+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1vr1 | ||||||
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タイトル | Specifity for Plasminogen Activator Inhibitor-1 | ||||||
要素 |
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キーワード | BLOOD CLOTTING/HYDROLASE INHIBITOR / THROMBIN (トロンビン) / BLOOD CLOTTING-HYDROLASE INHIBITOR COMPLEX | ||||||
機能・相同性 | 機能・相同性情報 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 / トロンビン / neutrophil-mediated killing of gram-negative bacterium / regulation of blood coagulation / 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 / トロンビン / neutrophil-mediated killing of gram-negative bacterium / regulation of blood coagulation / 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 / regulation of cytosolic calcium ion concentration / fibrinolysis / Intrinsic Pathway of Fibrin Clot Formation / Peptide ligand-binding receptors / positive regulation of release of sequestered calcium ion into cytosol / Regulation of Complement cascade / acute-phase response / Cell surface interactions at the vascular wall / lipopolysaccharide binding / negative regulation of proteolysis / positive regulation of receptor signaling pathway via JAK-STAT / growth factor activity / serine-type endopeptidase inhibitor activity / positive regulation of insulin secretion / 凝固・線溶系 / response to wounding / Golgi lumen / positive regulation of protein localization to nucleus / 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 / 凝固・線溶系 / antimicrobial humoral immune response mediated by antimicrobial peptide / 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 / blood microparticle / cell surface receptor signaling pathway / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / 小胞体 / signaling receptor binding / serine-type endopeptidase activity / calcium ion binding / positive regulation of cell population proliferation / タンパク質分解 / extracellular space / extracellular exosome / extracellular region / 細胞膜 類似検索 - 分子機能 | ||||||
生物種 | Homo sapiens (ヒト) Hirudo medicinalis (医用ビル) | ||||||
手法 | X線回折 / 分子置換 / 解像度: 1.9 Å | ||||||
データ登録者 | Dekker, R.J. / Eichinger, A. / Stoop, A.A. / Bode, W. / Pannekoek, H. / Horrevoets, A.J.G. | ||||||
引用 | ジャーナル: J.Mol.Biol. / 年: 1999 タイトル: The variable region-1 from tissue-type plasminogen activator confers specificity for plasminogen activator inhibitor-1 to thrombin by facilitating catalysis: release of a kinetic block ...タイトル: The variable region-1 from tissue-type plasminogen activator confers specificity for plasminogen activator inhibitor-1 to thrombin by facilitating catalysis: release of a kinetic block by a heterologous protein surface loop 著者: Dekker, R.J. / Eichinger, A. / Stoop, A.A. / Bode, W. / Pannekoek, H. / Horrevoets, A.J.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 | 1vr1.cif.gz | 71.5 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb1vr1.ent.gz | 55.4 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1vr1.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/vr/1vr1 ftp://data.pdbj.org/pub/pdb/validation_reports/vr/1vr1 | 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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1 |
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単位格子 |
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-要素
#1: タンパク質・ペプチド | 分子量: 3188.627 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: F2 / 発現宿主: Cricetinae gen. sp. (ネズミ) / 参照: UniProt: P00734, トロンビン |
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#2: タンパク質 | 分子量: 30186.732 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: F2 / 発現宿主: Cricetinae gen. sp. (ネズミ) / 参照: UniProt: P00734, トロンビン |
#3: タンパク質・ペプチド | 分子量: 1363.399 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Hirudo medicinalis (医用ビル) / 属: Homoヒト属 / 発現宿主: Cricetinae gen. sp. (ネズミ) / 参照: UniProt: P28504, UniProt: P01050*PLUS |
#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: 2.63 Å3/Da / 溶媒含有率: 53.3 % | |||||||||||||||||||||||||||||||||||
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結晶化 | pH: 7.6 / 詳細: pH 7.6 | |||||||||||||||||||||||||||||||||||
結晶化 | *PLUS 温度: 6 ℃ / 手法: 蒸気拡散法, ハンギングドロップ法 / 詳細: used to seeding / PH range low: 8.6 / PH range high: 7.4 | |||||||||||||||||||||||||||||||||||
溶液の組成 | *PLUS
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-データ収集
回折 | 平均測定温度: 289 K |
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放射光源 | 由来: 回転陽極 / 波長: 1.5418 |
検出器 | 検出器: AREA DETECTOR |
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 | 解像度: 1.9→19.9 Å / Num. obs: 24804 / % possible obs: 92.2 % / Observed criterion σ(I): 2 / 冗長度: 2.3 % / Rmerge(I) obs: 0.094 / Rsym value: 0.094 |
反射 シェル | *PLUS 最高解像度: 1.93 Å / 最低解像度: 2.04 Å / % possible obs: 81.8 % / Rmerge(I) obs: 0.439 |
-解析
ソフトウェア | 名称: REFMAC / 分類: 精密化 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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精密化 | 構造決定の手法: 分子置換 / 解像度: 1.9→19.9 Å / 交差検証法: THROUGHOUT / σ(F): 0
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原子変位パラメータ | Biso mean: 42.3 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 1.9→19.9 Å
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拘束条件 |
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精密化 | *PLUS 最高解像度: 1.9 Å / σ(F): 0 / Num. reflection Rfree: 2487 / % reflection Rfree: 10 % / Rfactor obs: 0.204 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
溶媒の処理 | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | *PLUS Biso mean: 42.3 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
拘束条件 | *PLUS
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