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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: 8bl0 | ||||||
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タイトル | Human Sirt6 in complex with the inhibitor S6023 and ADP-ribose | ||||||
![]() | NAD-dependent protein deacetylase sirtuin-6 | ||||||
![]() | HYDROLASE / Deacylase / Inhibitor | ||||||
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 / protein localization to site of double-strand break / NAD-dependent histone deacetylase activity / 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 / negative regulation of gene expression, epigenetic / regulation of double-strand break repair via homologous recombination / 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+ 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. | ||||||
資金援助 | ![]()
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![]() | ![]() タイトル: Development of novel Sirtuin 6 inhibitors and activators based on a protein crystallography-based fragment screen 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 | ![]() | 135.3 KB | 表示 | ![]() |
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PDB形式 | ![]() | 102 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 | ![]() | 1.5 MB | 表示 | ![]() |
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文書・詳細版 | ![]() | 1.6 MB | 表示 | |
XML形式データ | ![]() | 25.8 KB | 表示 | |
CIF形式データ | ![]() | 35.8 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 | ![]() 8ak5C ![]() 8ak6C ![]() 8ak7C ![]() 8ak8C ![]() 8ak9C ![]() 8akaC ![]() 8akbC ![]() 8akcC ![]() 8akdC ![]() 8akeC ![]() 8akfC ![]() 8akgC ![]() 8bl1C ![]() 8cnmC ![]() 8cnoC ![]() 5mf6S 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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非結晶学的対称性 (NCS) | NCSドメイン:
NCSドメイン領域: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 1 / Auth seq-ID: 15 - 297 / Label seq-ID: 9 - 291
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, protein acetyllysine N-acetyltransferase |
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-非ポリマー , 7種, 238分子 ![](data/chem/img/AR6.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/QTI.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/QTI.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
#2: 化合物 | #3: 化合物 | #4: 化合物 | #5: 化合物 | ChemComp-SO4 / #6: 化合物 | ChemComp-CL / #7: 化合物 | ChemComp-PEG / | #8: 水 | ChemComp-HOH / | |
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-詳細
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: 2.62 Å3/Da / 溶媒含有率: 53.01 % |
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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 / Serial crystal experiment: N |
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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: 0.9184 Å / 相対比: 1 |
反射 | 解像度: 1.82→47.56 Å / Num. obs: 59922 / % possible obs: 99 % / 冗長度: 16.7 % / Biso Wilson estimate: 39.344 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.18 / Net I/σ(I): 11.74 |
反射 シェル | 解像度: 1.82→1.93 Å / 冗長度: 16.1 % / Mean I/σ(I) obs: 0.83 / Num. unique obs: 9177 / CC1/2: 0.467 / Rrim(I) all: 3.26 / % possible all: 94.1 |
-位相決定
位相決定 | 手法: ![]() |
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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: 1.82→45.78 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.39 / SU ML: 0.073 / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.028 / ESU R Free: 0.027 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 / 溶媒モデル: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso max: 106.82 Å2 / Biso mean: 40.314 Å2 / Biso min: 20.99 Å2
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精密化ステップ | サイクル: final / 解像度: 1.82→45.78 Å
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拘束条件 |
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Refine LS restraints NCS | 数: 2145 / タイプ: TIGHT THERMAL / Rms dev position: 4 Å / Weight position: 0.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS精密化 シェル | 解像度: 1.822→1.87 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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