+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1qur | |||||||||
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タイトル | HUMAN ALPHA-THROMBIN IN COMPLEX WITH BIVALENT, BENZAMIDINE-BASED SYNTHETIC INHIBITOR | |||||||||
要素 |
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キーワード | HYDROLASE/HYDROLASE INHIBITOR / TRYPSIN LIKE SERINE PROTEASE / BLOOD COAGULATION / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | |||||||||
機能・相同性 | 機能・相同性情報 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 / positive regulation of receptor signaling pathway via JAK-STAT / Cell surface interactions at the vascular wall / lipopolysaccharide binding / 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 | Homo sapiens (ヒト) | |||||||||
手法 | X線回折 / 解像度: 2 Å | |||||||||
データ登録者 | Renatus, M. / Steinmetzer, T. | |||||||||
引用 | ジャーナル: Eur.J.Biochem. / 年: 1999 タイトル: Design and evaluation of novel bivalent thrombin inhibitors based on amidinophenylalanines. 著者: Steinmetzer, T. / Renatus, M. / Kunzel, S. / Eichinger, A. / Bode, W. / Wikstrom, P. / Hauptmann, J. / Sturzebecher, J. | |||||||||
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 | 1qur.cif.gz | 81.7 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb1qur.ent.gz | 59 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1qur.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
文書・要旨 | 1qur_validation.pdf.gz | 434.7 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 1qur_full_validation.pdf.gz | 442.6 KB | 表示 | |
XML形式データ | 1qur_validation.xml.gz | 16.2 KB | 表示 | |
CIF形式データ | 1qur_validation.cif.gz | 22.3 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/qu/1qur ftp://data.pdbj.org/pub/pdb/validation_reports/qu/1qur | HTTPS FTP |
-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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詳細 | The biological assembly of alpha-thrombin consists of the large and small subunit, linked by a disulfid bridge |
-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: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: P00734 |
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#2: タンパク質 | 分子量: 29594.055 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: P00734 |
#3: タンパク質・ペプチド | 分子量: 2404.564 Da / 分子数: 1 / 由来タイプ: 合成 詳細: The inhibitor was chemically synthesized AS COMBINATION OF ORGANIC AND SOLID PHASE PEPTIDE SYNTHESIS. THE ACTIVE SITE BINDING PORTION IS DERIVED FROM THE SYNTHETICAL INHIBITOR NAPAP,THE ...詳細: The inhibitor was chemically synthesized AS COMBINATION OF ORGANIC AND SOLID PHASE PEPTIDE SYNTHESIS. THE ACTIVE SITE BINDING PORTION IS DERIVED FROM THE SYNTHETICAL INHIBITOR NAPAP,THE SEQUENCE OF THE EXOSITE BINDING PORTION WAS DERIVED FROM THE NATURALLY OCCURING INHIBITOR HIRUDIN, ISOLATED FROM THE MEDICAL LEECH AND THE SYNTHETICALLY SYNTHESIZED EXOSITE INHIBITOR MDL-28,050. |
#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: 2.65 Å3/Da / 溶媒含有率: 53.65 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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結晶化 | 温度: 280 K / 手法: macro seeding 詳細: 100 mM Tris/HCl, 300-500 mM NaCl, 22-32% (w/v) PEG 8000, macro seeding, temperature 280K | |||||||||||||||||||||||||||||||||||||||||||||||||
結晶化 | *PLUS 温度: 6 ℃ / pH: 6 / 手法: 蒸気拡散法, ハンギングドロップ法 | |||||||||||||||||||||||||||||||||||||||||||||||||
溶液の組成 | *PLUS
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-データ収集
回折 | 平均測定温度: 290 K |
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放射光源 | 由来: 回転陽極 / タイプ: RIGAKU RU300 / 波長: 1.5418 |
検出器 | タイプ: MARRESEARCH / 検出器: IMAGE PLATE / 日付: 1998年11月23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: 1.5418 Å / 相対比: 1 |
反射 | 解像度: 1.98→9 Å / Num. all: 54304 / Num. obs: 23412 / % possible obs: 93.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / 冗長度: 2.3 % / Biso Wilson estimate: 21.604 Å2 / Rmerge(I) obs: 0.128 / Net I/σ(I): 4 |
反射 シェル | 解像度: 1.98→2.09 Å / 冗長度: 2 % / Rmerge(I) obs: 0.476 / Mean I/σ(I) obs: 1.2 / % possible all: 82 |
反射 シェル | *PLUS % possible obs: 82 % |
-解析
ソフトウェア |
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精密化 | 解像度: 2→9 Å / Data cutoff high rms absF: 10000 / σ(F): 0 / σ(I): 0 / 立体化学のターゲット値: Engh & Huber
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原子変位パラメータ |
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精密化ステップ | サイクル: LAST / 解像度: 2→9 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 2→2.03 Å / Total num. of bins used: 22 /
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Xplor file | Serial no: 1 / Param file: CNS_TOPPAR:protein_rep.param / Topol file: CNS_TOPPAR:water_rep.param | ||||||||||||||||||||||||||||
ソフトウェア | *PLUS 名称: CNS / 分類: refinement | ||||||||||||||||||||||||||||
精密化 | *PLUS 最高解像度: 2 Å / 最低解像度: 9 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.2085 / Rfactor Rfree: 0.2468 | ||||||||||||||||||||||||||||
溶媒の処理 | *PLUS | ||||||||||||||||||||||||||||
原子変位パラメータ | *PLUS | ||||||||||||||||||||||||||||
拘束条件 | *PLUS
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LS精密化 シェル | *PLUS Rfactor Rfree: 0.323 |