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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: 1c1u | |||||||||
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タイトル | RECRUITING ZINC TO MEDIATE POTENT, SPECIFIC INHIBITION OF SERINE PROTEASES | |||||||||
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![]() | BLOOD CLOTTING/HYDROLASE INHIBITOR / ZN(II)-MEDIATED SERINE PROTEASE INHIBITORS / PH DEPENDENCE / ZN(II) AFFINITY STUCTURE-BASED DRUG DESIGN / SERINE PROTEASE/INHIBITOR / BLOOD CLOTTING-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 / 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 | ![]() | |||||||||
![]() | Katz, B.A. / Luong, C. | |||||||||
![]() | ![]() タイトル: Design of potent selective zinc-mediated serine protease inhibitors. 著者: Katz, B.A. / Clark, J.M. / Finer-Moore, J.S. / Jenkins, T.E. / Johnson, C.R. / Ross, M.J. / Luong, C. / Moore, W.R. / Stroud, R.M. | |||||||||
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 | ![]() | 152.1 KB | 表示 | ![]() |
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PDB形式 | ![]() | 119.7 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 | ![]() | 724.8 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 734 KB | 表示 | |
XML形式データ | ![]() | 18.7 KB | 表示 | |
CIF形式データ | ![]() | 26.8 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
関連構造データ | ![]() 1c1nC ![]() 1c1oC ![]() 1c1pC ![]() 1c1qC ![]() 1c1rC ![]() 1c1tC ![]() 1c1vC ![]() 1c1wC ![]() 1c2dC ![]() 1c2eC ![]() 1c2fC ![]() 1c2gC ![]() 1c2hC ![]() 1c2iC ![]() 1c2jC ![]() 1c2kC ![]() 1c2lC ![]() 1c2mC ![]() 1xufC ![]() 1xugC ![]() 1xuhC ![]() 1xuiC ![]() 1xujC ![]() 1xukC C: 同じ文献を引用 ( |
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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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Components on special symmetry positions |
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要素
-タンパク質・ペプチド , 2種, 2分子 LI
#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) ![]() |
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#3: タンパク質・ペプチド | 分子量: 1491.528 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) ![]() |
-タンパク質 , 1種, 1分子 H
#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 詳細: COMPLEXED WITH (5-AMIDINO-2-BENZIMIDAZOLYL)(2-BENZIMIDAZOLYL)METHANE 由来: (天然) ![]() |
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-非ポリマー , 4種, 291分子 ![](data/chem/img/ZN.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/BAI.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/BAI.gif)
![](data/chem/img/HOH.gif)
#4: 化合物 | ChemComp-ZN / |
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#5: 化合物 | ChemComp-NA / |
#6: 化合物 | ChemComp-BAI / ( |
#7: 水 | ChemComp-HOH / |
-詳細
構成要素の詳細 | HIS_H57 IS MONOPROTONATED ON THE DELTA NITROGEN. HIS_H91 AND HIS_H119 ARE MONOPROTONATED ON THE ...HIS_H57 IS MONOPROTON |
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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: 2.62 Å3/Da / 溶媒含有率: 36.7 % |
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結晶化 | pH: 8.2 詳細: THROMBIN WAS PURCHASED FROM HAEMATOLOGIC TECHNOLOGIES, INC. AND ACETYL-HIRUDIN FROM BACHEM. THROMBIN WAS PREPARED AS DESCRIBED (SKRZPCZAK-JANKUN ET AL., 1991) .THROMBIN (1.0 MG/ML IN 50 MM ...詳細: THROMBIN WAS PURCHASED FROM HAEMATOLOGIC TECHNOLOGIES, INC. AND ACETYL-HIRUDIN FROM BACHEM. THROMBIN WAS PREPARED AS DESCRIBED (SKRZPCZAK-JANKUN ET AL., 1991) .THROMBIN (1.0 MG/ML IN 50 MM HEPES, 50 % GLYCEROL, PH 7.0) WAS INCUBATED WITH 1.0 MM ACETYL-HIRUDIN, 1.0 MM HEMI-BABIM, 1.0 MM ZN+2 FOR 1 HR AT 4 DEG C. GLYCEROL WAS REMOVED AND THE COMPLEX CONCENTRATED WITH A CENTRICON 10 ( AMICON) TO 8.6 MG/ML AS DETERMINED BY THE BIORAD PROTEIN ASSAY KIT USING BOVINE SERUM ALBUMIN. CRYSTALS OF THROMBIN-ACETYL-HIRUDIN-HEMI-BABIM-ZN+2 WERE GROWN IN HANGING DROPS BY VAPOR DIFFUSION AFTER STREAK SEEDING. THE DROPS WERE MADE FROM 5 MICROLITERS OF COMPLEX AND 5 MICROLITERS OF RESERVOIR SOLUTION ( 0.10 M TRIS,0.50 M NACL, 22 % (BY VOLUME) PEG 4K, PH 8.20). |
結晶化 | *PLUS 手法: unknown |
-データ収集
回折 | 平均測定温度: 298 K |
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放射光源 | 由来: ![]() |
検出器 | タイプ: RIGAKU RAXIS IV++ / 検出器: IMAGE PLATE / 日付: 1998年1月23日 / 詳細: MSC MIRRORS |
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: 1.45→38.78 Å / Num. obs: 35066 / % possible obs: 77 % / Observed criterion σ(I): 1 / 冗長度: 1.9 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 7.8 |
反射 シェル | 解像度: 1.75→1.83 Å / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 1.8 / % possible all: 50 |
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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: DIFFERENCE FOURIER PLUS REFINEMENT / 解像度: 1.75→7.5 Å / 交差検証法: X-PLOR / σ(F): 2 詳細: BULK SOLVENT TERMS INCLUDED IN FOB FILE CREATED WITH STANDARD X-PLOR SCRIPT.
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精密化ステップ | サイクル: LAST / 解像度: 1.75→7.5 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 1.75→1.83 Å / Total num. of bins used: 8
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Xplor file | Serial no: 1 / Param file: PARMALLH3X_TH1706ZN.PRO / Topol file: TOPALLH6X_TH1706ZN.PRO |