / Curtis, N.R. / Davis, R.P. / Douault, C. / Dickson, M.C. / Elwes, D. / Garton, N.S. / Gray, M. / Hayhow, T.G. / Hobbs, C.I. / ...著者: Liddle, J. / Atkinson, F.L. / Barker, M.D. / Carter, P.S. / Curtis, N.R. / Davis, R.P. / Douault, C. / Dickson, M.C. / Elwes, D. / Garton, N.S. / Gray, M. / Hayhow, T.G. / Hobbs, C.I. / Jones, E. / Leach, S. / Leavens, K. / Lewis, H.D. / McCleary, S. / Neu, M. / Patel, V.K. / Preston, A.G. / Ramirez-Molina, C. / Shipley, T.J. / Skone, P.A. / Smithers, N. / Somers, D.O. / Walker, A.L. / Watson, R.J. / Weingarten, G.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 | 3srv.cif.gz | 134.3 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb3srv.ent.gz | 103.2 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 3srv.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 | 3srv_validation.pdf.gz | 1.1 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 3srv_full_validation.pdf.gz | 1.1 MB | 表示 | |
XML形式データ | 3srv_validation.xml.gz | 26.8 KB | 表示 | |
CIF形式データ | 3srv_validation.cif.gz | 39.2 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/sr/3srv ftp://data.pdbj.org/pub/pdb/validation_reports/sr/3srv | 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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1 |
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2 |
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単位格子 |
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-要素
#1: タンパク質 | 分子量: 32161.992 Da / 分子数: 1 / 断片: KINASE DOMAIN (UNP Residues 360-635) / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: SYK 発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ) 株 (発現宿主): SF9 参照: UniProt: P43405, non-specific protein-tyrosine kinase | ||||
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#2: タンパク質 | 分子量: 32082.016 Da / 分子数: 1 / 断片: KINASE DOMAIN (UNP Residues 360-635) / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: SYK 発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ) 株 (発現宿主): SF9 参照: UniProt: P43405, non-specific protein-tyrosine kinase | ||||
#3: 化合物 | #4: 化合物 | ChemComp-GOL / #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: 2.25 Å3/Da / 溶媒含有率: 45.22 % |
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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: 6.5 詳細: 20% PEG3350, 0.2M Na-K-Phosphate, 0.1M Bis-Tris-Propane pH 6.5, 5mM DTT, 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: シンクロトロン / サイト: ESRF / ビームライン: ID29 / 波長: 0.9763 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
検出器 | タイプ: ADSC QUANTUM 315r / 検出器: CCD / 日付: 2010年6月23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: 0.9763 Å / 相対比: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
反射 | 解像度: 1.95→39.47 Å / Num. all: 38589 / Num. obs: 38589 / % possible obs: 94.7 % / 冗長度: 1.9 % / Biso Wilson estimate: 25.7 Å2 / Rsym value: 0.052 / Net I/σ(I): 11.1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
反射 シェル | Diffraction-ID: 1
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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: フーリエ合成 開始モデル: OTHER IN-HOUSE COORDINATES 解像度: 1.95→20 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.927 / WRfactor Rfree: 0.2359 / WRfactor Rwork: 0.1798 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8148 / SU B: 4.875 / SU ML: 0.137 / SU R Cruickshank DPI: 0.1942 / SU Rfree: 0.1739 / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.194 / ESU R Free: 0.174 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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溶媒の処理 | イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.4 Å / 溶媒モデル: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso max: 76.02 Å2 / Biso mean: 35.6065 Å2 / Biso min: 9.26 Å2
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精密化ステップ | サイクル: LAST / 解像度: 1.95→20 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 1.95→2 Å / Total num. of bins used: 20
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