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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: 1h8d | ||||||
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タイトル | X-ray structure of the human alpha-thrombin complex with a tripeptide phosphonate inhibitor. | ||||||
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![]() | HYDROLASE/HYDROLASE INHIBITOR / SERINE PROTEASE / 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 | ![]() ![]() ![]() | ||||||
![]() | Skordalakes, E. / Dodson, G.G. / Green, D. / Deadman, J. | ||||||
![]() | ![]() タイトル: Inhibition of Human Alpha-Thrombin by a Phosphonate Tripeptide Proceeds Via a Metastable Pentacoordinated Phosphorus Intermediate 著者: Skordalakes, E. / Dodson, G.G. / Green, D.S. / Goodwin, C.A. / Scully, M.F. / Hudson, H.R. / Kakkar, V.V. / Deadman, J.J. #1: ![]() タイトル: Inhibition of Trypsin and Thrombin by Amino (4-Amidinophenyl)Methanephosphonate Diphenyl Ester Derivatives: X-Ray and Molecular Models 著者: Bertrand, J.A. / Oleksyszyn, J. / Kam, C.M. / Boduszek, B. / Presnell, S. / Plaskon, R.R. / Suddath, F.L. / Powers, J.C. / Williams, L.D. | ||||||
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 | ![]() | 98.7 KB | 表示 | ![]() |
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PDB形式 | ![]() | 71.9 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 | ![]() | 938.2 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 954.4 KB | 表示 | |
XML形式データ | ![]() | 25 KB | 表示 | |
CIF形式データ | ![]() | 37.6 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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Components on special symmetry positions |
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要素
#1: タンパク質 | 分子量: 29797.395 Da / 分子数: 1 / 断片: THROMBIN HEAVY CHAIN / 由来タイプ: 天然 / 由来: (天然) ![]() |
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#2: タンパク質・ペプチド | 分子量: 1363.399 Da / 分子数: 1 / 断片: RESIDUES 55 TO 64 / 由来タイプ: 天然 / 由来: (天然) ![]() |
#3: タンパク質・ペプチド | 分子量: 3404.819 Da / 分子数: 1 / 断片: THROMBIN LIGHT CHAIN / 由来タイプ: 天然 / 由来: (天然) ![]() |
#4: 化合物 | ChemComp-PHW / |
#5: 水 | ChemComp-HOH / |
-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: 2.59 Å3/Da / 溶媒含有率: 54 % | ||||||||||||||||||||
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結晶化 | pH: 7.2 / 詳細: 20% PEG 8K, 0.05MM NAHPO4, 0.1M NACL, PH 7.20 | ||||||||||||||||||||
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: Skordalakes, E., (1997) J. Am. Chem. Soc., 119, 9935. | ||||||||||||||||||||
溶液の組成 | *PLUS
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-データ収集
回折 | 平均測定温度: 100 K |
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放射光源 | 由来: ![]() ![]() ![]() |
検出器 | 日付: 1998年6月7日 |
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: 1.488 Å / 相対比: 1 |
反射 | 解像度: 1.4→15 Å / Num. obs: 68615 / % possible obs: 95.4 % / Observed criterion σ(I): 5 / 冗長度: 3 % / Biso Wilson estimate: 16.27 Å2 / Rmerge(I) obs: 0.052 / Rsym value: 0.056 / Net I/σ(I): 23 |
反射 シェル | 解像度: 1.4→1.45 Å / 冗長度: 2 % / Rmerge(I) obs: 0.142 / Mean I/σ(I) obs: 6 / Rsym value: 0.131 / % possible all: 96.6 |
反射 | *PLUS 最低解像度: 8 Å / Num. obs: 66600 |
反射 シェル | *PLUS % possible obs: 95.5 % / Rmerge(I) obs: 0.136 / Mean I/σ(I) obs: 5.5 |
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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: 1HGT 解像度: 1.4→14 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: 18.5 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 1.4→14 Å
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拘束条件 |
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ソフトウェア | *PLUS 名称: REFMAC / 分類: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化 | *PLUS 最低解像度: 8 Å / Rfactor obs: 0.175 / Rfactor Rfree: 0.215 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
溶媒の処理 | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | *PLUS |