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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: 1hxf | ||||||
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タイトル | HUMAN THROMBIN COMPLEX WITH HIRUDIN VARIANT | ||||||
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![]() | HYDROLASE/HYDROLASE INHIBITOR / COMPLEX (SERINE PROTEASE INHIBITOR) / SULFATATION / MULTIGENE FAMILY / BLOOD COAGULATION / PLASMA / CALCIUM-BINDING / GLYCOPROTEIN / DUPLICATION / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
機能・相同性 | ![]() negative regulation of serine-type peptidase activity / positive regulation of lipid kinase activity / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / cytolysis by host of symbiont cells / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / thrombin / regulation of blood coagulation / neutrophil-mediated killing of gram-negative bacterium / ligand-gated ion channel signaling pathway ...negative regulation of serine-type peptidase activity / positive regulation of lipid kinase activity / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / cytolysis by host of symbiont cells / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / thrombin / regulation of blood coagulation / neutrophil-mediated killing of gram-negative bacterium / ligand-gated ion channel signaling pathway / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) / negative regulation of astrocyte differentiation / negative regulation of platelet activation / positive regulation of collagen biosynthetic process / negative regulation of cytokine production involved in inflammatory response / positive regulation of blood coagulation / negative regulation of fibrinolysis / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins / fibrinolysis / regulation of cytosolic calcium ion concentration / Intrinsic Pathway of Fibrin Clot Formation / Peptide ligand-binding receptors / positive regulation of release of sequestered calcium ion into cytosol / acute-phase response / Regulation of Complement cascade / negative regulation of proteolysis / Cell surface interactions at the vascular wall / lipopolysaccharide binding / positive regulation of receptor signaling pathway via JAK-STAT / growth factor activity / serine-type endopeptidase inhibitor activity / positive regulation of insulin secretion / platelet activation / response to wounding / positive regulation of protein localization to nucleus / Golgi lumen / antimicrobial humoral immune response mediated by antimicrobial peptide / 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 / blood coagulation / Thrombin signalling through proteinase activated receptors (PARs) / heparin binding / regulation of cell shape / positive regulation of cell growth / G alpha (q) signalling events / collagen-containing extracellular matrix / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell surface receptor signaling pathway / blood microparticle / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / serine-type endopeptidase activity / signaling receptor binding / calcium ion binding / positive regulation of cell population proliferation / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane 類似検索 - 分子機能 | ||||||
生物種 | ![]() ![]() | ||||||
手法 | ![]() | ||||||
![]() | Tulinsky, A. / Zhang, E. | ||||||
![]() | ![]() タイトル: The molecular environment of the Na+ binding site of thrombin. 著者: Zhang, E. / Tulinsky, A. #1: ![]() タイトル: The Na+ Binding Site of Thrombin 著者: Di Cera, E. / Guinto, E.R. / Vindigni, A. / Dang, Q.D. / Ayala, Y.M. / Wuyi, M. / Tulinsky, A. #2: ![]() タイトル: The Isomorphous Structures of Prethrombin2, Hirugen-, and Ppack-Thrombin: Changes Accompanying Activation and Exosite Binding to Thrombin 著者: Vijayalakshmi, J. / Padmanabhan, K.P. / Mann, K.G. / Tulinsky, A. #3: ![]() タイトル: Refined Structure of the Hirudin-Thrombin Complex 著者: Rydel, T.J. / Tulinsky, A. / Bode, W. / Huber, R. | ||||||
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 | ![]() | 75 KB | 表示 | ![]() |
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PDB形式 | ![]() | 55.3 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 | ![]() | 388.8 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 412 KB | 表示 | |
XML形式データ | ![]() | 10.4 KB | 表示 | |
CIF形式データ | ![]() | 15.3 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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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・ペプチド | 分子量: 4096.534 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() |
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#2: タンパク質 | 分子量: 29780.219 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() |
#3: タンパク質・ペプチド | 分子量: 1211.274 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() |
#4: 水 | ChemComp-HOH / |
構成要素の詳細 | THROMBIN IS CLEAVED BETWEEN RESIDUES 15 AND 16. CHAIN INDICATOR *L* IS USED FOR RESIDUES 1A - 14K ...THROMBIN IS CLEAVED BETWEEN RESIDUES 15 AND 16. CHAIN INDICATOR *L* IS USED FOR RESIDUES 1A - 14K AND CHAIN INDICATOR *H* IS USED FOR RESIDUES 16 - 244. CHAIN INDICATOR *I* IS USED FOR HIRUDIN 55 -64. RESIDUES 1 - 7 AND 34 - 36 OF CHAIN L ARE NOT IN ATOM LIST. THE LAST THREE C-TERMINAL RESIDUES ARE NOT IN ATOM LIST. |
-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: 2.62 Å3/Da / 溶媒含有率: 49 % | ||||||||||||||||||||||||||||||
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結晶化 | *PLUS pH: 8.5 / 手法: 蒸気拡散法 | ||||||||||||||||||||||||||||||
溶液の組成 | *PLUS
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-データ収集
放射光源 | 波長: 1.5418 |
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検出器 | タイプ: SIEMENS / 検出器: AREA DETECTOR / 日付: 1996年2月20日 |
放射 | 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 | Num. obs: 15885 / % possible obs: 70 % / Observed criterion σ(I): 1 / 冗長度: 2 % / Rmerge(I) obs: 0.048 |
反射 | *PLUS 最高解像度: 2.3 Å / Num. obs: 14047 / % possible obs: 91 % / Num. measured all: 44309 |
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解析
ソフトウェア |
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精密化 | 解像度: 2.1→7 Å / σ(F): 3 /
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原子変位パラメータ | Biso mean: 31 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 2.1→7 Å
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拘束条件 |
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ソフトウェア | *PLUS 名称: PROLSQ / 分類: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化 | *PLUS 最高解像度: 2.3 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
溶媒の処理 | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | *PLUS |