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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: 8f30 | ||||||
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タイトル | LSD1-CoREST in complex with AW2, long soaking | ||||||
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![]() | OXIDOREDUCTASE / Epigenetics / Histone demethylase / Drug resistance / Covalent inhibitor | ||||||
機能・相同性 | ![]() positive regulation of megakaryocyte differentiation / guanine metabolic process / regulation of DNA methylation-dependent heterochromatin formation / protein demethylation / [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase / FAD-dependent H3K4me/H3K4me3 demethylase activity / demethylase activity / telomeric repeat-containing RNA binding / histone H3K4 demethylase activity / muscle cell development ...positive regulation of megakaryocyte differentiation / guanine metabolic process / regulation of DNA methylation-dependent heterochromatin formation / protein demethylation / [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase / FAD-dependent H3K4me/H3K4me3 demethylase activity / demethylase activity / telomeric repeat-containing RNA binding / histone H3K4 demethylase activity / muscle cell development / neuron maturation / positive regulation of neural precursor cell proliferation / regulation of androgen receptor signaling pathway / MRF binding / DNA repair complex / DNA repair-dependent chromatin remodeling / nuclear androgen receptor binding / regulation of double-strand break repair via homologous recombination / positive regulation of neuroblast proliferation / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of stem cell proliferation / negative regulation of DNA binding / histone H3K9 demethylase activity / negative regulation of DNA damage response, signal transduction by p53 class mediator / histone deacetylase complex / positive regulation of cell size / histone demethylase activity / positive regulation of epithelial to mesenchymal transition / cellular response to cAMP / response to fungicide / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / transcription repressor complex / erythrocyte differentiation / nuclear receptor coactivator activity / negative regulation of protein binding / positive regulation of protein ubiquitination / Regulation of PTEN gene transcription / HDACs deacetylate histones / promoter-specific chromatin binding / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / HDMs demethylate histones / negative regulation of DNA-binding transcription factor activity / cellular response to gamma radiation / cerebral cortex development / positive regulation of neuron projection development / transcription corepressor activity / regulation of protein localization / cellular response to UV / p53 binding / chromatin organization / positive regulation of cold-induced thermogenesis / flavin adenine dinucleotide binding / Factors involved in megakaryocyte development and platelet production / DNA-binding transcription factor binding / Estrogen-dependent gene expression / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / Potential therapeutics for SARS / chromosome, telomeric region / transcription coactivator activity / oxidoreductase activity / chromatin remodeling / negative regulation of gene expression / negative regulation of DNA-templated transcription / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / enzyme binding / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / identical protein binding / nucleus 類似検索 - 分子機能 | ||||||
生物種 | ![]() | ||||||
手法 | ![]() ![]() ![]() | ||||||
![]() | Caroli, J. / Mattevi, A. | ||||||
資金援助 | ![]()
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![]() | ![]() タイトル: Distal drug resistance mutations promote covalent inhibitor-adduct Grob fragmentation in LSD1 著者: Caroli, J. / Mattevi, A. | ||||||
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 | ![]() | 178.8 KB | 表示 | ![]() |
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PDB形式 | ![]() | 135.1 KB | 表示 | ![]() |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
その他 | ![]() |
-検証レポート
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
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-関連構造データ
関連構造データ | ![]() 8bopC ![]() 8boxC ![]() 8f2zC ![]() 8f59C ![]() 8f6sC ![]() 8fdvC ![]() 8fj4C ![]() 8fj6C ![]() 8fj7C ![]() 8fqjC ![]() 8friC ![]() 8frqC ![]() 8frvC ![]() 8fskC ![]() 2v1dS S: 精密化の開始モデル C: 同じ文献を引用 ( |
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類似構造データ | 類似検索 - 機能・相同性 ![]() |
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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
#1: タンパク質 | 分子量: 95051.633 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() 参照: UniProt: O60341, [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase |
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#2: タンパク質 | 分子量: 16459.742 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() |
#3: 化合物 | ChemComp-XB6 / [( 分子量: 995.821 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C42H47N9O16P2 / タイプ: SUBJECT OF INVESTIGATION |
研究の焦点であるリガンドがあるか | Y |
-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: 5.64 Å3/Da / 溶媒含有率: 78.2 % |
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結晶化 | 温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 6.5 / 詳細: 1.2 Na/K Tartrate, 100 mM ADA pH 6.5 |
-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 PILATUS 12M / 検出器: PIXEL / 日付: 2022年5月11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: 0.9677 Å / 相対比: 1 |
反射 | 解像度: 3.1→47.57 Å / Num. obs: 45927 / % possible obs: 99.7 % / 冗長度: 13.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.231 / Rpim(I) all: 0.064 / Rrim(I) all: 0.24 / Χ2: 1.01 / Net I/σ(I): 10.4 / Num. measured all: 640118 |
反射 シェル | 解像度: 3.1→3.21 Å / % possible obs: 100 % / 冗長度: 14.5 % / Rmerge(I) obs: 3.495 / Num. measured all: 65117 / Num. unique obs: 4493 / CC1/2: 0.439 / Rpim(I) all: 0.945 / Rrim(I) all: 3.622 / Χ2: 1.05 / Net I/σ(I) obs: 1.1 |
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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: 2v1d 解像度: 3.1→47.57 Å / SU ML: 0.43 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 立体化学のターゲット値: ML
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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 | |||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 3.1→47.57 Å
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拘束条件 |
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LS精密化 シェル |
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