+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1hah | ||||||
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タイトル | THE ISOMORPHOUS STRUCTURES OF PRETHROMBIN2, HIRUGEN-AND PPACK-THROMBIN: CHANGES ACCOMPANYING ACTIVATION AND EXOSITE BINDING TO THROMBIN | ||||||
要素 |
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キーワード | COMPLEX(SERINE PROTEINASE/INHIBITOR) / COMPLEX(SERINE PROTEINASE-INHIBITOR) / COMPLEX(SERINE PROTEINASE-INHIBITOR) complex | ||||||
機能・相同性 | 機能・相同性情報 positive regulation of lipid kinase activity / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / cytolysis by host of symbiont cells / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / トロンビン / neutrophil-mediated killing of gram-negative bacterium / regulation of blood coagulation / ligand-gated ion channel signaling pathway / Defective F8 cleavage by thrombin ...positive regulation of lipid kinase activity / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / cytolysis by host of symbiont cells / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / トロンビン / neutrophil-mediated killing of gram-negative bacterium / regulation of blood coagulation / ligand-gated ion channel signaling pathway / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) / negative regulation of platelet activation / negative regulation of astrocyte differentiation / positive regulation of collagen biosynthetic process / negative regulation of cytokine production involved in inflammatory response / positive regulation of blood coagulation / negative regulation of fibrinolysis / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins / fibrinolysis / regulation of cytosolic calcium ion concentration / Intrinsic Pathway of Fibrin Clot Formation / Peptide ligand-binding receptors / positive regulation of release of sequestered calcium ion into cytosol / Regulation of Complement cascade / acute-phase response / Cell surface interactions at the vascular wall / lipopolysaccharide binding / negative regulation of proteolysis / positive regulation of receptor signaling pathway via JAK-STAT / growth factor activity / serine-type endopeptidase inhibitor activity / positive regulation of insulin secretion / 凝固・線溶系 / response to wounding / Golgi lumen / positive regulation of protein localization to nucleus / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of reactive oxygen species metabolic process / 凝固・線溶系 / antimicrobial humoral immune response mediated by antimicrobial peptide / Thrombin signalling through proteinase activated receptors (PARs) / heparin binding / regulation of cell shape / positive regulation of cell growth / G alpha (q) signalling events / collagen-containing extracellular matrix / blood microparticle / cell surface receptor signaling pathway / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / 小胞体 / signaling receptor binding / serine-type endopeptidase activity / calcium ion binding / positive regulation of cell population proliferation / 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) Hirudo medicinalis (医用ビル) | ||||||
手法 | X線回折 / 解像度: 2.3 Å | ||||||
データ登録者 | Tulinsky, A. / Vijayalakshmi, J. | ||||||
引用 | ジャーナル: Protein Sci. / 年: 1994 タイトル: The isomorphous structures of prethrombin2, hirugen-, and PPACK-thrombin: changes accompanying activation and exosite binding to thrombin. 著者: Vijayalakshmi, J. / Padmanabhan, K.P. / Mann, K.G. / Tulinsky, A. #1: ジャーナル: J.Mol.Biol. / 年: 1991 タイトル: Refined Structure of the Hirudin-Thrombin Complex 著者: Rydel, T.J. / Tulinsky, A. / Bode, W. / Huber, R. #2: ジャーナル: J.Mol.Biol. / 年: 1991 タイトル: Structure of the Hirugen and Hirulog 1 Complexes of Alpha-Thrombin 著者: Skrzypczak-Jankun, E. / Carperos, V.E. / Ravichandran, K.G. / Tulinsky, A. / Westbrook, M. / Maraganore, J.M. | ||||||
履歴 |
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Remark 700 | SHEET THE SHEET PRESENTED AS *B1* ON SHEET RECORDS BELOW IS ACTUALLY A SIX-STRANDED BETA-BARREL. ...SHEET THE SHEET PRESENTED AS *B1* ON SHEET RECORDS BELOW IS ACTUALLY A SIX-STRANDED BETA-BARREL. THIS IS REPRESENTED BY A SEVEN-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEET PRESENTED AS *B2* ON SHEET RECORDS BELOW IS ACTUALLY A SEVEN-STRANDED BETA-BARREL. THIS IS REPRESENTED BY AN EIGHT-STRANDED SHEET 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 | 1hah.cif.gz | 77.5 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb1hah.ent.gz | 59.8 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1hah.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/ha/1hah ftp://data.pdbj.org/pub/pdb/validation_reports/ha/1hah | 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: CIS PROLINE - PRO H 37 2: RESIDUE TYR I 63 IN THE HIRUGEN MOLECULE IS BONDED TO SULFATO- TYROSINE. | |||||||||
Components on special symmetry positions |
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-要素
#1: タンパク質・ペプチド | 分子量: 4096.534 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 参照: UniProt: P00734, トロンビン |
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#2: タンパク質 | 分子量: 29780.219 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 参照: UniProt: P00734, トロンビン |
#3: タンパク質・ペプチド | 分子量: 1363.399 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Hirudo medicinalis (医用ビル) / 参照: UniProt: P28507*PLUS |
#4: 糖 | ChemComp-NAG / |
#5: 水 | ChemComp-HOH / |
構成要素の詳細 | THROMBIN IS CLEAVED BETWEEN RESIDUES 15 AND 16. CHAIN INDICATOR *L* IS USED FOR RESIDUES 1H - 15 ...THROMBIN IS CLEAVED BETWEEN RESIDUES 15 AND 16. CHAIN INDICATOR *L* IS USED FOR RESIDUES 1H - 15 AND CHAIN INDICATOR *H* IS USED FOR RESIDUES 16 - 247. CHAIN INDICATOR *I* IS USED FOR N-ACETYLHIRU |
配列の詳細 | PEPTIDE ASP I 55 - LEU I 64 AT THE EXOSITE OF THROMBIN IS HIRUGEN MOLECULE, WHICH IS PART OF HIRUDIN 53 - 65. |
-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: 2.66 Å3/Da / 溶媒含有率: 53.79 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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結晶化 | *PLUS pH: 7.3 / 手法: microdialysis | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 15157 / % possible obs: 83 % / Rmerge(I) obs: 0.068 |
-解析
ソフトウェア |
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精密化 | 解像度: 2.3→7 Å / σ(F): 2 /
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精密化ステップ | サイクル: LAST / 解像度: 2.3→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/PROLSQ / 分類: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化 | *PLUS Rfactor obs: 0.114 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
溶媒の処理 | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | *PLUS Biso mean: 27.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
拘束条件 | *PLUS
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