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データを開く
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基本情報
登録情報 | データベース: PDB / ID: 1qtn | ||||||
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タイトル | CRYSTAL STRUCTURE OF THE COMPLEX OF CASPASE-8 WITH THE TETRAPEPTIDE INHIBITOR ACE-IETD-ALDEHYDE | ||||||
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![]() | HYDROLASE/HYDROLASE INHIBITOR / APOPTOSIS / DITHIANE-DIOL / CASPASE / CYSTEINE-PROTEASE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
機能・相同性 | ![]() caspase-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 ...caspase-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 / CLEC7A/inflammasome pathway / natural killer cell activation / 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 / extrinsic apoptotic signaling pathway / negative regulation of canonical NF-kappaB signal transduction / cysteine-type peptidase activity / regulation of cytokine production / T cell activation / 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 / response to estradiol / lamellipodium / peptidase activity / heart development / cell body / scaffold protein binding / angiogenesis / positive regulation of canonical NF-kappaB signal transduction / response to ethanol / mitochondrial outer membrane / response to lipopolysaccharide / cytoskeleton / 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 / mitochondrion / proteolysis / nucleoplasm / identical protein binding / cytoplasm / cytosol 類似検索 - 分子機能 | ||||||
生物種 | ![]() | ||||||
手法 | ![]() ![]() ![]() | ||||||
![]() | Watt, W. / Watenpaugh, K.D. | ||||||
![]() | ![]() タイトル: The atomic-resolution structure of human caspase-8, a key activator of apoptosis. 著者: Watt, W. / Koeplinger, K.A. / Mildner, A.M. / Heinrikson, R.L. / Tomasselli, A.G. / Watenpaugh, K.D. | ||||||
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構造の表示
構造ビューア | 分子: ![]() ![]() |
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ダウンロードとリンク
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ダウンロード
PDBx/mmCIF形式 | ![]() | 73.4 KB | 表示 | ![]() |
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PDB形式 | ![]() | 52 KB | 表示 | ![]() |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
その他 | ![]() |
-検証レポート
文書・要旨 | ![]() | 397.9 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 399.4 KB | 表示 | |
XML形式データ | ![]() | 7.1 KB | 表示 | |
CIF形式データ | ![]() | 12.2 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
関連構造データ | ![]() 1cp3S S: 精密化の開始モデル |
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類似構造データ |
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リンク
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集合体
登録構造単位 | ![]()
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単位格子 |
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Components on special symmetry positions |
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要素
#1: タンパク質 | 分子量: 18640.119 Da / 分子数: 1 / 断片: P18 FRAGMENT / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() 参照: UniProt: Q14790, 加水分解酵素; プロテアーゼ; ペプチド結合加水分解酵素; システインプロテアーゼ | ||||
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#2: タンパク質 | 分子量: 10901.364 Da / 分子数: 1 / 断片: P11 FRAGMENT / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() 参照: UniProt: Q14790, 加水分解酵素; プロテアーゼ; ペプチド結合加水分解酵素; システインプロテアーゼ | ||||
#3: タンパク質・ペプチド | | ||||
#4: 化合物 | #5: 水 | ChemComp-HOH / | 構成要素の詳細 | THERE IS A COVALENT BOND BETWEEN ATOM SG OF CYS360A AND ATOM C OF ASJ504C, FORMING A THIOHEMIAC | |
-実験情報
-実験
実験 | 手法: ![]() |
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試料調製
結晶 | マシュー密度: 2.42 Å3/Da / 溶媒含有率: 49.13 % | ||||||||||||||||||||||||||||||
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結晶化 | 温度: 282 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 8 詳細: 3 MICROLITERS PROTEIN (8.4 MG/ ML IN 20 MM TRISHCL, 100MM DTT AT PH 8.0) MIXED WITH 3 MICROLITERS WELL BUFFER (1.4 SODIUM CITRATE, 0.1M HEPES, AT PH 8.0) AT 4 DEG. C, VAPOR DIFFUSION, SITTING ...詳細: 3 MICROLITERS PROTEIN (8.4 MG/ ML IN 20 MM TRISHCL, 100MM DTT AT PH 8.0) MIXED WITH 3 MICROLITERS WELL BUFFER (1.4 SODIUM CITRATE, 0.1M HEPES, AT PH 8.0) AT 4 DEG. C, VAPOR DIFFUSION, SITTING DROP, temperature 282K | ||||||||||||||||||||||||||||||
結晶化 | *PLUS 温度: 4 ℃ | ||||||||||||||||||||||||||||||
溶液の組成 | *PLUS
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-データ収集
回折 | 平均測定温度: 105 K |
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放射光源 | 由来: ![]() ![]() ![]() |
検出器 | タイプ: BRUKER / 検出器: CCD / 日付: 1998年9月9日 / 詳細: NON-FOCUSING |
放射 | モノクロメーター: SILICON / 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: 1.03 Å / 相対比: 1 |
反射 | 解像度: 1.2→20 Å / Num. obs: 79890 / % possible obs: 87 % / Observed criterion σ(I): 0 / 冗長度: 3.73 % / Rmerge(I) obs: 0.068 |
反射 シェル | 解像度: 1.2→1.24 Å / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 2.35 / % possible all: 82 |
反射 | *PLUS Num. measured all: 298890 |
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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: ![]() 開始モデル: 1CP3 解像度: 1.2→8 Å / σ(F): 4 / 立体化学のターゲット値: ENGH & HUBER
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溶媒の処理 | 溶媒モデル: SWAT | |||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 1.2→8 Å
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拘束条件 |
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ソフトウェア | *PLUS 名称: SHELXL-97 / 分類: refinement | |||||||||||||||||||||||||||||||||
精密化 | *PLUS σ(F): 4 / % reflection Rfree: 5.3 % / Rfactor obs: 0.143 | |||||||||||||||||||||||||||||||||
溶媒の処理 | *PLUS | |||||||||||||||||||||||||||||||||
原子変位パラメータ | *PLUS | |||||||||||||||||||||||||||||||||
拘束条件 | *PLUS
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