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基本情報
登録情報 | データベース: PDB / ID: 4thn | ||||||
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タイトル | THE CRYSTAL STRUCTURE OF ALPHA-THROMBIN-HIRUNORM IV COMPLEX REVEALS A NOVEL SPECIFICITY SITE RECOGNITION MODE. | ||||||
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![]() | HYDROLASE/HYDROLASE INHIBITOR / COMPLEX (SERINE PROTEASE-INHIBITOR) / THROMBIN SYNTHETIC INHIBITORS / ANTITHROMBOTICS / HIRUDIN-LIKE BINDING MODE / HIRUNORMS / THROMBIN / 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 / 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 / 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 | ![]() ![]() | ||||||
![]() | Lombardi, A. / De Simone, G. / Nastri, F. / Galdiero, S. / Della Morte, R. / Staiano, N. / Pedone, C. / Bolognesi, M. / Pavone, V. | ||||||
![]() | ![]() タイトル: The crystal structure of alpha-thrombin-hirunorm IV complex reveals a novel specificity site recognition mode. 著者: Lombardi, A. / De Simone, G. / Nastri, F. / Galdiero, S. / Della Morte, R. / Staiano, N. / Pedone, C. / Bolognesi, M. / Pavone, V. #1: ![]() 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 2D, J.W. #2: ![]() タイトル: Hirunorms are True Hirudin Mimetics. The Crystal Structure of Human Alpha-Thrombin-Hirunorm V Complex 著者: De Simone, G. / Lombardi, A. / Galdiero, S. / Nastri, F. / Della Morte, R. / Staiano, N. / Pedone, C. / Bolognesi, M. / Pavone, V. #3: ![]() タイトル: Rational Design of True Hirudin Mimetics: Synthesis and Characterization of Multisite-Directed Alpha-Thrombin Inhibitors 著者: Lombardi, A. / Nastri, F. / Della Morte, R. / Rossi, A. / De Rosa, A. / Staiano, N. / Pedone, C. / Pavone, V. #4: ![]() 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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PDBx/mmCIF形式 | ![]() | 78.6 KB | 表示 | ![]() |
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PDB形式 | ![]() | 59.6 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 |
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-関連構造データ
関連構造データ | ![]() 1hahS S: 精密化の開始モデル |
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類似構造データ |
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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
#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: 3016.274 Da / 分子数: 1 / 由来タイプ: 組換発現 / 詳細: CHEMICAL SYNTHESIS |
#4: 糖 | ChemComp-NAG / |
#5: 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 *I* IS USED FOR HIRUNORM IV. |
-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: 2.58 Å3/Da / 溶媒含有率: 52.33 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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結晶化 | pH: 7 / 詳細: pH 7.0 | ||||||||||||||||||||||||||||||||||||||||||||||||
結晶 | *PLUS 溶媒含有率: 49 % | ||||||||||||||||||||||||||||||||||||||||||||||||
結晶化 | *PLUS 温度: 4 ℃ / 手法: 蒸気拡散法 | ||||||||||||||||||||||||||||||||||||||||||||||||
溶液の組成 | *PLUS
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-データ収集
回折 | 平均測定温度: 293 K |
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放射光源 | 波長: 1.5418 |
検出器 | タイプ: RIGAKU RAXIS II / 検出器: IMAGE PLATE / 日付: 1996年6月1日 / 詳細: COLLIMATOR |
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 | 解像度: 2.5→20 Å / Num. obs: 12580 / % possible obs: 96.3 % / Observed criterion σ(I): 1.5 / 冗長度: 2.6 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 5 |
反射 シェル | 解像度: 2.5→2.63 Å / 冗長度: 2.6 % / Rmerge(I) obs: 0.439 / Mean I/σ(I) obs: 1.6 / % possible all: 97.4 |
反射 | *PLUS Num. measured all: 33294 |
反射 シェル | *PLUS % possible obs: 97.4 % |
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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 1HAH (J. VIJAYALAKSHMI ET AL., PROTEIN SCI. 3, 2254-71) 解像度: 2.5→20 Å / σ(F): 0
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溶媒の処理 | Bsol: 147.6 Å2 / ksol: 0.768 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 2.5→20 Å
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拘束条件 |
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ソフトウェア | *PLUS 名称: TNT / バージョン: 5E / 分類: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
拘束条件 | *PLUS
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