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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: 6hoy | ||||||
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タイトル | Human Sirt6 in complex with ADP-ribose and the inhibitor trichostatin A | ||||||
![]() | NAD-dependent protein deacetylase sirtuin-6 | ||||||
![]() | HYDROLASE / Deacylase / Inhibitor / Hydroxamate / Non-competitive / Isoform-selective | ||||||
機能・相同性 | ![]() NAD-dependent histone H3K56 deacetylase activity / NAD-dependent histone H3K18 deacetylase activity / NAD-dependent histone H3K9 deacetylase activity / protein delipidation / ketone biosynthetic process / regulation of lipid catabolic process / NAD+-protein-lysine ADP-ribosyltransferase activity / chromosome, subtelomeric region / NAD-dependent protein demyristoylase activity / NAD-dependent protein depalmitoylase activity ...NAD-dependent histone H3K56 deacetylase activity / NAD-dependent histone H3K18 deacetylase activity / NAD-dependent histone H3K9 deacetylase activity / protein delipidation / ketone biosynthetic process / regulation of lipid catabolic process / NAD+-protein-lysine ADP-ribosyltransferase activity / chromosome, subtelomeric region / NAD-dependent protein demyristoylase activity / NAD-dependent protein depalmitoylase activity / NAD+-protein-arginine ADP-ribosyltransferase activity / positive regulation of protein localization to chromatin / DNA damage sensor activity / positive regulation of stem cell differentiation / positive regulation of blood vessel branching / NAD-dependent protein lysine deacetylase activity / retrotransposon silencing / protein acetyllysine N-acetyltransferase / cardiac muscle cell differentiation / positive regulation of chondrocyte proliferation / pericentric heterochromatin formation / positive regulation of telomere maintenance / protein deacetylation / negative regulation of glucose import / NAD-dependent histone deacetylase activity / protein localization to site of double-strand break / TORC2 complex binding / lncRNA binding / negative regulation of glycolytic process / negative regulation of protein localization to chromatin / positive regulation of double-strand break repair / DNA repair-dependent chromatin remodeling / positive regulation of vascular endothelial cell proliferation / negative regulation of protein import into nucleus / regulation of double-strand break repair via homologous recombination / negative regulation of gene expression, epigenetic / positive regulation of stem cell population maintenance / positive regulation of stem cell proliferation / regulation of protein secretion / negative regulation of transcription elongation by RNA polymerase II / NAD+-protein ADP-ribosyltransferase activity / negative regulation of cellular senescence / site of DNA damage / regulation of lipid metabolic process / 転移酵素; グリコシル基を移すもの; 五炭糖残基を移すもの / NAD+-protein poly-ADP-ribosyltransferase activity / NAD+ binding / subtelomeric heterochromatin formation / positive regulation of fat cell differentiation / regulation of protein localization to plasma membrane / pericentric heterochromatin / negative regulation of gluconeogenesis / response to UV / nucleosome binding / 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 / nucleotidyltransferase activity / positive regulation of protein export from nucleus / determination of adult lifespan / circadian regulation of gene expression / protein destabilization / base-excision repair / regulation of circadian rhythm / positive regulation of insulin secretion / chromatin DNA binding / Pre-NOTCH Transcription and Translation / transcription corepressor activity / positive regulation of fibroblast proliferation / double-strand break repair / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / glucose homeostasis / positive regulation of cold-induced thermogenesis / site of double-strand break / Processing of DNA double-strand break ends / damaged DNA binding / chromatin remodeling / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / chromatin binding / chromatin / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / protein homodimerization activity / zinc ion binding / nucleoplasm / nucleus 類似検索 - 分子機能 | ||||||
生物種 | ![]() | ||||||
手法 | ![]() ![]() ![]() | ||||||
![]() | You, W. / Steegborn, C. | ||||||
![]() | ![]() タイトル: Structural Basis of Sirtuin 6 Inhibition by the Hydroxamate Trichostatin A: Implications for Protein Deacylase Drug Development. 著者: You, W. / Steegborn, C. | ||||||
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 | ![]() | 140.1 KB | 表示 | ![]() |
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PDB形式 | ![]() | 106.2 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 | ![]() | 1.4 MB | 表示 | ![]() |
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文書・詳細版 | ![]() | 1.4 MB | 表示 | |
XML形式データ | ![]() | 28.2 KB | 表示 | |
CIF形式データ | ![]() | 39.5 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
関連構造データ | ![]() 5mf6S S: 精密化の開始モデル |
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類似構造データ |
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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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Components on special symmetry positions |
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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:
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要素
-タンパク質 , 1種, 2分子 AB
#1: タンパク質 | 分子量: 33631.594 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() 参照: UniProt: Q8N6T7, 加水分解酵素; ペプチド以外のCN結合加水分解酵素; 鎖状アミドに作用 |
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-非ポリマー , 7種, 351分子 ![](data/chem/img/AR6.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/TSN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/TSN.gif)
![](data/chem/img/HOH.gif)
#2: 化合物 | #3: 化合物 | #4: 化合物 | #5: 化合物 | #6: 化合物 | ChemComp-SO4 / #7: 化合物 | #8: 水 | ChemComp-HOH / | |
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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: 2.62 Å3/Da / 溶媒含有率: 53.06 % |
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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: 5.7 詳細: 1.6 M (NH4)2SO4, 10% PEG 400, and Bis-Tris buffer pH 5.7 PH範囲: 5.7-6.2 |
-データ収集
回折 | 平均測定温度: 100 K | |||||||||||||||
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放射光源 | 由来: ![]() ![]() ![]() | |||||||||||||||
検出器 | タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2018年7月12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: 0.918 Å / 相対比: 1 | |||||||||||||||
Reflection twin |
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反射 | 解像度: 1.7→47.89 Å / Num. obs: 74416 / % possible obs: 99.9 % / Observed criterion σ(I): 0.87 / 冗長度: 11.4 % / Biso Wilson estimate: 34.27 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.15 / Net I/σ(I): 10.56 | |||||||||||||||
反射 シェル | 解像度: 1.7→1.8 Å / 冗長度: 11.6 % / Mean I/σ(I) obs: 0.87 / Num. unique obs: 11954 / CC1/2: 0.436 / Rrim(I) all: 2.47 / % possible all: 99.6 |
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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: 5MF6 解像度: 1.7→45.65 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.26 / SU ML: 0.044 / 交差検証法: THROUGHOUT / ESU R: 0.017 / ESU R Free: 0.018 / 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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溶媒の処理 | イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 34.477 Å2
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精密化ステップ | サイクル: 1 / 解像度: 1.7→45.65 Å
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拘束条件 |
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