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基本情報
登録情報 | データベース: PDB / ID: 5tmn | |||||||||
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タイトル | Slow-and fast-binding inhibitors of thermolysin display different modes of binding. crystallographic analysis of extended phosphonamidate transition-state analogues | |||||||||
![]() | THERMOLYSIN | |||||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / METALLOPROTEINASE / HYDROLASE-HYDROLASE INHIBITOR complex | |||||||||
機能・相同性 | ![]() thermolysin / metalloendopeptidase activity / proteolysis / extracellular region / metal ion binding 類似検索 - 分子機能 | |||||||||
生物種 | ![]() ![]() | |||||||||
手法 | ![]() | |||||||||
![]() | Holden, H.M. / Tronrud, D.E. / Monzingo, A.F. / Weaver, L.H. / Matthews, B.W. | |||||||||
![]() | ![]() タイトル: Slow- and fast-binding inhibitors of thermolysin display different modes of binding: crystallographic analysis of extended phosphonamidate transition-state analogues. 著者: Holden, H.M. / Tronrud, D.E. / Monzingo, A.F. / Weaver, L.H. / Matthews, B.W. #1: ![]() タイトル: Structures of Two Thermolysin-Inhibitor Complexes that Differ by a Single Hydrogen Bond 著者: Tronrud, D.E. / Holden, H.M. / Matthews, B.W. #2: ![]() タイトル: Crystallographic Structural Analysis of Phosphoramidates as Inhibitors and Transition-State Analogs of Thermolysin 著者: Tronrud, D.E. / Monzingo, A.F. / Matthews, B.W. #3: ![]() タイトル: Binding of N-Carboxymethyl Dipepetide Inhibitors to Thermolysin Determined by X-Ray Crystallography. A Novel Class of Transition-State Analogues for Zinc Peptidases 著者: Monzingo, A.F. / Matthews, B.W. #4: ![]() タイトル: An Interactive Computer Graphics Study of Thermolysin-Catalyzed Peptide Cleavage and Inhibition by N-Carboxymethyl Dipeptides 著者: Hangauer, D.G. / Monzingo, A.F. / Matthews, B.W. #5: ![]() タイトル: Structural Analysis of the Inhibition of Thermolysin by an Active-Site-Directed Irreversible Inhibitor 著者: Holmes, M.A. / Tronrud, D.E. / Matthews, B.W. #6: ![]() タイトル: Structure of a Mercaptan-Thermolysin Complex Illustrates Mode of Inhibition of Zinc Proteases by Substrate-Analogue Mercaptans 著者: Monzingo, A.F. / Matthews, B.W. #7: ![]() タイトル: Structure of Thermolysin Refined at 1.6 Angstroms Resolution 著者: Holmes, M.A. / Matthews, B.W. #8: ![]() タイトル: Binding of Hydroxamic Acid Inhibitors to Crystalline Thermolysin Suggests a Pentacoordinate Zinc Intermediate in Catalysis 著者: Holmes, M.A. / Matthews, B.W. #9: ![]() タイトル: Binding of the Biproduct Analog L-Benzylsuccinic Acid to Thermolysin Determined by X-Ray Crystallography 著者: Bolognesi, M.C. / Matthews, B.W. #10: ![]() タイトル: Comparison of the Structures of Carboxypeptidase a and Thermolysin 著者: Kester, W.R. / Matthews, B.W. #11: ![]() タイトル: A Crystallographic Study of the Complex of Phosphoramidon with Thermolysin. A Model for the Presumed Catalytic Transition State and for the Binding of Extended Substrates 著者: Weaver, L.H. / Kester, W.R. / Matthews, B.W. #12: ![]() タイトル: Crystallographic Study of the Binding of Dipeptide Inhibitors to Thermolysin. Implications for the Mechanism of Catalysis 著者: Kester, W.R. / Matthews, B.W. #13: ![]() タイトル: Role of Calcium in the Thermal Stability of Thermolysin 著者: Dahlquist, F.W. / Long, J.W. / Bigbee, W.L. #14: ![]() タイトル: Evidence of Homologous Relationship between Thermolysin and Neutral Protease a of Bacillus Subtilis 著者: Levy, P.L. / Pangburn, M.K. / Burstein, Y. / Ericsson, L.H. / Neurath, H. / Walsh, K.A. #15: ![]() タイトル: The Structure and Stability of Thermolysin 著者: Weaver, L.H. / Kester, W.R. / Teneyck, L.F. / Matthews, B.W. #16: ![]() タイトル: The Conformation of Thermolysin 著者: Matthews, B.W. / Weaver, L.H. / Kester, W.R. #17: ![]() タイトル: Binding of Lanthanide Ions to Thermolysin 著者: Matthews, B.W. / Weaver, L.H. #18: ![]() タイトル: The Structure of Thermolysin. An Electron Density Map at 2.3 Angstroms