+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1ets | ||||||
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タイトル | REFINED 2.3 ANGSTROMS X-RAY CRYSTAL STRUCTURE OF BOVINE THROMBIN COMPLEXES FORMED WITH THE BENZAMIDINE AND ARGININE-BASED THROMBIN INHIBITORS NAPAP, 4-TAPAP AND MQPA: A STARTING POINT FOR IMPROVING ANTITHROMBOTICS | ||||||
要素 | (EPSILON-THROMBIN) x 2 | ||||||
キーワード | HYDROLASE/HYDROLASE inhibitor / SERINE PROTEINASE (セリンプロテアーゼ) / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
機能・相同性 | 機能・相同性情報 fibrinogen binding / トロンビン / protein polymerization / positive regulation of blood coagulation / acute-phase response / 凝固・線溶系 / collagen-containing extracellular matrix / serine-type endopeptidase activity / calcium ion binding / タンパク質分解 / extracellular space 類似検索 - 分子機能 | ||||||
生物種 | Bos taurus (ウシ) | ||||||
手法 | X線回折 / 解像度: 2.3 Å | ||||||
データ登録者 | Bode, W. / Brandstetter, H. | ||||||
引用 | ジャーナル: J.Mol.Biol. / 年: 1992 タイトル: Refined 2.3 A X-ray crystal structure of bovine thrombin complexes formed with the benzamidine and arginine-based thrombin inhibitors NAPAP, 4-TAPAP and MQPA. A starting point for improving antithrombotics. 著者: Brandstetter, H. / Turk, D. / Hoeffken, H.W. / Grosse, D. / Sturzebecher, J. / Martin, P.D. / Edwards, B.F. / Bode, W. #1: ジャーナル: To be Published タイトル: Crystallographic Determination of Thrombin Complexes with Small Synthetic Inhibitors as a Starting Point for the Receptor-Based Design of Antithrombotics 著者: Bode, W. / Brandstetter, H. / Turk, D. / Bauer, M. / Stuerzebecher, J. #2: ジャーナル: To be Published タイトル: X-Ray Crystal Structure of Thrombin in Complex with D-Phe-Pro-Arg and with Small Benzamidine and Arginine-Based "Non-Peptidic" Inhibitors 著者: Bode, W. #3: ジャーナル: Protein Sci. / 年: 1992 タイトル: The Refined 1.9-Angstroms X-Ray Crystal Structure of D-Phe-Pro-Arg Chloromethylketone-Inhibited Human Alpha-Thrombin: Structure Analysis, Overall Structure, Electrostatic Properties, ...タイトル: The Refined 1.9-Angstroms X-Ray Crystal Structure of D-Phe-Pro-Arg Chloromethylketone-Inhibited Human Alpha-Thrombin: Structure Analysis, Overall Structure, Electrostatic Properties, Detailed Active-Site Geometry, and Structure-Function Relationships 著者: Bode, W. / Turk, D. / Karshikov, A. #4: ジャーナル: FEBS Lett. / 年: 1991 タイトル: Geometry of Binding of the Nalpha-Tosylated Piperidides of M-Amidino-, P-Amidino-and P-Guanidino Phenylalanine to Thrombin and Trypsin: X-Ray Crystal Structures of Their Trypsin ...タイトル: Geometry of Binding of the Nalpha-Tosylated Piperidides of M-Amidino-, P-Amidino-and P-Guanidino Phenylalanine to Thrombin and Trypsin: X-Ray Crystal Structures of Their Trypsin Complexes and Modeling of Their Thrombin Complexes 著者: Turk, D. / Stuerzebecher, J. / Bode, W. #5: ジャーナル: Eur.J.Biochem. / 年: 1990 タイトル: Geometry of Binding of the Benzamidine-and Arginine-Based Inhibitors N-Alpha-(2-Naphthyl-Sulphonyl-Glycyl)-Dl-P-Amidinophenylalanyl-Piperidine (Napap) and (2R,4R)-4-Methyl-1-[N-Alpha-(3- ...タイトル: Geometry of Binding of the Benzamidine-and Arginine-Based Inhibitors N-Alpha-(2-Naphthyl-Sulphonyl-Glycyl)-Dl-P-Amidinophenylalanyl-Piperidine (Napap) and (2R,4R)-4-Methyl-1-[N-Alpha-(3-Methyl-1,2,3,4-Tetrahydro-8-Quinolinesulphonyl)-L-Arginyl]-2-Piperidine Carboxylic Acid (Mqpa) to Human Alpha-Thrombin: X-Ray Crystallographic Determination of the Napap-Trypsin Complex and Modeling of Napap-Thrombin and Mqpa-Thrombin 著者: Bode, W. / Turk, D. / Stuerzebecher, J. #6: ジャーナル: Embo J. / 年: 1989 タイトル: The Refined 1.9 Angstroms Crystal Structure of Human Alpha-Thrombin: Interaction with D-Phe-Pro-Arg Chloromethylketone and Significance of the Tyr-Pro-Pro-Trp Insertion Segment 著者: Bode, W. / Mayr, I. / Baumann, U. / Huber, R. / Stone, S.R. / Hofsteenge, J. | ||||||
