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データを開く
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基本情報
登録情報 | データベース: PDB / ID: 6xq9 | ||||||
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タイトル | Receptor for Advanced Glycation End Products VC1 domain in complex with Fragments 1 & 13 | ||||||
![]() | Advanced glycosylation end product-specific receptor | ||||||
![]() | SIGNALING PROTEIN / RAGE / IG-like domain / receptor / Advanced Glycation End Products | ||||||
機能・相同性 | ![]() regulation of CD4-positive, alpha-beta T cell activation / negative regulation of blood circulation / advanced glycation end-product receptor activity / positive regulation of endothelin production / regulation of T cell mediated cytotoxicity / glucose mediated signaling pathway / negative regulation of long-term synaptic depression / positive regulation of monocyte extravasation / positive regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process / positive regulation of dendritic cell differentiation ...regulation of CD4-positive, alpha-beta T cell activation / negative regulation of blood circulation / advanced glycation end-product receptor activity / positive regulation of endothelin production / regulation of T cell mediated cytotoxicity / glucose mediated signaling pathway / negative regulation of long-term synaptic depression / positive regulation of monocyte extravasation / positive regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process / positive regulation of dendritic cell differentiation / regulation of p38MAPK cascade / regulation of non-canonical NF-kappaB signal transduction / scavenger receptor activity / induction of positive chemotaxis / transcytosis / protein localization to membrane / positive regulation of monocyte chemotactic protein-1 production / positive regulation of heterotypic cell-cell adhesion / S100 protein binding / regulation of long-term synaptic potentiation / regulation of spontaneous synaptic transmission / laminin receptor activity / positive regulation of p38MAPK cascade / negative regulation of interleukin-10 production / positive regulation of activated T cell proliferation / response to amyloid-beta / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling / transport across blood-brain barrier / negative regulation of long-term synaptic potentiation / positive regulation of chemokine production / positive regulation of interleukin-12 production / positive regulation of interleukin-1 beta production / astrocyte activation / positive regulation of JNK cascade / microglial cell activation / TAK1-dependent IKK and NF-kappa-B activation / regulation of synaptic plasticity / fibrillar center / response to wounding / positive regulation of non-canonical NF-kappaB signal transduction / cellular response to amyloid-beta / transmembrane signaling receptor activity / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / neuron projection development / cell junction / signaling receptor activity / positive regulation of NF-kappaB transcription factor activity / amyloid-beta binding / regulation of inflammatory response / postsynapse / molecular adaptor activity / learning or memory / cell surface receptor signaling pathway / positive regulation of ERK1 and ERK2 cascade / response to hypoxia / inflammatory response / positive regulation of protein phosphorylation / apical plasma membrane / protein-containing complex binding / cell surface / extracellular region / identical protein binding / plasma membrane 類似検索 - 分子機能 | ||||||
生物種 | ![]() | ||||||
手法 | ![]() ![]() ![]() | ||||||
![]() | Salay, L.E. / Kozlyuk, N. / Gilston, B.A. / Gogliotti, R.D. / Christov, P.P. / Kim, K. / Ovee, M. / Waterson, A.G. / Chazin, W.J. | ||||||
資金援助 | ![]()
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![]() | ![]() タイトル: A fragment-based approach to discovery of Receptor for Advanced Glycation End products inhibitors. 著者: Kozlyuk, N. / Gilston, B.A. / Salay, L.E. / Gogliotti, R.D. / Christov, P.P. / Kim, K. / Ovee, M. / Waterson, A.G. / Chazin, W.J. | ||||||
履歴 |
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構造の表示
構造ビューア | 分子: ![]() ![]() |
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ダウンロードとリンク
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ダウンロード
PDBx/mmCIF形式 | ![]() | 199.2 KB | 表示 | ![]() |
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PDB形式 | ![]() | 140.8 KB | 表示 | ![]() |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
その他 | ![]() |
-検証レポート
文書・要旨 | ![]() | 2 MB | 表示 | ![]() |
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文書・詳細版 | ![]() | 2 MB | 表示 | |
XML形式データ | ![]() | 19.6 KB | 表示 | |
CIF形式データ | ![]() | 26.1 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-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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非結晶学的対称性 (NCS) | NCSドメイン:
NCSドメイン領域:
NCS oper: (Code: givenMatrix: (0.502026601379, -0.864851981748, 0.000584101949087), (-0.864848899824, -0.502026443228, -0.00241469939158), (0.00238159217812, 0.000707083400855, -0.999996914021) ...NCS oper: (Code: given Matrix: (0.502026601379, -0.864851981748, 0.000584101949087), ベクター: |
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要素
#1: タンパク質 | 分子量: 23131.494 Da / 分子数: 2 / 断片: VC1 domain, resdues 23-231 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() #2: 化合物 | ChemComp-ACT / #3: 化合物 | ChemComp-V6S / #4: 化合物 | #5: 水 | ChemComp-HOH / | 研究の焦点であるリガンドがあるか | Y | |
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-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: 3.32 Å3/Da / 溶媒含有率: 63 % |
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結晶化 | 温度: 277 K / 手法: 蒸気拡散法, ハンギングドロップ法 / 詳細: 2.5 M NaOAc (pH 7.5) |
-データ収集
回折 | 平均測定温度: 100 K / Serial crystal experiment: N |
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放射光源 | 由来: ![]() ![]() ![]() |
検出器 | タイプ: RAYONIX MX-300 / 検出器: CCD / 日付: 2018年7月24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: 0.97857 Å / 相対比: 1 |
反射 | 解像度: 2.3→50 Å / Num. obs: 52826 / % possible obs: 99.73 % / 冗長度: 5.7 % / Biso Wilson estimate: 31.43 Å2 / Rpim(I) all: 0.019 / Rrim(I) all: 0.063 / Net I/av σ(I): 29.94 / Net I/σ(I): 29.9 |
反射 シェル | 解像度: 2.3→2.38 Å / 冗長度: 5.7 % / Mean I/σ(I) obs: 18.38 / Num. unique obs: 5258 / Rpim(I) all: 0.05 / Rrim(I) all: 0.166 / % possible all: 98.43 |
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解析
ソフトウェア |
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精密化 | 構造決定の手法: ![]() 開始モデル: 4LP4 解像度: 2.3→34.06 Å / SU ML: 0.2929 / 交差検証法: FREE R-VALUE / σ(F): 1.39 / 位相誤差: 26.6772 立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
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溶媒の処理 | 減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 40.9 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 2.3→34.06 Å
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拘束条件 |
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Refine LS restraints NCS | タイプ: Torsion NCS / Rms dev position: 0.573947506322 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS精密化 シェル |
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