+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1za4 | |||||||||
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タイトル | Crystal Structure of the Thrombospondin-1 N-terminal Domain in Complex with Arixtra | |||||||||
要素 | Thrombospondin 1 | |||||||||
キーワード | CELL ADHESION (細胞接着) / TSP-1 / NTSP-1 / HBD / ARIXTRA | |||||||||
機能・相同性 | 機能・相同性情報 negative regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / collagen V binding / negative regulation of dendritic cell antigen processing and presentation / negative regulation of nitric oxide mediated signal transduction / chronic inflammatory response / negative regulation of sprouting angiogenesis / negative regulation of endothelial cell chemotaxis / Defective B3GALTL causes PpS / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / O-glycosylation of TSR domain-containing proteins ...negative regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / collagen V binding / negative regulation of dendritic cell antigen processing and presentation / negative regulation of nitric oxide mediated signal transduction / chronic inflammatory response / negative regulation of sprouting angiogenesis / negative regulation of endothelial cell chemotaxis / Defective B3GALTL causes PpS / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / O-glycosylation of TSR domain-containing proteins / positive regulation of transforming growth factor beta1 production / negative regulation of fibroblast growth factor receptor signaling pathway / negative regulation of long-chain fatty acid import across plasma membrane / negative regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / engulfment of apoptotic cell / low-density lipoprotein particle binding / negative regulation of focal adhesion assembly / fibrinogen complex / peptide cross-linking / positive regulation of chemotaxis / fibrinogen binding / Signaling by PDGF / Α顆粒 / negative regulation of interleukin-12 production / negative regulation of cell migration involved in sprouting angiogenesis / negative regulation of plasminogen activation / positive regulation of macrophage activation / transforming growth factor beta binding / positive regulation of endothelial cell apoptotic process / negative regulation of endothelial cell migration / positive regulation of fibroblast migration / 血管新生 / proteoglycan binding / extracellular matrix structural constituent / Syndecan interactions / endopeptidase inhibitor activity / negative regulation of cell-matrix adhesion / phosphatidylserine binding / positive regulation of macrophage chemotaxis / negative regulation of cGMP-mediated signaling / negative regulation of endothelial cell proliferation / response to testosterone / fibroblast growth factor binding / behavioral response to pain / positive regulation of transforming growth factor beta receptor signaling pathway / negative regulation of blood vessel endothelial cell migration / response to magnesium ion / fibronectin binding / response to unfolded protein / positive regulation of blood vessel endothelial cell migration / laminin binding / Integrin cell surface interactions / positive regulation of blood coagulation / negative regulation of fibrinolysis / response to glucose / response to mechanical stimulus / positive regulation of phosphorylation / 細胞外マトリックス / response to endoplasmic reticulum stress / negative regulation of angiogenesis / positive regulation of endothelial cell migration / positive regulation of translation / platelet alpha granule lumen / response to progesterone / 筋小胞体 / 分泌 / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of smooth muscle cell proliferation / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / positive regulation of MAP kinase activity / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / cellular response to growth factor stimulus / response to calcium ion / positive regulation of angiogenesis / positive regulation of reactive oxygen species metabolic process / 遊走 / integrin binding / positive regulation of tumor necrosis factor production / Platelet degranulation / cellular response to heat / heparin binding / cellular response to tumor necrosis factor / collagen-containing extracellular matrix / protease binding / response to hypoxia / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / 細胞接着 / positive regulation of cell migration / 免疫応答 / response to xenobiotic stimulus / 炎症 / 小胞体 / negative regulation of cell population proliferation / external side of plasma membrane / apoptotic process / calcium ion binding / positive regulation of cell population proliferation / negative regulation of apoptotic process / 細胞膜 / 小胞体 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 / 多波長異常分散 / 解像度: 1.9 Å | |||||||||
データ登録者 | Tan, K. / Wang, J.H. / Lawler, J. | |||||||||
引用 | ジャーナル: Structure / 年: 2006 タイトル: The Structures of the Thrombospondin-1 N-terminal Domain and its Complex with a Synthetic Pentameric Heparin 著者: Tan, K. / Duquette, M. / Liu, J.H. / Zhang, R. / Joachimiak, A. / Wang, J.H. / Lawler, J. | |||||||||
履歴 |
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Remark 600 | HETEROGEN ARIXTRA (FONDAPARINUX SODIUM) IS A SYNTHETIC MODIFIED PENTAMERIC HEPARIN. THE COMPLETE ...HETEROGEN ARIXTRA (FONDAPARINUX SODIUM) IS A SYNTHETIC MODIFIED PENTAMERIC HEPARIN. THE COMPLETE ARIXTRA MOLECULE WAS NOT OBSERVED. SGN, N,O6-DISULFO-GLUCOSAMINE IS PART OF ARIXTRA MOLECULE (DEFINED AS FIFTH UNIT) AND SO4, SULFATE IONS ARE ALSO PART OF ARIXTRA MOLECULE (FRAGMENTS FROM THE REST OF THE UNITS). |
-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 | 1za4.cif.gz | 52.9 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb1za4.ent.gz | 40 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1za4.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/za/1za4 ftp://data.pdbj.org/pub/pdb/validation_reports/za/1za4 | 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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-要素
#1: タンパク質 | 分子量: 27649.893 Da / 分子数: 1 / 断片: N-terminal Domain / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: THBS1, TSP, TSP1 / プラスミド: pMT/BiP/v5-His A / 属 (発現宿主): Drosophila / 発現宿主: Drosophila (ハエ) / 株 (発現宿主): Drosophila S2 cell / 参照: UniProt: P07996 | ||
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#2: 糖 | ChemComp-SGN / | ||
#3: 化合物 | ChemComp-SO4 / #4: 水 | ChemComp-HOH / | |
-実験情報
-実験
実験 | 手法: X線回折 / 使用した結晶の数: 2 |
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-試料調製
結晶 | マシュー密度: 2 Å3/Da / 溶媒含有率: 37.3 % |
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結晶化 | 温度: 298 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 4.6 詳細: 30% PEG1500 AND 0.1 M NAAC , pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-データ収集
回折 |
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放射光源 |
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検出器 |
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放射 |
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放射波長 |
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反射 | 解像度: 1.9→50 Å / Num. obs: 30776 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / 冗長度: 4.4 % / Biso Wilson estimate: 28.7 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 27.1 | ||||||||||||||||||
反射 シェル | 解像度: 1.9→1.97 Å / 冗長度: 2.8 % / Rmerge(I) obs: 0.359 / Mean I/σ(I) obs: 1.85 / Num. unique all: 2479 / % possible all: 78.2 |
-解析
ソフトウェア |
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精密化 | 構造決定の手法: 多波長異常分散 / 解像度: 1.9→25 Å / σ(F): 3 / 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: 34.2 Å2 | |||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.31 Å / Luzzati d res low obs: 3 Å / Luzzati sigma a obs: 0.15 Å | |||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 1.9→25 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 1.9→1.97 Å /
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