+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1ucy | |||||||||
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タイトル | THROMBIN COMPLEXED WITH FIBRINOPEPTIDE A ALPHA (RESIDUES 7-19). THREE COMPLEXES, ONE WITH EPSILON-THROMBIN AND TWO WITH ALPHA-THROMBIN | |||||||||
要素 |
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キーワード | COMPLEX (SERINE PROTEASE/COAGULATION) / COMPLEX (SERINE PROTEASE-COAGULATION) / SERINE (セリン) / PROTEASE (プロテアーゼ) / THROMBIN (トロンビン) / COMPLEX (SERINE PROTEASE-COAGULATION) 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 / 凝固・線溶系 / collagen-containing extracellular matrix / 獲得免疫系 / serine-type endopeptidase activity ...fibrinogen binding / トロンビン / protein polymerization / positive regulation of blood coagulation / acute-phase response / 凝固・線溶系 / 凝固・線溶系 / collagen-containing extracellular matrix / 獲得免疫系 / serine-type endopeptidase activity / 自然免疫系 / calcium ion binding / タンパク質分解 / extracellular space / extracellular region 類似検索 - 分子機能 | |||||||||
生物種 | Bos taurus (ウシ) | |||||||||
手法 | X線回折 / 解像度: 2.2 Å | |||||||||
データ登録者 | Martin, P. / Edwards, B. | |||||||||
引用 | ジャーナル: Biochemistry / 年: 1996 タイトル: Bovine thrombin complexed with an uncleavable analog of residues 7-19 of fibrinogen A alpha: geometry of the catalytic triad and interactions of the P1', P2', and P3' substrate residues. 著者: Martin, P.D. / Malkowski, M.G. / DiMaio, J. / Konishi, Y. / Ni, F. / Edwards, B.F. | |||||||||
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 | 1ucy.cif.gz | 214.4 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb1ucy.ent.gz | 170.8 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1ucy.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/uc/1ucy ftp://data.pdbj.org/pub/pdb/validation_reports/uc/1ucy | 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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3 |
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単位格子 |
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-要素
-タンパク質・ペプチド , 2種, 6分子 LJMFGI
#1: タンパク質・ペプチド | 分子量: 5735.240 Da / 分子数: 3 / 由来タイプ: 天然 詳細: CHYMOTRYPSINOGEN NUMBERING (RATHER THAN SEQUENTIAL) SYSTEM IS USED, BASED ON THE TOPOLOGICAL ALIGNMENT WITH THE STRUCTURE OF CHYMOTRYPSINOGEN (H.BRANDSTETTER ET AL., 1992, J.MOL.BIOL., V. ...詳細: CHYMOTRYPSINOGEN NUMBERING (RATHER THAN SEQUENTIAL) SYSTEM IS USED, BASED ON THE TOPOLOGICAL ALIGNMENT WITH THE STRUCTURE OF CHYMOTRYPSINOGEN (H.BRANDSTETTER ET AL., 1992, J.MOL.BIOL., V. 226, 1085). THE N-TERMINUS OF THE FIBRINOPEPTIDE IS ACETYLATED. FIBRINOPEPTIDE SEQUENCE NUMBERS ARE ACE 6 TO ARG 19. A NEW RESIDUE, OPR, HAS BEEN DEFINED FOR THE ARG/GLY COMBINATION IN WHICH THE AMIDE NITROGEN HAS BEEN REPLACED WITH A CH2, MAKING THE NORMAL AMIDE BOND BETWEEN THESE TWO RESIDUES A KETONE BOND. THE FIBRINOPEPTIDE NUMBERING IS CONSEQUENTLY INCREMENTED BY 1 AFTER THIS RESIDUE IN KEEPING WITH THE FIBRINOGEN NUMBERING SCHEME. THERE ARE ALTERNATE CONFORMATIONS FOR RESIDUES PRO 18 AND ARG 19 IN FIBRINOPEPTIDE III. 由来: (天然) Bos taurus (ウシ) / 組織: BLOOD血液 / 参照: UniProt: P00735, トロンビン #4: タンパク質・ペプチド | 分子量: 1356.508 Da / 分子数: 3 / Fragment: RESIDUES 7 - 19 / 由来タイプ: 組換発現 詳細: THREE COMPLEXES ARE PRESENTED, ONE WITH EPSILON-THROMBIN AND TWO WITH ALPHA-THROMBIN 参照: UniProt: P12803, UniProt: P68108*PLUS |
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-タンパク質 , 3種, 4分子 HEKN
