+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 3kjq | ||||||
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タイトル | Caspase 8 with covalent inhibitor | ||||||
要素 | (Caspase-8カスパーゼ-8) x 2 | ||||||
キーワード | HYDROLASE (加水分解酵素) / caspase 8 (カスパーゼ-8) / Apoptosis (アポトーシス) / kinetics / Peptidomimetic Inhibitor / urazole / Disease mutation / Phosphoprotein / Protease (プロテアーゼ) / Thiol protease (システインプロテアーゼ) / Zymogen (酵素前駆体) / Allosteric (アロステリック効果) | ||||||
機能・相同性 | 機能・相同性情報 カスパーゼ-8 / death effector domain binding / syncytiotrophoblast cell differentiation involved in labyrinthine layer development / FasL/ CD95L signaling / TRAIL signaling / CD95 death-inducing signaling complex / ripoptosome / TRAIL-activated apoptotic signaling pathway / Defective RIPK1-mediated regulated necrosis / Apoptotic execution phase ...カスパーゼ-8 / death effector domain binding / syncytiotrophoblast cell differentiation involved in labyrinthine layer development / FasL/ CD95L signaling / TRAIL signaling / CD95 death-inducing signaling complex / ripoptosome / TRAIL-activated apoptotic signaling pathway / Defective RIPK1-mediated regulated necrosis / Apoptotic execution phase / Activation, myristolyation of BID and translocation to mitochondria / TRIF-mediated programmed cell death / TLR3-mediated TICAM1-dependent programmed cell death / Microbial modulation of RIPK1-mediated regulated necrosis / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 / Caspase activation via Death Receptors in the presence of ligand / positive regulation of macrophage differentiation / self proteolysis / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / response to cobalt ion / cysteine-type endopeptidase activity involved in apoptotic signaling pathway / death-inducing signaling complex / natural killer cell activation / CLEC7A/inflammasome pathway / negative regulation of necroptotic process / activation of cysteine-type endopeptidase activity / regulation of tumor necrosis factor-mediated signaling pathway / tumor necrosis factor receptor binding / death receptor binding / cysteine-type endopeptidase activity involved in apoptotic process / TNFR1-induced proapoptotic signaling / execution phase of apoptosis / RIPK1-mediated regulated necrosis / B cell activation / regulation of innate immune response / Apoptotic cleavage of cellular proteins / pyroptotic inflammatory response / positive regulation of proteolysis / macrophage differentiation / protein maturation / cellular response to organic cyclic compound / extrinsic apoptotic signaling pathway via death domain receptors / Caspase-mediated cleavage of cytoskeletal proteins / response to tumor necrosis factor / negative regulation of canonical NF-kappaB signal transduction / extrinsic apoptotic signaling pathway / cysteine-type peptidase activity / regulation of cytokine production / T細胞 / proteolysis involved in protein catabolic process / positive regulation of interleukin-1 beta production / Regulation of NF-kappa B signaling / apoptotic signaling pathway / Regulation of TNFR1 signaling / NOD1/2 Signaling Pathway / Regulation of necroptotic cell death / cellular response to mechanical stimulus / positive regulation of neuron apoptotic process / lamellipodium / response to estradiol / heart development / peptidase activity / cell body / scaffold protein binding / 血管新生 / positive regulation of canonical NF-kappaB signal transduction / response to ethanol / mitochondrial outer membrane / response to lipopolysaccharide / 細胞骨格 / positive regulation of cell migration / positive regulation of apoptotic process / cysteine-type endopeptidase activity / apoptotic process / ubiquitin protein ligase binding / protein-containing complex binding / protein-containing complex / ミトコンドリア / タンパク質分解 / 核質 / identical protein binding / 細胞質基質 / 細胞質 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: 1.8 Å | ||||||
データ登録者 | Kamtekar, S. / Watt, W. / Finzel, B.C. / Harris, M.S. / Blinn, J. / Wang, Z. / Tomasselli, A.G. | ||||||
引用 | ジャーナル: Biochim.Biophys.Acta / 年: 2010 タイトル: Kinetic and structural characterization of caspase-3 and caspase-8 inhibition by a novel class of irreversible inhibitors. 著者: Wang, Z. / Watt, W. / Brooks, N.A. / Harris, M.S. / Urban, J. / Boatman, D. / McMillan, M. / Kahn, M. / Heinrikson, R.L. / Finzel, B.C. / Wittwer, A.J. / Blinn, J. / Kamtekar, S. / Tomasselli, A.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 | 3kjq.cif.gz | 62.4 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb3kjq.ent.gz | 49 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 3kjq.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/kj/3kjq ftp://data.pdbj.org/pub/pdb/validation_reports/kj/3kjq | 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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単位格子 |
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-要素
#1: タンパク質 | 分子量: 18640.119 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: CASP8, MCH5 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q14790, カスパーゼ-8 | ||
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#2: タンパク質 | 分子量: 10901.364 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: CASP8, MCH5 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q14790, カスパーゼ-8 | ||
#3: 化合物 | #4: 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: 2.62 Å3/Da / 溶媒含有率: 52.99 % |
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結晶化 | 温度: 277 K / 手法: 蒸気拡散法 / pH: 7.8 詳細: 2 microliters of 100 mM inhibitor stock in DMSO was added to 100 microliters of 8.4 mg/mL protein in 20 mM Tris, 100 mM DTT, pH 8.0. Protein solution was mixed with an equal volume of well ...詳細: 2 microliters of 100 mM inhibitor stock in DMSO was added to 100 microliters of 8.4 mg/mL protein in 20 mM Tris, 100 mM DTT, pH 8.0. Protein solution was mixed with an equal volume of well solution (1.0-1.1 M Citrate, 50 mM HEPES or PIPES pH 6.5, 25 mM DTT), VAPOR DIFFUSION, temperature 277K |
-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: APS / ビームライン: 17-ID / 波長: 1 Å |
検出器 | タイプ: ADSC QUANTUM 210 / 検出器: CCD |
放射 | モノクロメーター: Si(111) double-crystal monochromator 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: 1.8→20 Å / Num. all: 29350 / Num. obs: 29346 / % possible obs: 99.6 % |
反射 シェル | 解像度: 1.8→1.85 Å / % possible all: 96.9 |
-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 / 解像度: 1.8→19.94 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.936 / SU B: 1.957 / SU ML: 0.063 / 交差検証法: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.11 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD / 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 12.497 Å2
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精密化ステップ | サイクル: LAST / 解像度: 1.8→19.94 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 1.8→1.846 Å / Total num. of bins used: 20
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