+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 3hkj | ||||||
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タイトル | Crystal structure of human thrombin mutant W215A/E217A in complex with the extracellular fragment of human PAR1 | ||||||
要素 |
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キーワード | HYDROLASE / Serine protease / Acute phase / Blood coagulation / Cleavage on pair of basic residues / Disease mutation / Disulfide bond / Gamma-carboxyglutamic acid / Glycoprotein / Kringle / Protease / Secreted / Zymogen / Cell membrane / G-protein coupled receptor / Membrane / Phosphoprotein / Receptor / Transducer / Transmembrane | ||||||
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 / platelet dense tubular network / cell-cell junction maintenance / establishment of synaptic specificity at neuromuscular junction / regulation of interleukin-1 beta production / platelet dense granule organization / connective tissue replacement involved in inflammatory response wound healing ...negative regulation of renin secretion into blood stream / dendritic cell homeostasis / negative regulation of glomerular filtration / thrombin-activated receptor activity / platelet dense tubular network / cell-cell junction maintenance / establishment of synaptic specificity at neuromuscular junction / regulation of interleukin-1 beta production / platelet dense granule organization / connective tissue replacement involved in inflammatory response wound healing / trans-synaptic signaling by endocannabinoid, modulating synaptic transmission / regulation of sensory perception of pain / positive regulation of smooth muscle contraction / 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 / thrombin / regulation of blood coagulation / neutrophil-mediated killing of gram-negative bacterium / 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 astrocyte differentiation / negative regulation of platelet activation / G-protein alpha-subunit binding / positive regulation of collagen biosynthetic process / negative regulation of cytokine production involved in inflammatory response / anatomical structure morphogenesis / 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 / release of sequestered calcium ion into cytosol / homeostasis of number of cells within a tissue / 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 / positive regulation of GTPase activity / caveola / acute-phase response / Regulation of Complement cascade / positive regulation of interleukin-8 production / G protein-coupled receptor activity / negative regulation of proteolysis / Cell surface interactions at the vascular wall / lipopolysaccharide binding / positive regulation of receptor signaling pathway via JAK-STAT / growth factor activity / regulation of synaptic plasticity / neuromuscular junction / positive regulation of insulin secretion / platelet activation / response to wounding / positive regulation of protein localization to nucleus / Golgi lumen / antimicrobial humoral immune response mediated by antimicrobial peptide / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / activation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of interleukin-6 production / G-protein beta-subunit binding / positive regulation of reactive oxygen species metabolic process / blood coagulation / late endosome / Thrombin signalling through proteinase activated receptors (PARs) / phospholipase C-activating G protein-coupled receptor signaling pathway / heparin binding / regulation of cell shape / positive regulation of cytosolic calcium ion concentration / positive regulation of cell growth / G alpha (q) signalling events / postsynaptic membrane / positive regulation of canonical NF-kappaB signal transduction / collagen-containing extracellular matrix / negative regulation of neuron apoptotic process / response to lipopolysaccharide / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of ERK1 and ERK2 cascade / cell surface receptor signaling pathway / early endosome / blood microparticle / positive regulation of cell migration / inflammatory response / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / negative regulation of cell population proliferation / endoplasmic reticulum lumen / serine-type endopeptidase activity / signaling receptor binding 類似検索 - 分子機能 | ||||||
