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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: 1hut | ||||||
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タイトル | THE STRUCTURE OF ALPHA-THROMBIN INHIBITED BY A 15-MER SINGLE-STRANDED DNA APTAMER | ||||||
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![]() | HYDROLASE/HYDROLASE INHIBITOR/DNA / THROMBIN / BLOOD CLOTTING / HYDROLASE-HYDROLASE INHIBITOR-DNA COMPLEX | ||||||
機能・相同性 | ![]() cytolysis by host of symbiont cells / thrombospondin receptor activity / thrombin-activated receptor signaling pathway / Defective factor XII causes hereditary angioedema / thrombin / negative regulation of astrocyte differentiation / regulation of blood coagulation / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / neutrophil-mediated killing of gram-negative bacterium / Defective F8 cleavage by thrombin ...cytolysis by host of symbiont cells / thrombospondin receptor activity / thrombin-activated receptor signaling pathway / Defective factor XII causes hereditary angioedema / thrombin / negative regulation of astrocyte differentiation / regulation of blood coagulation / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / neutrophil-mediated killing of gram-negative bacterium / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) / ligand-gated ion channel signaling pathway / positive regulation of collagen biosynthetic process / negative regulation of platelet activation / negative regulation of blood coagulation / positive regulation of blood coagulation / negative regulation of fibrinolysis / regulation of cytosolic calcium ion concentration / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Gamma-carboxylation of protein precursors / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins / fibrinolysis / Intrinsic Pathway of Fibrin Clot Formation / negative regulation of proteolysis / negative regulation of cytokine production involved in inflammatory response / positive regulation of release of sequestered calcium ion into cytosol / Peptide ligand-binding receptors / Regulation of Complement cascade / acute-phase response / Cell surface interactions at the vascular wall / positive regulation of receptor signaling pathway via JAK-STAT / lipopolysaccharide binding / growth factor activity / positive regulation of insulin secretion / platelet activation / response to wounding / positive regulation of protein localization to nucleus / Golgi lumen / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of reactive oxygen species metabolic process / antimicrobial humoral immune response mediated by antimicrobial peptide / blood coagulation / regulation of cell shape / heparin binding / Thrombin signalling through proteinase activated receptors (PARs) / : / positive regulation of cell growth / blood microparticle / G alpha (q) signalling events / cell surface receptor signaling pathway / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor ligand activity / endoplasmic reticulum lumen / signaling receptor binding / serine-type endopeptidase activity / positive regulation of cell population proliferation / calcium ion binding / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane 類似検索 - 分子機能 | ||||||
生物種 | ![]() | ||||||
手法 | ![]() | ||||||
![]() | Padmanabhan, K. / Padmanabhan, K.P. / Ferrara, J.D. / Sadler, J.E. / Tulinsky, A. | ||||||
![]() | ![]() タイトル: The structure of alpha-thrombin inhibited by a 15-mer single-stranded DNA aptamer. 著者: Padmanabhan, K. / Padmanabhan, K.P. / Ferrara, J.D. / Sadler, J.E. / Tulinsky, A. | ||||||
履歴 |
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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 | ![]() | 86.9 KB | 表示 | ![]() |
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PDB形式 | ![]() | 62.1 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 | ![]() | 469 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 552.4 KB | 表示 | |
XML形式データ | ![]() | 20.2 KB | 表示 | |
CIF形式データ | ![]() | 28.6 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
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リンク
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集合体
登録構造単位 | ![]()
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1 |
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単位格子 |
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要素
#1: DNA鎖 | 分子量: 4743.051 Da / 分子数: 1 / 由来タイプ: 合成 |
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#2: タンパク質・ペプチド | 分子量: 4096.534 Da / 分子数: 1 / Fragment: RESIDUES 328-363 / 由来タイプ: 天然 / 由来: (天然) ![]() |
#3: タンパク質 | 分子量: 29780.219 Da / 分子数: 1 / Fragment: RESIDUES 364-622 / 由来タイプ: 天然 / 由来: (天然) ![]() |
#4: 化合物 | ChemComp-0G7 / |
#5: 水 | ChemComp-HOH / |
Has protein modification | Y |
配列の詳細 | CHYMOTRYPSIN NUMBERING SYSTEM IS USED BASED ON THE TOPOLOGICAL ALIGNMENT WITH THE STRUCTURE OF ...CHYMOTRYPS |
-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: 2.78 Å3/Da / 溶媒含有率: 55.72 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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結晶化 | *PLUS pH: 7.3 / 手法: 蒸気拡散法, ハンギングドロップ法 / 詳細: Skrzypczak, J., (1991) J. Mol. Biol., 221, 1379. | ||||||||||||||||||||||||||||||||||||||||||||||||
溶液の組成 | *PLUS
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-データ収集
放射光源 | 由来: ![]() |
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検出器 | タイプ: RIGAKU RAXIS II / 検出器: IMAGE PLATE |
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 | 最高解像度: 2.87 Å / Num. obs: 6990 |
反射 | *PLUS % possible obs: 67 % / Observed criterion σ(F): 1 / Num. measured all: 12408 / Rmerge F obs: 0.116 |
反射 シェル | *PLUS 最高解像度: 2.87 Å / 最低解像度: 2.9 Å / % possible obs: 32 % |
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解析
ソフトウェア | 名称: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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精密化 | 最高解像度: 2.9 Å /
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精密化ステップ | サイクル: LAST / 最高解像度: 2.9 Å
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拘束条件 |
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ソフトウェア | *PLUS 名称: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化 | *PLUS Rfactor obs: 0.159 / Rfactor Rwork: 0.159 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
溶媒の処理 | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
拘束条件 | *PLUS タイプ: x_angle_d / Dev ideal: 3.3 |