+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1c1w | |||||||||
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タイトル | RECRUITING ZINC TO MEDIATE POTENT, SPECIFIC INHIBITION OF SERINE PROTEASES | |||||||||
要素 |
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キーワード | HYDROLASE/HYDROLASE INHIBITOR / ZN(II)-MEDIATED SERINE PROTEASE INHIBITORS / PH DEPENDENCE / ZN(II) AFFINITY STUCTURE-BASED DRUG DESIGN / SERINE PROTEASE/INHIBITOR / BLOOD CLOTTING / 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 / 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 | Homo sapiens (ヒト) Hirudo medicinalis (医用ビル) | |||||||||
手法 | X線回折 / DIFFERENCE FOURIER PLUS REFINEMENT / 解像度: 1.9 Å | |||||||||
データ登録者 | Katz, B.A. / Luong, C. | |||||||||
引用 | ジャーナル: Nature / 年: 1998 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: 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 | 1c1w.cif.gz | 150.2 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb1c1w.ent.gz | 118 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1c1w.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 | 1c1w_validation.pdf.gz | 754 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 1c1w_full_validation.pdf.gz | 764.3 KB | 表示 | |
XML形式データ | 1c1w_validation.xml.gz | 18.1 KB | 表示 | |
CIF形式データ | 1c1w_validation.cif.gz | 25.6 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/c1/1c1w ftp://data.pdbj.org/pub/pdb/validation_reports/c1/1c1w | HTTPS FTP |
-関連構造データ
関連構造データ | 1c1nC 1c1oC 1c1pC 1c1qC 1c1rC 1c1tC 1c1uC 1c1vC 1c2dC 1c2eC 1c2fC 1c2gC 1c2hC 1c2iC 1c2jC 1c2kC 1c2lC 1c2mC 1xufC 1xugC 1xuhC 1xuiC 1xujC 1xukC C: 同じ文献を引用 (文献) |
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類似構造データ |
-リンク
-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 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: P00734, thrombin |
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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: 天然 / 由来: (天然) Hirudo medicinalis (医用ビル) / 参照: UniProt: P28504 |
-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 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: P00734, thrombin |
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-非ポリマー , 4種, 244分子
#4: 化合物 | #5: 化合物 | ChemComp-NA / | #6: 化合物 | ChemComp-BAH / | #7: 水 | ChemComp-HOH / | |
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-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: 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: 2.58 Å3/Da / 溶媒含有率: 52.38 % |
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結晶化 | pH: 9 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 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-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 7.00). A CO-CRYSTAL WAS SOAKED IN 30 % PEG 4K,0.50 M NACL, 0.10 M TRIS, 0.4 MM ZN+2, PH 9.00, SATURATED IN KETO- BABIM AND CONTAINING 2 % DMSO. |
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: 回転陽極 / 波長: 1.5418 |
検出器 | タイプ: RIGAKU RAXIS IV++ / 検出器: IMAGE PLATE / 日付: 1998年2月18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: 1.9→35.9 Å / Num. obs: 25689 / % possible obs: 65 % / Observed criterion σ(I): 1 / 冗長度: 1.6 % / Rmerge(I) obs: 0.116 / Net I/σ(I): 5.5 |
反射 シェル | 解像度: 1.9→1.98 Å / Rmerge(I) obs: 0.246 / Mean I/σ(I) obs: 2.1 / % possible all: 36.7 |
-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: 1.9→7.5 Å / 交差検証法: X-PLOR / σ(F): 2.2 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: 1.9→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: 1.9→1.98 Å / Total num. of bins used: 8
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Xplor file |
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