Resolution 著者: Colman, P.M. / Jansonius, J.N. / Matthews, B.W. #19: ![]() タイトル: Amino-Acid Sequence of Thermolysin 著者: Titani, K. / Hermodson, M.A. / Ericsson, L.H. / Walsh, K.A. / Neurath, H. #20: ![]() タイトル: Three Dimensional Structure of Thermolysin 著者: Matthews, B.W. / Jansonius, J.N. / Colman, P.M. / Schoenborn, B.P. / Duporque, D. #21: ![]() タイトル: Structure of Thermolysin 著者: Matthews, B.W. / Colman, P.M. / Jansonius, J.N. / Titani, K. / Walsh, K.A. / Neurath, H. #22: ![]() タイトル: The Gamma Turn. Evidence for a New Folded Conformation in Proteins 著者: Matthews, B.W. #23: ![]() タイトル: Rare Earths as Isomorphous Calcium Replacements for Protein Crystallography 著者: Colman, P.M. / Weaver, L.H. / Matthews, B.W. | |||||||||
履歴 |
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Remark 650 | HELIX TURNS 14, 20 AND 21 OF TABLE VIII IN THE PAPER CITED AS REFERENCE 10 ABOVE WERE NOT INCLUDED ...HELIX TURNS 14, 20 AND 21 OF TABLE VIII IN THE PAPER CITED AS REFERENCE 10 ABOVE WERE NOT INCLUDED IN THE TURN RECORDS BELOW BECAUSE THESE CORRESPOND TO HELICAL SUBSTRUCTURES SPECIFIED IN THE HELIX RECORDS. | |||||||||
Remark 700 | SHEET THE *ACTIVE-SITE* SHEET SUBSTRUCTURE OF THIS MOLECULE HAS ONE EDGE-STRAND COMPRISED OF TWO ...SHEET THE *ACTIVE-SITE* SHEET SUBSTRUCTURE OF THIS MOLECULE HAS ONE EDGE-STRAND COMPRISED OF TWO DISTINCT SEQUENCES OF THE POLYPEPTIDE CHAIN. TO REPRESENT THIS FEATURE AN EXTRA SHEET IS DEFINED. STRANDS 2,3,4,5 OF S1 ARE IDENTICAL TO STRANDS 2,3,4,5 OF S2. |
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構造の表示
構造ビューア | 分子: ![]() ![]() |
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PDBx/mmCIF形式 | ![]() | 83.6 KB | 表示 | ![]() |
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その他 | ![]() |
-検証レポート
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
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-関連構造データ
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リンク
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集合体
登録構造単位 | ![]()
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単位格子 |
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Atom site foot note | 1: RESIDUE 51 IS A CIS-PROLINE. / 2: ATOMS 2619 - 2622 LIE IN SUBSITE S1(PRIME). / 3: ATOMS 2627 - 2630 LIE IN SUBSITE S2(PRIME). / 4: ATOMS 2613 AND 2614 ARE BONDED TO THE ZINC ATOM. |
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要素
#1: タンパク質 | 分子量: 34362.305 Da / 分子数: 1 / 由来タイプ: 組換発現 由来: (組換発現) ![]() ![]() 参照: UniProt: P00800, thermolysin | ||||||
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#2: 化合物 | ChemComp-0PJ / | ||||||
#3: 化合物 | ChemComp-CA / #4: 化合物 | ChemComp-ZN / | #5: 水 | ChemComp-HOH / | 構成要素の詳細 | THE ACTIVE SITE CLEFT OF THERMOLYSIN CONTAINS AT LEAST FOUR SUBSITES S1, S1(PRIME), S2, AND ...THE ACTIVE SITE CLEFT OF THERMOLYSI | |
-実験情報
-実験
実験 | 手法: ![]() |
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試料調製
結晶 | マシュー密度: 2.41 Å3/Da / 溶媒含有率: 49.01 % | ||||||||||||||||||||||||||||||
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結晶化 | *PLUS pH: 7.2 / 手法: unknown / 詳細: Holmes, M.A., (1982) J.Mol.Biol., 160, 623. | ||||||||||||||||||||||||||||||
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: 1.6 Å / Num. obs: 31799 / Num. measured all: 72525 / Rmerge(I) obs: 0.056 |
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解析
ソフトウェア | 名称: TNT / 分類: 精密化 | ||||||||||||||||||||||||||||||
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精密化 | Rfactor obs: 0.177 / 最高解像度: 1.6 Å | ||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 最高解像度: 1.6 Å
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拘束条件 |
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精密化 | *PLUS 最低解像度: 10 Å / Num. reflection obs: 31627 | ||||||||||||||||||||||||||||||
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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