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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: 7lmw | ||||||
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タイトル | Receptor for Advanced Glycation End Products VC1 domain in complex with 3-(3-((4-(4-carboxyphenoxy)benzyl)oxy)phenyl)-1H-indole-2-carboxylic acid | ||||||
![]() | Advanced glycosylation end product-specific receptor | ||||||
![]() | SIGNALING PROTEIN / RAGE / inhibitor / 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 / neuron projection development / positive regulation of tumor necrosis factor production / 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 / positive regulation of ERK1 and ERK2 cascade / cell surface receptor signaling pathway / 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 | ![]() | 205.9 KB | 表示 | ![]() |
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PDB形式 | ![]() | 136.1 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 | ![]() | 2.2 MB | 表示 | ![]() |
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文書・詳細版 | ![]() | 2.2 MB | 表示 | |
XML形式データ | ![]() | 19 KB | 表示 | |
CIF形式データ | ![]() | 25.2 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: (0.499801329889, 0.866139930126, 0.000502077895275), (0.86613978514, -0.499800603513, -0.00110874999045), (-0.000709393804183, 0.000989024360075, -0.999999259295) ...NCS oper: (Code: given Matrix: (0.499801329889, 0.866139930126, 0.000502077895275), 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-Y6P / #3: 化合物 | ChemComp-ACT / #4: 化合物 | ChemComp-CL / | #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: 3.31 Å3/Da / 溶媒含有率: 62.88 % |
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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: DECTRIS EIGER X 9M / 検出器: PIXEL / 日付: 2019年8月8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: 1.0781 Å / 相対比: 1 |
反射 | 解像度: 2.5→50 Å / Num. obs: 20999 / % possible obs: 99.81 % / 冗長度: 2.7 % / Biso Wilson estimate: 40.82 Å2 / Rpim(I) all: 0.037 / Rrim(I) all: 0.086 / Net I/av σ(I): 13 / Net I/σ(I): 13 |
反射 シェル | 解像度: 2.5→2.82 Å / 冗長度: 2.8 % / Mean I/σ(I) obs: 2.6 / Num. unique obs: 6412 / Rpim(I) all: 0.199 / Rrim(I) all: 0.461 / % possible all: 100 |
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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: 2.5→33.41 Å / SU ML: 0.2934 / 交差検証法: FREE R-VALUE / σ(F): 1.39 / 位相誤差: 26.9002 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: 47.62 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 2.5→33.41 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: 0.391811878839 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS精密化 シェル |
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精密化 TLS | 手法: refined / Origin x: -30.7033228783 Å / Origin y: -17.7833227908 Å / Origin z: 19.8555031182 Å
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精密化 TLSグループ | Selection details: all |