+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1nro | ||||||
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タイトル | CRYSTALLOGRAPHIC STRUCTURES OF THROMBIN COMPLEXED WITH THROMBIN RECEPTOR PEPTIDES: EXISTENCE OF EXPECTED AND NOVEL BINDING MODES | ||||||
要素 |
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キーワード | SERINE PROTEINASE/RECEPTOR (セリン) / SERINE PROTEINASE-RECEPTOR complex (セリン) | ||||||
機能・相同性 | 機能・相同性情報 negative regulation of renin secretion into blood stream / dendritic cell homeostasis / negative regulation of glomerular filtration / thrombin-activated receptor activity / establishment of synaptic specificity at neuromuscular junction / platelet dense tubular network / cell-cell junction maintenance / regulation of interleukin-1 beta production / connective tissue replacement involved in inflammatory response wound healing / platelet dense granule organization ...negative regulation of renin secretion into blood stream / dendritic cell homeostasis / negative regulation of glomerular filtration / thrombin-activated receptor activity / establishment of synaptic specificity at neuromuscular junction / platelet dense tubular network / cell-cell junction maintenance / regulation of interleukin-1 beta production / connective tissue replacement involved in inflammatory response wound healing / platelet dense granule organization / trans-synaptic signaling by endocannabinoid, modulating synaptic transmission / regulation of sensory perception of pain / positive regulation of smooth muscle contraction / protein kinase C-activating G protein-coupled receptor signaling pathway / positive regulation of calcium ion transport / positive regulation of Rho protein signal transduction / 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) / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / negative regulation of platelet activation / negative regulation of astrocyte differentiation / G-protein alpha-subunit binding / anatomical structure morphogenesis / 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 / homeostasis of number of cells within a tissue / release of sequestered calcium ion into cytosol / positive regulation of vasoconstriction / 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 / カベオラ / G protein-coupled receptor activity / positive regulation of interleukin-8 production / 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 / neuromuscular junction / positive regulation of insulin secretion / 凝固・線溶系 / positive regulation of GTPase activity / response to wounding / positive regulation of interleukin-6 production / 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) / G-protein beta-subunit binding / activation of cysteine-type endopeptidase activity involved in apoptotic process / 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) / late endosome / heparin binding / phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of cytosolic calcium ion concentration / regulation of cell shape / postsynaptic membrane / positive regulation of cell growth / G alpha (q) signalling events / collagen-containing extracellular matrix / blood microparticle / positive regulation of canonical NF-kappaB signal transduction / negative regulation of neuron apoptotic process / response to lipopolysaccharide / positive regulation of MAPK cascade / positive regulation of ERK1 and ERK2 cascade / cell surface receptor signaling pathway / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / エンドソーム / positive regulation of cell migration / 炎症 / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / 小胞体 / negative regulation of cell population proliferation / signaling receptor binding / serine-type endopeptidase activity / calcium ion binding 類似検索 - 分子機能 | ||||||
生物種 | Homo sapiens (ヒト) | ||||||
手法 | X線回折 / 解像度: 3.1 Å | ||||||
データ登録者 | Tulinsky, A. / Mathews, I.I. | ||||||
引用 | ジャーナル: Biochemistry / 年: 1994 タイトル: Crystallographic structures of thrombin complexed with thrombin receptor peptides: existence of expected and novel binding modes. 著者: Mathews, I.I. / Padmanabhan, K.P. / Ganesh, V. / Tulinsky, A. / Ishii, M. / Chen, J. / Turck, C.W. / Coughlin, S.R. / Fenton 2nd., J.W. #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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-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 | 1nro.cif.gz | 71.3 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb1nro.ent.gz | 56.5 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1nro.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/nr/1nro ftp://data.pdbj.org/pub/pdb/validation_reports/nr/1nro | 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: A FEW SIDE CHAINS IN BOTH THROMBIN AND RECEPTOR PEPTIDE DO NOT HAVE WELL-DEFINED ELECTRON DENSITY. THESE ATOMS HAVE BEEN GIVEN OCCUPANCIES OF 0.01 IN THIS ENTRY. |
-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: 3382.644 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: P25116 |
#4: 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 *R* IS USED FOR NRP. |
-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: 2.75 Å3/Da / 溶媒含有率: 55.23 % | |||||||||||||||
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結晶化 | *PLUS pH: 8.5 / 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: 3.1 Å / % possible obs: 88 % / Rmerge F obs: 0.071 |
-解析
ソフトウェア | 名称: PROLSQ / 分類: 精密化 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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精密化 | 解像度: 3.1→7 Å / σ(F): 2 詳細: A FEW SIDE CHAINS IN BOTH THROMBIN AND RECEPTOR PEPTIDE DO NOT HAVE WELL-DEFINED ELECTRON DENSITY. THESE ATOMS HAVE BEEN GIVEN OCCUPANCIES OF 0.01 IN THIS ENTRY.
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精密化ステップ | サイクル: LAST / 解像度: 3.1→7 Å
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拘束条件 |
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ソフトウェア | *PLUS 名称: PROLSQ / 分類: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化 | *PLUS Rfactor obs: 0.171 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
溶媒の処理 | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | *PLUS Biso mean: 29 Å2 |