#2: タンパク質 | 分子量: 17525.346 Da / 分子数: 1 / 由来タイプ: 天然 詳細: CHYMOTRYPSINOGEN NUMBERING (RATHER THAN SEQUENTIAL) SYSTEM IS USED, BASED ON THE TOPOLOGICAL ALIGNMENT WITH THE STRUCTURE OF CHYMOTRYPSINOGEN (H.BRANDSTETTER ET AL., 1992, J.MOL.BIOL., V. ...詳細: CHYMOTRYPSINOGEN NUMBERING (RATHER THAN SEQUENTIAL) SYSTEM IS USED, BASED ON THE TOPOLOGICAL ALIGNMENT WITH THE STRUCTURE OF CHYMOTRYPSINOGEN (H.BRANDSTETTER ET AL., 1992, J.MOL.BIOL., V. 226, 1085). THE N-TERMINUS OF THE FIBRINOPEPTIDE IS ACETYLATED. FIBRINOPEPTIDE SEQUENCE NUMBERS ARE ACE 6 TO ARG 19. A NEW RESIDUE, OPR, HAS BEEN DEFINED FOR THE ARG/GLY COMBINATION IN WHICH THE AMIDE NITROGEN HAS BEEN REPLACED WITH A CH2, MAKING THE NORMAL AMIDE BOND BETWEEN THESE TWO RESIDUES A KETONE BOND. THE FIBRINOPEPTIDE NUMBERING IS CONSEQUENTLY INCREMENTED BY 1 AFTER THIS RESIDUE IN KEEPING WITH THE FIBRINOGEN NUMBERING SCHEME. THERE ARE ALTERNATE CONFORMATIONS FOR RESIDUES PRO 18 AND ARG 19 IN FIBRINOPEPTIDE III. 由来: (天然) Bos taurus (ウシ) / 組織: BLOOD血液 / 参照: UniProt: P00735, トロンビン |
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#3: タンパク質 | 分子量: 12265.071 Da / 分子数: 1 / 由来タイプ: 天然 詳細: CHYMOTRYPSINOGEN NUMBERING (RATHER THAN SEQUENTIAL) SYSTEM IS USED, BASED ON THE TOPOLOGICAL ALIGNMENT WITH THE STRUCTURE OF CHYMOTRYPSINOGEN (H.BRANDSTETTER ET AL., 1992, J.MOL.BIOL., V. ...詳細: CHYMOTRYPSINOGEN NUMBERING (RATHER THAN SEQUENTIAL) SYSTEM IS USED, BASED ON THE TOPOLOGICAL ALIGNMENT WITH THE STRUCTURE OF CHYMOTRYPSINOGEN (H.BRANDSTETTER ET AL., 1992, J.MOL.BIOL., V. 226, 1085). THE N-TERMINUS OF THE FIBRINOPEPTIDE IS ACETYLATED. FIBRINOPEPTIDE SEQUENCE NUMBERS ARE ACE 6 TO ARG 19. A NEW RESIDUE, OPR, HAS BEEN DEFINED FOR THE ARG/GLY COMBINATION IN WHICH THE AMIDE NITROGEN HAS BEEN REPLACED WITH A CH2, MAKING THE NORMAL AMIDE BOND BETWEEN THESE TWO RESIDUES A KETONE BOND. THE FIBRINOPEPTIDE NUMBERING IS CONSEQUENTLY INCREMENTED BY 1 AFTER THIS RESIDUE IN KEEPING WITH THE FIBRINOGEN NUMBERING SCHEME. THERE ARE ALTERNATE CONFORMATIONS FOR RESIDUES PRO 18 AND ARG 19 IN FIBRINOPEPTIDE III. 由来: (天然) Bos taurus (ウシ) / 組織: BLOOD血液 / 参照: UniProt: P00735, トロンビン |
#5: タンパク質 | 分子量: 29772.422 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 組織: BLOOD血液 / 参照: UniProt: P00735, トロンビン |
-非ポリマー , 1種, 733分子
#6: 水 | ChemComp-HOH / |
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-詳細
配列の詳細 | CHYMOTRYPSINOGEN NUMBERING (RATHER THAN SEQUENTIAL) SYSTEM IS USED, BASED ON THE TOPOLOGICAL ...CHYMOTRYPS |
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-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: 3.13 Å3/Da / 溶媒含有率: 60.73 % |
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結晶化 | *PLUS pH: 8 / 手法: 蒸気拡散法, ハンギングドロップ法 / 詳細: Martin, P.D., (1992) J. Biol. Chem., 267, 7911. |
溶液の組成 | *PLUS 濃度: 40 % / 一般名: ammonium sulfate |
-データ収集
検出器 | タイプ: SIEMENS / 検出器: X1000 MULTIWIRE |
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反射 | 解像度: 2.2→7 Å / Num. obs: 45875 / Observed criterion σ(I): 1 |
反射 シェル | 解像度: 2.2→2.3 Å / Rsym value: 0.072 / % possible all: 15 |
反射 | *PLUS Num. measured all: 117995 / Rmerge(I) obs: 0.072 |
反射 シェル | *PLUS % possible obs: 15 % |
-解析
ソフトウェア |
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精密化 | 解像度: 2.2→7 Å / Rfactor Rwork: 0.171 / Rfactor obs: 0.171 / σ(F): 1 詳細: THERE ARE THREE INDEPENDENT COMPLEXES IN THE ASYMMETRIC UNIT. COMPLEX I IS EPSILON THROMBIN (ADDITIONAL CHAIN BREAK BETWEEN RESIDUES 149A AND 149B), AND MOLECULES II AND III ARE ALPHA ...詳細: THERE ARE THREE INDEPENDENT COMPLEXES IN THE ASYMMETRIC UNIT. COMPLEX I IS EPSILON THROMBIN (ADDITIONAL CHAIN BREAK BETWEEN RESIDUES 149A AND 149B), AND MOLECULES II AND III ARE ALPHA THROMBIN. FIBRINOPEPTIDES I AND II HAVE OCCUPANCIES THAT MAKES THE AVERAGE SIDE CHAIN B OF OPR-16 ROUGHLY EQUAL TO THAT IN FIBRINOPEPTIDE III. THE DEPOSITORS DO NOT SEE ANY DENSITY AT ALL FOR THROMBIN RESIDUES 1U - 1I, AND POOR DENSITY FOR THE N AND C TERMINI OF THE LIGHT CHAINS, THE C TERMINUS OF THE HEAVY CHAINS, AND THE FIVE RESIDUES BORDERING 149B IN MOLECULES II AND III. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.25 Å / Luzzati sigma a obs: 0.29 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 2.2→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 / 分類: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
拘束条件 | *PLUS
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