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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: 1abi | |||||||||
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タイトル | STRUCTURE OF THE HIRULOG 3-THROMBIN COMPLEX AND NATURE OF THE S' SUBSITES OF SUBSTRATES AND INHIBITORS | |||||||||
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![]() | HYDROLASE/HYDROLASE INHIBITOR / HYDROLASE(SERINE PROTEINASE) / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | |||||||||
機能・相同性 | ![]() 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 ...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 | ![]() | |||||||||
![]() | Qiu, X. / Tulinsky, A. | |||||||||
![]() | ![]() タイトル: Structure of the hirulog 3-thrombin complex and nature of the S' subsites of substrates and inhibitors. 著者: Qiu, X. / Padmanabhan, K.P. / Carperos, V.E. / Tulinsky, A. / Kline, T. / Maraganore, J.M. / Fenton 2nd., J.W. #1: ![]() タイトル: Structure of the Hirugen and Hirulog 1 Complexes of Alpha-Thrombin 著者: Skrzypczak-Jankun, E. / Carperos, V. / Ravichandran, K.G. / Tulinsky, A. / Westbrook, M. / Maraganore, J.M. #2: ![]() タイトル: The Structure of a Complex of Recombinant Hirudin and Human Alpha-Thrombin 著者: Rydel, T.J. / Ravichandran, K.G. / Tulinsky, A. / Bode, W. / Huber, R. / Roitsch, C. / Fenton II, J.W. #3: ![]() タイトル: The Refined 1.9 Angstroms Crystal Structure of Human Alpha-Thrombin: Interaction with D-Phe-Pro-Arg Chloromethylketone and Significance of the Tyr-Pro-Pro-Trp Insertion Segment 著者: Bode, W. / Mayr, I. / Baumann, U. / Huber, R. / Stone, S.R. / Hofsteenge, J. | |||||||||
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 | ![]() | 83.4 KB | 表示 | ![]() |
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PDB形式 | ![]() | 60.4 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 | ![]() | 390.5 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 420.2 KB | 表示 | |
XML形式データ | ![]() | 12.5 KB | 表示 | |
CIF形式データ | ![]() | 18.8 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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Atom site foot note | 1: CIS PROLINE - PRO H 37 / 2: RESIDUE I 1 IS D-PHENYLALANINE. | ||||||||
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: 組換発現 / 由来: (組換発現) ![]() |
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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: 組換発現 / 由来: (組換発現) ![]() |
#3: タンパク質・ペプチド | 分子量: 2154.251 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 1H - 15 ...THROMBIN IS CLEAVED BETWEEN RESIDUES 15 AND 16. CHAIN INDICATOR *L* IS USED FOR RESIDUES 1H - 15 AND CHAIN INDICATOR *H* IS USED FOR RESIDUES 16 - 247. CHAIN INDICATOR *I* IS USED FOR HIRULOG 3. |
非ポリマーの詳細 | CAUTION SHOULD BE TAKEN IF SOLVENT MOLECULES WITH OCCUPANCY LESS THAN 0.5 ARE USED IN ANY ...CAUTION SHOULD BE TAKEN IF SOLVENT MOLECULES WITH OCCUPANCY LESS THAN 0.5 ARE USED IN ANY STRUCTURAL |
-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: 2.56 Å3/Da / 溶媒含有率: 51.99 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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結晶化 | *PLUS 温度: 8 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 7.3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
溶液の組成 | *PLUS
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-データ収集
放射 | 散乱光タイプ: x-ray |
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放射波長 | 相対比: 1 |
反射 | *PLUS 最高解像度: 2.3 Å / 最低解像度: 2.5 Å / Num. obs: 12167 / % possible obs: 77 % / Num. measured all: 59257 / Rmerge(I) obs: 2 / Rmerge F obs: 0.045 |
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解析
ソフトウェア | 名称: PROLSQ / 分類: 精密化 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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精密化 | 解像度: 2.3→7 Å / Rfactor obs: 0.132 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 2.3→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 / 最低解像度: 7 Å / Rfactor obs: 0.132 / Num. reflection obs: 11408 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
溶媒の処理 | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | *PLUS Biso mean: 26 Å2 |