+
データを開く
-
基本情報
登録情報 | データベース: PDB / ID: 1qhr | ||||||
---|---|---|---|---|---|---|---|
タイトル | NOVEL COVALENT ACTIVE SITE THROMBIN INHIBITORS | ||||||
![]() |
| ||||||
![]() | BLOOD CLOTTING/HYDROLASE INHIBITOR / PROTEINASE / BLOOD COAGULATION / TRYPSIN LIKE PROTEINASE / COMPLEX (SERINE PROTEASE-INHIBITOR) / BLOOD CLOTTING-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 / 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 / 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 / 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 / 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 / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell surface receptor signaling pathway / 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 | ![]() | ||||||
![]() | Jhoti, H. / Cleasby, A. / Reid, S. / Thomas, P. / Wonacott, A. | ||||||
![]() | ![]() タイトル: Crystal structures of thrombin complexed to a novel series of synthetic inhibitors containing a 5,5-trans-lactone template. 著者: Jhoti, H. / Cleasby, A. / Reid, S. / Thomas, P.J. / Weir, M. / Wonacott, A. | ||||||
履歴 |
|
-
構造の表示
構造ビューア | 分子: ![]() ![]() |
---|
-
ダウンロードとリンク
-
ダウンロード
PDBx/mmCIF形式 | ![]() | 81.1 KB | 表示 | ![]() |
---|---|---|---|---|
PDB形式 | ![]() | 60 KB | 表示 | ![]() |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
その他 | ![]() |
-検証レポート
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
---|
-関連構造データ
-
リンク
-
集合体
登録構造単位 | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
単位格子 |
|
-
要素
#1: タンパク質・ペプチド | 分子量: 4096.534 Da / 分子数: 1 / 断片: LIGHT CHAIN / 由来タイプ: 天然 / 由来: (天然) ![]() |
---|---|
#2: タンパク質 | 分子量: 29780.219 Da / 分子数: 1 / 断片: HEAVY CHAIN / 由来タイプ: 天然 / 由来: (天然) ![]() |
#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: 合成 詳細: THIS PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE FOR THIS PEPTIDE OCCURS NATURALLY IN MEDICINAL LEECH (HIRUDO MEDICINALIS). 由来: (合成) ![]() |
#4: 化合物 | ChemComp-157 / |
#5: 水 | ChemComp-HOH / |
非ポリマーの詳細 | GR15: ACTIVE SITE DIRECTED, ACYLATING INHIBITOR OF THROMBIN. |
-実験情報
-実験
実験 | 手法: ![]() |
---|
-
試料調製
結晶 | マシュー密度: 2.62 Å3/Da / 溶媒含有率: 53.11 % | ||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
結晶化 | pH: 7 詳細: CRYSTALS WERE GROWN BY MACROSEEDING A SOLUTION OF 100MM HEPES PH 7.0, 22% PEG4K, 200MM NACL. PROTEIN CONCENTRATION OF 5MG/ML. | ||||||||||||||||||||||||||||||||||||||||||||||||
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
|
-データ収集
回折 | 平均測定温度: 290 K |
---|---|
放射光源 | 由来: ![]() |
検出器 | タイプ: ENRAF-NONIUS / 検出器: AREA DETECTOR / 詳細: MONOCHROMATOR |
放射 | モノクロメーター: GRAPHITE / 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: 2→30 Å / Num. obs: 21972 / % possible obs: 98 % / 冗長度: 2.2 % / Rsym value: 0.06 |
反射 | *PLUS Rmerge(I) obs: 0.058 |
-
解析
ソフトウェア |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
精密化 | 構造決定の手法: OTHER / 解像度: 2.2→15 Å / σ(F): 2 /
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 2.2→15 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
拘束条件 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ソフトウェア | *PLUS 名称: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化 | *PLUS 最高解像度: 2.2 Å / 最低解像度: 15 Å / σ(F): 2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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_deg / Dev ideal: 3.1 |