+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1o3p | ||||||
---|---|---|---|---|---|---|---|
タイトル | Elaborate Manifold of Short Hydrogen Bond Arrays Mediating Binding of Active Site-Directed Serine Protease Inhibitors | ||||||
要素 | (Urokinase-type plasminogen activatorウロキナーゼ) x 2 | ||||||
キーワード | BLOOD CLOTTING (凝固・線溶系) / hydrolase (加水分解酵素) / serine protease (セリンプロテアーゼ) / short hydrogen bond / inhibition mechanism / shift of pKa / trypsin (トリプシン) / thrombin (トロンビン) / urokinase (ウロキナーゼ) / factor Xa (第X因子) | ||||||
機能・相同性 | 機能・相同性情報 ウロキナーゼ / 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 ...ウロキナーゼ / 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 / tertiary granule membrane / regulation of cell adhesion mediated by integrin / negative regulation of fibrinolysis / specific granule membrane / regulation of cell adhesion / serine protease inhibitor complex / fibrinolysis / 走化性 / 凝固・線溶系 / 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 / 細胞膜 / シグナル伝達 / タンパク質分解 / extracellular space / extracellular exosome / extracellular region / 細胞膜 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: 1.81 Å | ||||||
データ登録者 | 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. ...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. / Hui, H.C. / Breitenbucher, J.G. / Allen, D. / Janc, J.W. | ||||||
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. / Hui, H.C. / Breitenbucher, J.G. ...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. / Hui, H.C. / Breitenbucher, J.G. / Allen, D. / Janc, J.W. | ||||||
履歴 |
|
-構造の表示
構造ビューア | 分子: MolmilJmol/JSmol |
---|
-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 1o3p.cif.gz | 136.2 KB | 表示 | PDBx/mmCIF形式 |
---|---|---|---|---|
PDB形式 | pdb1o3p.ent.gz | 108.5 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1o3p.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/o3/1o3p ftp://data.pdbj.org/pub/pdb/validation_reports/o3/1o3p | HTTPS FTP |
---|
-関連構造データ
関連構造データ | 1o2gC 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 C: 同じ文献を引用 (文献) |
---|---|
類似構造データ |
-リンク
-集合体
登録構造単位 |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
単位格子 |
| ||||||||||||
Components on special symmetry positions |
|
-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) / 遺伝子: PLAU / プラスミド: PPIC9LMWUPA / 発現宿主: Pichia pastoris (菌類) / 参照: UniProt: P00749, ウロキナーゼ | ||||
---|---|---|---|---|---|
#2: タンパク質 | 分子量: 28435.428 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) / 遺伝子: PLAU / プラスミド: PPIC9LMWUPA / 発現宿主: Pichia pastoris (菌類) / 参照: UniProt: P00749, ウロキナーゼ | ||||
#3: 化合物 | #4: 化合物 | ChemComp-655 / | #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 |
---|
-試料調製
結晶 | マシュー密度: 2 Å3/Da / 溶媒含有率: 38.5 % |
---|---|
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 |
-データ収集
回折 | 平均測定温度: 298 K |
---|---|
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: 2000年4月11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: 1.81→41.66 Å / Num. all: 22960 / Num. obs: 15430 / % possible obs: 67.2 % / Observed criterion σ(I): 0.8 / 冗長度: 2 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 6.1 |
反射 シェル | 解像度: 1.81→1.89 Å / % possible obs: 36.6 % / Rmerge(I) obs: 0.215 / Num. unique all: 2749 |
-解析
ソフトウェア |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
精密化 | 構造決定の手法: フーリエ合成 / 解像度: 1.81→7 Å / 交差検証法: THROUGHOUT / σ(F): 1.6 / 立体化学のターゲット値: X-PLOR force field 詳細: Only Leu_A9 to Lys_A16 are included for the A-chain. Residues prior and after these residues are not visible (disordered). Residues after Lys_B243 are not visible (disordered). Residues ...詳細: Only Leu_A9 to Lys_A16 are included for the A-chain. Residues prior and after these residues are not visible (disordered). Residues after Lys_B243 are not visible (disordered). Residues simultaneously refined in two or more conformations are: Lys_A10, Met_B47, Glu_B84, Glu_B86, Leu_B123, Thr_B139, Gln_B192, Arg_B217, Leu_B235. HIS_H57 IS doubly protonated. HIS_H91 and His_H119 are MONOPROTONATED ON the epsilon nitrogen Disordered waters are: HOH382 which is close to conformation 1 of Arg_B217; HOH582 which is close to a symmetry-related equivalent of itself; HOH721 which is close to conformation 1 of Lys_A10; HOH1010 which is close to a symmetry-related equivalent of itself; Some of the waters may correspond to the disordered or mobile termini of the light chain. 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_849, and OgSer195, and O6' of the inhibitor. These atoms form a very short multi-centered hydrogen-bonding network.
| ||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 1.81→7 Å
| ||||||||||||||||||||
拘束条件 |
|