+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1o2g | |||||||||
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タイトル | Elaborate Manifold of Short Hydrogen Bond Arrays Mediating Binding of Active Site-Directed Serine Protease Inhibitors | |||||||||
要素 |
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キーワード | BLOOD CLOTTING / HYDROLASE/INHIBITOR / serine protease / short hydrogen bond / inhibition mechanism / shift of pKa / trypsin / thrombin / urokinase / factor Xa / hydrolase / HYDROLASE-HYDROLASE INHIBITOR COMPLEX / 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 / 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 | Homo sapiens (ヒト) Hirudo medicinalis (医用ビル) | |||||||||
手法 | X線回折 / フーリエ合成 / 解像度: 1.58 Å | |||||||||
データ登録者 | Katz, B.A. / Elrod, K. / Verner, E. / Mackman, R.L. / Luong, C. / Shrader, W. / Sendzik, M. / Spencer, J.R. / Sprengeler, P.A. / Kolesnikov, A. ...Katz, B.A. / Elrod, K. / Verner, E. / Mackman, R.L. / Luong, C. / Shrader, W. / Sendzik, M. / Spencer, J.R. / Sprengeler, P.A. / Kolesnikov, A. / Tai, W.F. / Hui, H. / Breitenbucher, G. / Allen, D. / Janc, J. | |||||||||
引用 | ジャーナル: J.Mol.Biol. / 年: 2003 タイトル: Elaborate Manifold of Short Hydrogen Bond Arrays Mediating Binding of Active Site-Directed Serine Protease Inhibitors 著者: Katz, B.A. / Elrod, K. / Verner, E. / Mackman, R.L. / Luong, C. / Shrader, W.D. / Sendzik, M. / Spencer, J.R. / Sprengeler, P.A. / Kolesnikov, A. / Tai, V.W.-F. / Hui, H.C. / Breitenbucher, J. ...著者: Katz, B.A. / Elrod, K. / Verner, E. / Mackman, R.L. / Luong, C. / Shrader, W.D. / Sendzik, M. / Spencer, J.R. / Sprengeler, P.A. / Kolesnikov, A. / Tai, V.W.-F. / Hui, H.C. / Breitenbucher, J.G. / Allen, D. / Janc, J.W. | |||||||||
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 | 1o2g.cif.gz | 152.3 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb1o2g.ent.gz | 121.2 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1o2g.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 | 1o2g_validation.pdf.gz | 731.3 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 1o2g_full_validation.pdf.gz | 735.4 KB | 表示 | |
XML形式データ | 1o2g_validation.xml.gz | 18.3 KB | 表示 | |
CIF形式データ | 1o2g_validation.cif.gz | 26.6 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/o2/1o2g ftp://data.pdbj.org/pub/pdb/validation_reports/o2/1o2g | HTTPS FTP |
-関連構造データ
関連構造データ | 1o2hC 1o2iC 1o2jC 1o2kC 1o2lC 1o2mC 1o2nC 1o2oC 1o2pC 1o2qC 1o2rC 1o2sC 1o2tC 1o2uC 1o2vC 1o2wC 1o2xC 1o2yC 1o2zC 1o30C 1o31C 1o32C 1o33C 1o34C 1o35C 1o36C 1o37C 1o38C 1o39C 1o3aC 1o3bC 1o3cC 1o3dC 1o3eC 1o3fC 1o3gC 1o3hC 1o3iC 1o3jC 1o3kC 1o3lC 1o3mC 1o3nC 1o3oC 1o3pC 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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1 |
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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, RESIDUES 328-363 / 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: 合成 / 由来: (合成) 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 / 断片: HEAVY CHAIN, RESIDUES 364-620 / 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 , 3種, 310分子
#4: 化合物 | ChemComp-NA / |
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#5: 化合物 | ChemComp-696 / |
#6: 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: 2.59 Å3/Da / 溶媒含有率: 52.6 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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結晶化 | 温度: 298 K / 手法: 蒸気拡散法 / pH: 6.5 詳細: 2-propanol, PEG 4000, pH 6.5, vapor diffusion at 298 K, pH 6.50 | |||||||||||||||||||||||||||||||||||||||||||||||||
結晶化 | *PLUS pH: 7 / 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: 285 K / Ambient temp details: Crystal Cooler |
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放射光源 | 由来: 回転陽極 / タイプ: RIGAKU RUH3R / 波長: 1.5418 |
検出器 | タイプ: RIGAKU RAXIS IV++ / 検出器: IMAGE PLATE / 日付: 2002年6月4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: 1.58→32.19 Å / Num. all: 49555 / Num. obs: 45048 / % possible obs: 90.91 % / Observed criterion σ(I): 0 / 冗長度: 2 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 9.6 |
反射 シェル | 解像度: 1.58→1.65 Å / % possible obs: 48.34 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 1.2 / Num. unique all: 7062 |
反射 | *PLUS 最高解像度: 1.38 Å / Num. obs: 46254 / Num. measured all: 93493 |
反射 シェル | *PLUS Rmerge(I) obs: 0.34 |
-解析
ソフトウェア |
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精密化 | 構造決定の手法: フーリエ合成 / 解像度: 1.58→7 Å / 交差検証法: THROUGHOUT / σ(F): 0.7 詳細: Met_H84, Leu_H130, Val_H157, Pro_H166, and Ile_H174 were simultaneously refined in two conformations. No density was observed for Thr147, Trp148, Thr149, Ala149A, Asn149B, Val149C, Gly149D, ...詳細: Met_H84, Leu_H130, Val_H157, Pro_H166, and Ile_H174 were simultaneously refined in two conformations. No density was observed for Thr147, Trp148, Thr149, Ala149A, Asn149B, Val149C, Gly149D, and Lys149E in the autolysis loop, and these residues are not included in the model. In the non-active site peptide inhibitor (acetylhirudin) the tyrosine hydroxyl is sulfonated. HOH477, OgSer195 and O6' of the inhibitor make a 3-centered short hydrogen bond array. Disordered waters include: HOH395 is close to a symmetry related equivalent of itself. HOH396 is close to a symmetry related equivalent of itself. HOH397 is close to a symmetry related equivalent of itself. HIS_H57 IS doubly protonated. HIS_H91 and His_H119 are monoprotonated on the epsilon nitrogen
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精密化ステップ | サイクル: LAST / 解像度: 1.58→7 Å
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拘束条件 |
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精密化 | *PLUS 最高解像度: 1.58 Å / % reflection Rfree: 10 % / Rfactor Rwork: 0.222 | ||||||||||||||||||||
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 最高解像度: 1.58 Å / 最低解像度: 1.65 Å / Rfactor Rfree: 0.25 |