履歴 |
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Remark 700 | SHEET THE SHEETS PRESENTED AS *S1* AND *S2* ON SHEET RECORDS BELOW ARE ACTUALLY SIX-STRANDED BETA- ...SHEET THE SHEETS PRESENTED AS *S1* AND *S2* ON SHEET RECORDS BELOW ARE ACTUALLY SIX-STRANDED BETA-BARRELS. THESE ARE REPRESENTED BY SEVEN-STRANDED SHEETS IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-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 | 1ets.cif.gz | 97.3 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb1ets.ent.gz | 79.7 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1ets.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/et/1ets ftp://data.pdbj.org/pub/pdb/validation_reports/et/1ets | 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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Atom site foot note | 1: RESIDUE PRO H 37 IS A CIS PROLINE. |
-要素
#1: タンパク質・ペプチド | 分子量: 5735.240 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Bos taurus (ウシ) / 参照: UniProt: P00735, トロンビン |
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#2: タンパク質 | 分子量: 29772.422 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Bos taurus (ウシ) / 参照: UniProt: P00735, トロンビン |
#3: 化合物 | ChemComp-MID / |
#4: 水 | ChemComp-HOH / |
非ポリマーの詳細 | AMIDINOPHENYLALANINE (OF NAPAP) BINDS TO S1 SPECIFICITY POCKET, PIPERIDINE TO S2 AND NAPHLYL GROUP ...AMIDINOPHE |
配列の詳細 | THE NUMBERING OF THROMBIN RESIDUES IS BASED ON TOPOLOGICA |
-実験情報
-実験
実験 | 手法: X線回折 |
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-試料調製
結晶 | マシュー密度: 2.85 Å3/Da / 溶媒含有率: 56.85 % | ||||||||||||||||||||||||||||||
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結晶化 | *PLUS 温度: 20 ℃ / pH: 8 / 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
放射 | 散乱光タイプ: x-ray |
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放射波長 | 相対比: 1 |
反射 | *PLUS 最高解像度: 2.3 Å / Num. obs: 13578 / % possible obs: 78 % / Observed criterion σ(I): 2 / Num. measured all: 84833 / Rmerge(I) obs: 0.142 |
-解析
ソフトウェア |
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精密化 | 解像度: 2.3→8 Å / Rfactor Rwork: 0.178 / Rfactor obs: 0.178 詳細: THERE IS A CLEAVAGE IN THE CHAIN AT THR 149A - SER 149B IN THE INSERTION LOOP OF THROMBIN. THE AUTHORS DO NOT SEE THIS CLEAVAGE DUE TO DISORDER AT BOTH FLANKING REGIONS. NOTE THAT THE ...詳細: THERE IS A CLEAVAGE IN THE CHAIN AT THR 149A - SER 149B IN THE INSERTION LOOP OF THROMBIN. THE AUTHORS DO NOT SEE THIS CLEAVAGE DUE TO DISORDER AT BOTH FLANKING REGIONS. NOTE THAT THE OCCUPANCY OF RESIDUES 148 - 149E IS GIVEN AS 0.0 INDICATING THAT THEY WERE NOT SEEN IN THE ELECTRON DENSITY MAPS. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 2.3→8 Å
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拘束条件 |
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ソフトウェア | *PLUS 名称: X-PLOR / 分類: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化 | *PLUS 最高解像度: 2.3 Å / 最低解像度: 8 Å / Num. reflection obs: 12503 / Rfactor obs: 0.178 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
溶媒の処理 | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | *PLUS Biso mean: 40 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
拘束条件 | *PLUS タイプ: x_angle_d / Dev ideal: 3.089 |