+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1gi8 | ||||||
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タイトル | A NOVEL SERINE PROTEASE INHIBITION MOTIF INVOLVING A MULTI-CENTERED SHORT HYDROGEN BONDING NETWORK AT THE ACTIVE SITE | ||||||
要素 | (UROKINASE-TYPE PLASMINOGEN ACTIVATOR) x 2 | ||||||
キーワード | BLOOD CLOTTING / hydrolase / three-centered / very short hydrogen bond / oxyanion hole water / shift of pKa of His57 / structure-based drug design / specificity / urokinase / trypsin / thrombin / Zn+2-mediated inhibition | ||||||
機能・相同性 | 機能・相同性情報 u-plasminogen activator / regulation of smooth muscle cell-matrix adhesion / urokinase plasminogen activator signaling pathway / regulation of plasminogen activation / regulation of fibrinolysis / regulation of wound healing / protein complex involved in cell-matrix adhesion / negative regulation of plasminogen activation / regulation of smooth muscle cell migration / regulation of signaling receptor activity ...u-plasminogen activator / regulation of smooth muscle cell-matrix adhesion / urokinase plasminogen activator signaling pathway / regulation of plasminogen activation / regulation of fibrinolysis / regulation of wound healing / protein complex involved in cell-matrix adhesion / negative regulation of plasminogen activation / regulation of smooth muscle cell migration / regulation of signaling receptor activity / serine-type endopeptidase complex / Dissolution of Fibrin Clot / smooth muscle cell migration / plasminogen activation / regulation of cell adhesion mediated by integrin / tertiary granule membrane / negative regulation of fibrinolysis / regulation of cell adhesion / specific granule membrane / serine protease inhibitor complex / fibrinolysis / chemotaxis / blood coagulation / regulation of cell population proliferation / response to hypoxia / positive regulation of cell migration / external side of plasma membrane / serine-type endopeptidase activity / focal adhesion / Neutrophil degranulation / cell surface / signal transduction / 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 / フーリエ合成 / 解像度: 1.75 Å | ||||||
データ登録者 | Katz, B.A. / Elrod, K. / Luong, C. / Rice, M. / Mackman, R.L. / Sprengeler, P.A. / Spencer, J. / Hatayte, J. / Janc, J. / Link, J. ...Katz, B.A. / Elrod, K. / Luong, C. / Rice, M. / Mackman, R.L. / Sprengeler, P.A. / Spencer, J. / Hatayte, J. / Janc, J. / Link, J. / Litvak, J. / Rai, R. / Rice, K. / Sideris, S. / Verner, E. / Young, W. | ||||||
引用 | ジャーナル: J.Mol.Biol. / 年: 2001 タイトル: A novel serine protease inhibition motif involving a multi-centered short hydrogen bonding network at the active site. 著者: Katz, B.A. / Elrod, K. / Luong, C. / Rice, M.J. / Mackman, R.L. / Sprengeler, P.A. / Spencer, J. / Hataye, J. / Janc, J. / Link, J. / Litvak, J. / Rai, R. / Rice, K. / Sideris, S. / Verner, E. / Young, 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 | 1gi8.cif.gz | 138.3 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb1gi8.ent.gz | 110.3 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1gi8.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
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/gi/1gi8 ftp://data.pdbj.org/pub/pdb/validation_reports/gi/1gi8 | HTTPS FTP |
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-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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Components on special symmetry positions |
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-要素
#1: タンパク質・ペプチド | 分子量: 2708.183 Da / 分子数: 1 / 断片: SHORT CHAIN / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 解説: CHEM.BIOL. 7, 299-312, 2000 / プラスミド: PPIC9LMWUPA / 発現宿主: Pichia pastoris (菌類) / 参照: UniProt: P00749 | ||||
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#2: タンパク質 | 分子量: 27579.473 Da / 分子数: 1 / 断片: CATALYTIC DOMAIN / Mutation: N145A / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 解説: CHEM.BIOL. 7, 299-312, 2000 / プラスミド: PPIC9LMWUPA / 発現宿主: Pichia pastoris (菌類) / 参照: UniProt: P00749, u-plasminogen activator | ||||
#3: 化合物 | #4: 化合物 | ChemComp-BMZ / | #5: 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: 2.03 Å3/Da / 溶媒含有率: 39.47 % | |||||||||||||||||||||||||||||||||||
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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 手法: 蒸気拡散法, ハンギングドロップ法 / PH range low: 8.2 / PH range high: 7.5 | |||||||||||||||||||||||||||||||||||
溶液の組成 | *PLUS
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-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 / タイプ: RIGAKU RU200 / 波長: 1.5418 |
検出器 | タイプ: RIGAKU RAXIS IV / 検出器: IMAGE PLATE / 日付: 1999年7月19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: 1.43→40.95 Å / Num. all: 45525 / Num. obs: 20030 / % possible obs: 44 % / Observed criterion σ(I): 1 / 冗長度: 1.9 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 6 |
反射 シェル | 解像度: 1.7→1.85 Å / Rmerge(I) obs: 0.327 / Num. unique all: 1930 / % possible all: 31.9 |
反射 | *PLUS 冗長度: 1.9 % / Num. measured all: 38325 |
-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: 1.75→7 Å / 交差検証法: THROUGHOUT / σ(F): 2 / 立体化学のターゲット値: X-PLOR force field 詳細: Only Leu_A9 to Thr_A17 are included for the A-chain. Residues prior and after these residues are not visible (disordered). Residues after Thr_B242 are not visible (disordered). Residues ...詳細: Only Leu_A9 to Thr_A17 are included for the A-chain. Residues prior and after these residues are not visible (disordered). Residues after Thr_B242 are not visible (disordered). Residues simultaneously refined in two or more conformations are: Ile_B17, Thr_B22, Met_B47, Asp_B97, Thr_B139, Arg_B166. Disordered waters are: HOH11 which is close to HOH12; HOH90 which is close to a symmetry-related equivalent of itself; HOH373 which is close to HOH374; HOH497 which is close to a symmetry-related equivalent of itself; HOH681 which is close to HOH682; HOH940 which is close to HOH941, which in turn is close to HOH942; HOH980 which is close to HOH981; HOH1013 which is close to a symmetry-related equivalent of itself; HOH1017 which is close to a symmetry-related equivalent of itself; HOH1031 which is close to a symmetry-related equivalent of itself; No energy terms between citrate 1 and 2 are included because they are hydrogen-bonded to one another via an unusually short hydrogen bond between carboxylate / hydroxyl groups. No energy terms are included among HOH_591, and OgSer195, and O6' of the inhibitor. These atoms form a very short multi-centered hydrogen-bonding network.
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精密化ステップ | サイクル: LAST / 解像度: 1.75→7 Å
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拘束条件 |
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ソフトウェア | *PLUS 名称: X-PLOR / バージョン: 3.851 / 分類: refinement | ||||||||||||||||||||
精密化 | *PLUS 最低解像度: 7 Å / σ(F): 2 / % reflection Rfree: 10 % / Rfactor all: 0.204 / Rfactor obs: 0.2 / Rfactor Rwork: 0.2 | ||||||||||||||||||||
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: 1.75 Å / 最低解像度: 1.83 Å / Rfactor Rfree: 0.261 / Rfactor obs: 0.205 |