+
データを開く
-
基本情報
登録情報 | データベース: PDB / ID: 1gi7 | ||||||
---|---|---|---|---|---|---|---|
タイトル | A NOVEL SERINE PROTEASE INHIBITION MOTIF INVOLVING A MULTI-CENTERED SHORT HYDROGEN BONDING NETWORK AT THE ACTIVE SITE | ||||||
![]() | (UROKINASE-TYPE PLASMINOGEN ACTIVATOR) x 2 | ||||||
![]() | 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 | ![]() 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 | ![]() | ||||||
手法 | ![]() ![]() ![]() | ||||||
![]() | 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. | ||||||
![]() | ![]() 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 |
|
-
構造の表示
構造ビューア | 分子: ![]() ![]() |
---|
-
ダウンロードとリンク
-
ダウンロード
PDBx/mmCIF形式 | ![]() | 128.1 KB | 表示 | ![]() |
---|---|---|---|---|
PDB形式 | ![]() | 101.6 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 | ![]() | 666.6 KB | 表示 | ![]() |
---|---|---|---|---|
文書・詳細版 | ![]() | 674.3 KB | 表示 | |
XML形式データ | ![]() | 16.1 KB | 表示 | |
CIF形式データ | ![]() | 23.4 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
-
リンク
-
集合体
登録構造単位 | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
単位格子 |
|
-
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) ![]() ![]() | ||
---|---|---|---|
#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) ![]() ![]() | ||
#3: 化合物 | ChemComp-120 / | ||
#4: 化合物 | #5: 水 | ChemComp-HOH / | |
-実験情報
-実験
実験 | 手法: ![]() |
---|
-
試料調製
結晶 | マシュー密度: 2.06 Å3/Da / 溶媒含有率: 40.15 % | |||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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
|
-データ収集
回折 | 平均測定温度: 277 K |
---|---|
放射光源 | 由来: ![]() ![]() ![]() |
検出器 | タイプ: MARRESEARCH / 検出器: IMAGE PLATE / 日付: 2000年6月25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: 0.97 Å / 相対比: 1 |
反射 | 解像度: 1.79→40.95 Å / Num. obs: 21259 / % possible obs: 90.2 % / Observed criterion σ(I): 0 / 冗長度: 1.7 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 7.6 |
反射 シェル | 解像度: 1.79→1.87 Å / Num. unique all: 843 / % possible all: 40.1 |
反射 | *PLUS Num. measured all: 35745 |
-
解析
ソフトウェア |
| ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
精密化 | 構造決定の手法: ![]() 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: Met B47, Thr B139, Arg B166, Gln B192, Ser B202 Disordered waters are: HOH510 which is close to a symmetry-related equivalent of HOH511; 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.
| ||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 1.79→7.5 Å
| ||||||||||||||||
拘束条件 |
| ||||||||||||||||
ソフトウェア | *PLUS 名称: ![]() | ||||||||||||||||
精密化 | *PLUS 最低解像度: 7.5 Å / σ(F): 2.5 / % reflection Rfree: 10 % / Rfactor all: 0.188 / Rfactor obs: 0.185 / Rfactor Rfree: 0.22 | ||||||||||||||||
溶媒の処理 | *PLUS | ||||||||||||||||
原子変位パラメータ | *PLUS | ||||||||||||||||
拘束条件 | *PLUS
| ||||||||||||||||
LS精密化 シェル | *PLUS 最高解像度: 1.79 Å / 最低解像度: 1.87 Å / Rfactor Rfree: 0.22 / Rfactor obs: 0.188 |