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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: 1ba8 | ||||||
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タイトル | THROMBIN INHIBITOR WITH A RIGID TRIPEPTIDYL ALDEHYDES | ||||||
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![]() | HYDROLASE/HYDROLASE INHIBITOR / 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 | ![]() ![]() | ||||||
![]() | Krishnan, R. / Zhang, E. / Hakansson, K. / Arni, R.K. / Tulinsky, A. / Lim-Wilby, M.S.L. / Levy, O.E. / Semple, J.E. / Brunck, T.K. | ||||||
![]() | ![]() タイトル: Highly selective mechanism-based thrombin inhibitors: structures of thrombin and trypsin inhibited with rigid peptidyl aldehydes. 著者: Krishnan, R. / Zhang, E. / Hakansson, K. / Arni, R.K. / Tulinsky, A. / Lim-Wilby, M.S. / Levy, O.E. / Semple, J.E. / Brunck, T.K. | ||||||
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 | ![]() | 75.7 KB | 表示 | ![]() |
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PDB形式 | ![]() | 57.2 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 | ![]() | 478.4 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 500 KB | 表示 | |
XML形式データ | ![]() | 11.5 KB | 表示 | |
CIF形式データ | ![]() | 16.8 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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要素
-タンパク質・ペプチド , 2種, 2分子 AC
#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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#3: タンパク質・ペプチド | 分子量: 1561.577 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() |
-タンパク質 / 糖 , 2種, 2分子 B![](data/chem/img/NAG.gif)
![](data/chem/img/NAG.gif)
#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) ![]() |
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#5: 糖 | ChemComp-NAG / |
-非ポリマー , 2種, 159分子 ![](data/chem/img/0IT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#4: 化合物 | ChemComp-0IT / |
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#6: 水 | ChemComp-HOH / |
-詳細
非ポリマーの詳細 | THE ACTIVE SITE SER 195 IS CLOSE TO THE CARBONYL CARBON (C2) OF THE ALDEHYDE GROUP OF THE INHIBITOR ...THE ACTIVE SITE SER 195 IS CLOSE TO THE CARBONYL CARBON (C2) OF THE ALDEHYDE GROUP OF THE INHIBITOR BUT DOES NOT FORM A TETRAHEDRA |
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-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: 2.5 Å3/Da / 溶媒含有率: 51 % | ||||||||||||||||||||||||
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結晶化 | pH: 7.5 / 詳細: pH 7.5 | ||||||||||||||||||||||||
結晶 | *PLUS | ||||||||||||||||||||||||
結晶化 | *PLUS 手法: 蒸気拡散法, ハンギングドロップ法 / 詳細: used to seeding | ||||||||||||||||||||||||
溶液の組成 | *PLUS
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-データ収集
回折 | 平均測定温度: 300 K |
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放射光源 | 波長: 1.5418 |
検出器 | タイプ: RIGAKU / 検出器: IMAGE PLATE / 日付: 1995年8月1日 |
放射 | モノクロメーター: NI FILTER / 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: 1.8→15 Å / Num. obs: 22257 / % possible obs: 61 % / Observed criterion σ(I): 2.5 / 冗長度: 2.5 % / Rmerge(I) obs: 0.045 / Rsym value: 0.12 / Net I/σ(I): 14 |
反射 シェル | 解像度: 1.8→2 Å / 冗長度: 2 % / Rmerge(I) obs: 0.07 / Mean I/σ(I) obs: 2.5 / Rsym value: 0.25 / % possible all: 38 |
反射 | *PLUS 冗長度: 1.8 % / Num. measured all: 40769 / Rmerge(I) obs: 0.078 |
反射 シェル | *PLUS % possible obs: 38 % / Rmerge(I) obs: 0.184 |
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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: PDB ENTRY 1TMB 解像度: 1.8→7 Å / 交差検証法: THROUGHOUT / σ(F): 4 詳細: RESIDUES 148 - 149 IN THE B CHAIN WERE DISORDERED AND ARE NOT INCLUDED IN THE COORDINATES.
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原子変位パラメータ | Biso mean: 26.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.2 Å / Luzzati d res low obs: 7 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 1.8→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 Rfactor obs: 0.152 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
溶媒の処理 | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | *PLUS |