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基本情報
登録情報 | データベース: PDB / ID: 1doj | ||||||
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タイトル | Crystal structure of human alpha-thrombin*RWJ-51438 complex at 1.7 A | ||||||
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![]() | HYDROLASE/HYDROLASE INHIBITOR / thrombin / serine protease / enzyme inhibition / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
機能・相同性 | ![]() 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 ...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) / negative regulation of astrocyte differentiation / negative regulation of platelet activation / 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 / regulation of cytosolic calcium ion concentration / fibrinolysis / Intrinsic Pathway of Fibrin Clot Formation / Peptide ligand-binding receptors / positive regulation of release of sequestered calcium ion into cytosol / acute-phase response / Regulation of Complement cascade / 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 / serine-type endopeptidase inhibitor activity / positive regulation of insulin secretion / platelet activation / response to wounding / positive regulation of protein localization to nucleus / Golgi lumen / 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 / antimicrobial humoral immune response mediated by antimicrobial peptide / blood coagulation / 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 / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell surface receptor signaling pathway / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / serine-type endopeptidase activity / signaling receptor binding / calcium ion binding / positive regulation of cell population proliferation / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane 類似検索 - 分子機能 | ||||||
生物種 | ![]() | ||||||
手法 | ![]() | ||||||
![]() | Recacha, R. / Costanzo, M.J. / Maryanoff, B.E. / Carson, M. / DeLucas, L. / Chattopadhyay, D. | ||||||
![]() | ![]() タイトル: Structure of human alpha-thrombin complexed with RWJ-51438 at 1.7 A: unusual perturbation of the 60A-60I insertion loop. 著者: Recacha, R. / Costanzo, M.J. / Maryanoff, B.E. / Carson, M. / DeLucas, L. / Chattopadhyay, D. #1: ![]() タイトル: Structure of the Hirulog 3-Thrombin Complex and Nature of the S' Subsites of Substrates and Inhibitors 著者: Qiu, X. / Padmanabhan, K.P. / Carperos, V.E. / Tulinsky, A. / Kline, T. / Maraganore, J.M. / Fenton II, J.W. #2: ![]() タイトル: Crystal Structure of Thrombin with Thiazole-Containing Inhibitors: Probes of the S1' Binding Site 著者: Matthews, J.H. / Krishnan, R. / Costanzo, M.J. / Maryanoff, B.E. / Tulinsky, A. #3: ![]() タイトル: The Refined 1.9-A X-ray Crystal Structure of D-Pro-Phe-Arg Chloromethylketone-Inhibited Human Alpha-Thrombin: Structure Analysis, Overall Structure, Electrostatic Properties, Detailed ...タイトル: The Refined 1.9-A X-ray Crystal Structure of D-Pro-Phe-Arg Chloromethylketone-Inhibited Human Alpha-Thrombin: Structure Analysis, Overall Structure, Electrostatic Properties, Detailed Active-Site Geometry, and Structure-Function Relationships 著者: Bode, W. / Turk, D. / Karshikov, A. | ||||||
履歴 |
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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 | ![]() | 88.2 KB | 表示 | ![]() |
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PDB形式 | ![]() | 63.7 KB | 表示 | ![]() |
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その他 | ![]() |
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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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要素
-タンパク質 / タンパク質・ペプチド / 糖 , 3種, 3分子 AB![](data/chem/img/NAG.gif)
![](data/chem/img/NAG.gif)
#1: タンパク質 | 分子量: 33858.730 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() |
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#2: タンパク質・ペプチド | 分子量: 1491.528 Da / 分子数: 1 / Fragment: FRAGMENT OF HIRUDIN / 由来タイプ: 合成 / 詳細: Hirugen, comes from hirudin / 参照: UniProt: P09945, UniProt: P28504*PLUS |
#4: 糖 | ChemComp-NAG / |
-非ポリマー , 3種, 352分子 ![](data/chem/img/1Z0.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#3: 化合物 | ChemComp-1Z0 / | ||
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#5: 化合物 | #6: 水 | ChemComp-HOH / | |
-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: 2.47 Å3/Da / 溶媒含有率: 50.21 % | |||||||||||||||||||||||||||||||||||
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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: 6.5 詳細: 0.75 sodium acetate, 0.01% (w/v), 20% polyethylene glycol 4000 (w/v), pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K | |||||||||||||||||||||||||||||||||||
結晶化 | *PLUS pH: 7.3 | |||||||||||||||||||||||||||||||||||
溶液の組成 | *PLUS
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-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: ![]() |
検出器 | タイプ: RIGAKU / 検出器: IMAGE PLATE / 日付: 1998年3月4日 |
放射 | 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: 1.5418 Å / 相対比: 1 |
反射 | 解像度: 1.66→99 Å / Num. all: 126549 / Num. obs: 126549 / % possible obs: 87.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / 冗長度: 5 % / Biso Wilson estimate: 16.2 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 16.3 |
反射 シェル | 最高解像度: 1.66 Å / 冗長度: 3 % / Rmerge(I) obs: 0.2 / % possible all: 87.1 |
反射 | *PLUS Num. obs: 42979 / Num. measured all: 289770 |
反射 シェル | *PLUS 最低解像度: 1.72 Å / % possible obs: 43 % / Rmerge(I) obs: 0.2 |
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解析
ソフトウェア |
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精密化 | 解像度: 1.7→8 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1520225.35 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / 交差検証法: THROUGHOUT / σ(F): 3 / σ(I): 0 / 詳細: The Bijvoet differences were used in phasing
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溶媒の処理 | 溶媒モデル: FLAT MODEL / Bsol: 93.48 Å2 / ksol: 0.49 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 19.5 Å2
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Refine analyze |
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精密化ステップ | サイクル: LAST / 解像度: 1.7→8 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 1.7→1.81 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file |
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ソフトウェア | *PLUS 名称: ![]() | ||||||||||||||||||||||||||||||||||||||||||||
精密化 | *PLUS Num. reflection obs: 35906 / σ(F): 3 / % reflection Rfree: 4.5 % / Rfactor obs: 0.196 / Rfactor Rfree: 0.232 | ||||||||||||||||||||||||||||||||||||||||||||
溶媒の処理 | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | *PLUS Biso mean: 19.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||
拘束条件 | *PLUS
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LS精密化 シェル | *PLUS Rfactor Rfree: 0.298 / % reflection Rfree: 10 % / Rfactor Rwork: 0.276 |