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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: 6l71 | ||||||
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タイトル | Sirtuin 2 demyristoylation native intermediate I & II mixture | ||||||
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![]() | TRANSFERASE / Sirtuin / myristoylation / intermediate | ||||||
機能・相同性 | ![]() cellular response to caloric restriction / negative regulation of oligodendrocyte progenitor proliferation / cellular lipid catabolic process / negative regulation of striated muscle tissue development / NAD-dependent histone H4K16 deacetylase activity / positive regulation of meiotic nuclear division / positive regulation of attachment of spindle microtubules to kinetochore / NAD-dependent protein demyristoylase activity / NAD-dependent protein depalmitoylase activity / paranodal junction ...cellular response to caloric restriction / negative regulation of oligodendrocyte progenitor proliferation / cellular lipid catabolic process / negative regulation of striated muscle tissue development / NAD-dependent histone H4K16 deacetylase activity / positive regulation of meiotic nuclear division / positive regulation of attachment of spindle microtubules to kinetochore / NAD-dependent protein demyristoylase activity / NAD-dependent protein depalmitoylase activity / paranodal junction / tubulin deacetylation / lateral loop / NLRP3 inflammasome complex assembly / peptidyl-lysine deacetylation / mitotic nuclear membrane reassembly / negative regulation of NLRP3 inflammasome complex assembly / tubulin deacetylase activity / regulation of exit from mitosis / paranode region of axon / NAD-dependent protein lysine deacetylase activity / Schmidt-Lanterman incisure / positive regulation of fatty acid biosynthetic process / myelination in peripheral nervous system / rDNA heterochromatin formation / protein acetyllysine N-acetyltransferase / chromatin silencing complex / regulation of phosphorylation / Initiation of Nuclear Envelope (NE) Reformation / protein deacetylation / NAD-dependent histone deacetylase activity / positive regulation of oocyte maturation / juxtaparanode region of axon / protein lysine deacetylase activity / meiotic spindle / response to redox state / regulation of myelination / histone acetyltransferase binding / histone deacetylase activity / negative regulation of fat cell differentiation / negative regulation of peptidyl-threonine phosphorylation / positive regulation of execution phase of apoptosis / glial cell projection / positive regulation of cell division / NAD+-protein poly-ADP-ribosyltransferase activity / NAD+ binding / subtelomeric heterochromatin formation / negative regulation of reactive oxygen species metabolic process / positive regulation of DNA binding / heterochromatin / epigenetic regulation of gene expression / heterochromatin formation / 転移酵素; アシル基を移すもの; アミノアシル基以外のアシル基を移すもの / cellular response to epinephrine stimulus / substantia nigra development / centriole / negative regulation of autophagy / meiotic cell cycle / ubiquitin binding / negative regulation of protein catabolic process / mitotic spindle / autophagy / histone deacetylase binding / spindle / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / myelin sheath / chromosome / cellular response to oxidative stress / midbody / growth cone / cellular response to hypoxia / perikaryon / proteasome-mediated ubiquitin-dependent protein catabolic process / DNA-binding transcription factor binding / microtubule / chromosome, telomeric region / regulation of cell cycle / cell division / innate immune response / negative regulation of DNA-templated transcription / centrosome / chromatin binding / nucleolus / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / mitochondrion / zinc ion binding / nucleus / plasma membrane / cytoplasm / cytosol 類似検索 - 分子機能 | ||||||
生物種 | ![]() synthetic construct (人工物) | ||||||
手法 | ![]() ![]() ![]() | ||||||
![]() | Chen, L.F. | ||||||
資金援助 | ![]()
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![]() | ![]() タイトル: Sirtuin 2 protein with H3K18 myristoylated peptide 著者: Chen, L.F. | ||||||
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 | ![]() | 89.7 KB | 表示 | ![]() |
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PDB形式 | ![]() | 63.7 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 | ![]() | 1.2 MB | 表示 | ![]() |
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文書・詳細版 | ![]() | 1.2 MB | 表示 | |
XML形式データ | ![]() | 18.5 KB | 表示 | |
CIF形式データ | ![]() | 26 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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要素
-タンパク質 / タンパク質・ペプチド , 2種, 2分子 AC
#1: タンパク質 | 分子量: 34404.691 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() 参照: UniProt: Q8IXJ6, protein acetyllysine N-acetyltransferase |
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#2: タンパク質・ペプチド | 分子量: 713.868 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) synthetic construct (人工物) |
-非ポリマー , 4種, 226分子 ![](data/chem/img/NCA.gif)
![](data/chem/img/YOY.gif)
![](data/chem/img/YDD.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/YOY.gif)
![](data/chem/img/YDD.gif)
![](data/chem/img/HOH.gif)
#3: 化合物 | ChemComp-NCA / |
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#4: 化合物 | ChemComp-YOY / [[( |
#5: 化合物 | ChemComp-YDD / [[( |
#6: 水 | ChemComp-HOH / |
-詳細
研究の焦点であるリガンドがあるか | Y |
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非ポリマーの詳細 | YDD and YOY are in alternate confirmations of each other. |
-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: 2.33 Å3/Da / 溶媒含有率: 47.32 % |
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結晶化 | 温度: 291 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 6.5 / 詳細: 0.1M MES, pH 6.5, 6%-20% (w/v) PEG 10000 |
-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: ADSC QUANTUM 315r / 検出器: CCD / 日付: 2019年3月23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: 0.9793 Å / 相対比: 1 |
反射 | 解像度: 2.109→50 Å / Num. obs: 18062 / % possible obs: 96.7 % / 冗長度: 5.9 % / CC1/2: 0.989 / Net I/σ(I): 11 |
反射 シェル | 解像度: 2.109→2.15 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 712 / CC1/2: 0.601 |
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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: 4R8M 解像度: 2.109→27.924 Å / SU ML: 0.23 / 交差検証法: THROUGHOUT / σ(F): 1.36 / 位相誤差: 25.47
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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 | ||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso max: 100.95 Å2 / Biso mean: 34.6187 Å2 / Biso min: 7.91 Å2 | ||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: final / 解像度: 2.109→27.924 Å
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拘束条件 |
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LS精密化 シェル | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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