生物種 | Homo sapiens (ヒト) | ||||||
手法 | X線回折 / シンクロトロン / 分子置換 / 解像度: 2.6 Å | ||||||
データ登録者 | Gandhi, P.S. / Page, M.J. / Chen, Z. / Bush-Pelc, L. / Di Cera, E. | ||||||
引用 | ジャーナル: J.Biol.Chem. / 年: 2009 タイトル: Mechanism of the Anticoagulant Activity of Thrombin Mutant W215A/E217A. 著者: Gandhi, P.S. / Page, M.J. / Chen, Z. / Bush-Pelc, L. / Di Cera, E. #1: ジャーナル: J.Biol.Chem. / 年: 2004 タイトル: The anticoagulant thrombin mutant W215A/E217A has a collapsed primary specificity pocket. 著者: Pineda, A.O. / Chen, Z.W. / Caccia, S. / Cantwell, A.M. / Savvides, S.N. / Waksman, G. / Mathews, F.S. / Di Cera, E. | ||||||
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 | 3hkj.cif.gz | 133.3 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb3hkj.ent.gz | 103.1 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 3hkj.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
文書・要旨 | 3hkj_validation.pdf.gz | 497.1 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 3hkj_full_validation.pdf.gz | 515.3 KB | 表示 | |
XML形式データ | 3hkj_validation.xml.gz | 26.8 KB | 表示 | |
CIF形式データ | 3hkj_validation.cif.gz | 36.6 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/hk/3hkj ftp://data.pdbj.org/pub/pdb/validation_reports/hk/3hkj | HTTPS FTP |
-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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2 |
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単位格子 |
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詳細 | THE BIOLOGICAL ASSEMBLY CONSISTS OF A, B AND C CHAINS. |
-要素
#1: タンパク質・ペプチド | 分子量: 3647.075 Da / 分子数: 2 / 断片: Light chain: UNP residues 333-363 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: F2 / Cell (発現宿主): BHK cells / 器官 (発現宿主): baby hamster kidney 発現宿主: Cricetulus griseus (モンゴルキヌゲネズミ) 参照: UniProt: P00734, thrombin #2: タンパク質 | 分子量: 29607.055 Da / 分子数: 2 / 断片: Heavy chain: UNP residues 364-622 / Mutation: W215A, E217A / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: F2 / Cell (発現宿主): BHK cells / 器官 (発現宿主): baby hamster kidney 発現宿主: Cricetulus griseus (モンゴルキヌゲネズミ) 参照: UniProt: P00734, thrombin #3: タンパク質・ペプチド | 分子量: 2673.862 Da / 分子数: 2 / 断片: Extracellular fragment: UNP residues 42-62 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: F2R, CF2R, PAR1, TR / Cell (発現宿主): BHK cells / 器官 (発現宿主): baby hamster kidney 発現宿主: Cricetulus griseus (モンゴルキヌゲネズミ) 参照: UniProt: P25116 #4: 糖 | #5: 水 | ChemComp-HOH / | |
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-実験情報
-実験
実験 | 手法: X線回折 / 使用した結晶の数: 1 |
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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: 56.92 % |
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結晶化 | 温度: 295 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 7.5 詳細: 100mM HEPES pH 7.5, 20% PEG 10000, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-データ収集
回折 | 平均測定温度: 100 K |
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放射光源 | 由来: シンクロトロン / サイト: APS / ビームライン: 14-BM-C / 波長: 0.9 Å |
検出器 | タイプ: ADSC QUANTUM 315 / 検出器: CCD / 日付: 2008年10月27日 |
放射 | モノクロメーター: Bent Ge(111) / プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray |
放射波長 | 波長: 0.9 Å / 相対比: 1 |
反射 | 解像度: 2.6→40 Å / Num. all: 24771 / Num. obs: 22864 / % possible obs: 93.4 % / Observed criterion σ(I): -3 / 冗長度: 3 % / Biso Wilson estimate: 31.7 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 18.5 |
反射 シェル | 解像度: 2.6→2.69 Å / 冗長度: 2.6 % / Rmerge(I) obs: 0.199 / Mean I/σ(I) obs: 4.2 / Num. unique all: 1956 / % possible all: 79.3 |
-解析
ソフトウェア |
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精密化 | 構造決定の手法: 分子置換 開始モデル: PDB entry 1TQ0 解像度: 2.6→37.17 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 127702.59 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / 交差検証法: THROUGHOUT / σ(F): 0 / σ(I): 0 / 立体化学のターゲット値: Engh & Huber
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原子変位パラメータ | Biso mean: 40.8 Å2 | ||||||||||||||||||||
Refine analyze |
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精密化ステップ | サイクル: LAST / 解像度: 2.6→37.17 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 2.6→2.76 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
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