+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 5ip5 | ||||||
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タイトル | Human DJ-1 complexed with Na-K-tartrate | ||||||
要素 | Protein deglycase DJ-1 | ||||||
キーワード | HYDROLASE (加水分解酵素) / Na-K-tartrate / Parkinson's diseases / DJ-1 / oxidative stress (酸化ストレス) | ||||||
機能・相同性 | 機能・相同性情報 tyrosine 3-monooxygenase activator activity / cellular response to glyoxal / L-dopa decarboxylase activator activity / peptidyl-cysteine deglycation / peptidyl-arginine deglycation / peptidyl-lysine deglycation / protein deglycation, methylglyoxal removal / glutathione deglycation / detoxification of hydrogen peroxide / methylglyoxal catabolic process to lactate ...tyrosine 3-monooxygenase activator activity / cellular response to glyoxal / L-dopa decarboxylase activator activity / peptidyl-cysteine deglycation / peptidyl-arginine deglycation / peptidyl-lysine deglycation / protein deglycation, methylglyoxal removal / glutathione deglycation / detoxification of hydrogen peroxide / methylglyoxal catabolic process to lactate / guanine deglycation, methylglyoxal removal / cellular detoxification of methylglyoxal / regulation of supramolecular fiber organization / negative regulation of death-inducing signaling complex assembly / negative regulation of TRAIL-activated apoptotic signaling pathway / positive regulation of pyrroline-5-carboxylate reductase activity / positive regulation of tyrosine 3-monooxygenase activity / positive regulation of L-dopa biosynthetic process / positive regulation of L-dopa decarboxylase activity / negative regulation of hydrogen peroxide-induced neuron intrinsic apoptotic signaling pathway / glyoxalase (glycolic acid-forming) activity / negative regulation of protein K48-linked deubiquitination / negative regulation of ubiquitin-specific protease activity / protein deglycation, glyoxal removal / guanine deglycation, glyoxal removal / glyoxal metabolic process / negative regulation of nitrosative stress-induced intrinsic apoptotic signaling pathway / detection of oxidative stress / glycolate biosynthetic process / guanine deglycation / positive regulation of NAD(P)H oxidase activity / detoxification of mercury ion / protein deglycase / methylglyoxal metabolic process / positive regulation of mitochondrial electron transport, NADH to ubiquinone / mercury ion binding / protein deglycase activity / oxidoreductase activity, acting on peroxide as acceptor / positive regulation of dopamine biosynthetic process / superoxide dismutase copper chaperone activity / positive regulation of acute inflammatory response to antigenic stimulus / positive regulation of autophagy of mitochondrion / lactate biosynthetic process / negative regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / cellular detoxification of aldehyde / positive regulation of superoxide dismutase activity / small protein activating enzyme binding / 加水分解酵素; エステル加水分解酵素; 3価のアルコールのエステル加水分解酵素 / regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / negative regulation of ubiquitin-protein transferase activity / peroxiredoxin activity / detoxification of copper ion / negative regulation of protein acetylation / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / positive regulation of transcription regulatory region DNA binding / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / positive regulation of androgen receptor activity / membrane hyperpolarization / protein deglycosylation / negative regulation of protein sumoylation / negative regulation of protein export from nucleus / regulation of androgen receptor signaling pathway / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / cupric ion binding / oxygen sensor activity / ubiquitin-like protein conjugating enzyme binding / insulin secretion / 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 / positive regulation of reactive oxygen species biosynthetic process / dopamine uptake involved in synaptic transmission / nuclear androgen receptor binding / hydrogen peroxide metabolic process / ubiquitin-specific protease binding / cytokine binding / cuprous ion binding / 脱分極 / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / single fertilization / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / regulation of neuron apoptotic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / negative regulation of reactive oxygen species biosynthetic process / negative regulation of protein ubiquitination / activation of protein kinase B activity / mitochondrion organization / adult locomotory behavior / SUMOylation of transcription cofactors / regulation of mitochondrial membrane potential / negative regulation of protein phosphorylation / negative regulation of protein binding / positive regulation of interleukin-8 production / negative regulation of extrinsic apoptotic signaling pathway / 接着結合 / Late endosomal microautophagy / negative regulation of protein kinase activity / positive regulation of protein-containing complex assembly / ミトコンドリア / PML body / オートファジー / kinase binding 類似検索 - 分子機能 | ||||||
生物種 | Homo sapiens (ヒト) | ||||||
手法 | X線回折 / シンクロトロン / 分子置換 / 解像度: 1.66 Å | ||||||
データ登録者 | Lee, S. / Cha, S.-S. / An, Y.J. | ||||||
引用 | ジャーナル: To Be Published タイトル: Human DJ-1 complexed with Na-K-tartrate 著者: Lee, S. / Cha, S.-S. / An, Y.J. | ||||||
履歴 |
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-構造の表示
構造ビューア | 分子: MolmilJmol/JSmol |
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-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 5ip5.cif.gz | 54 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb5ip5.ent.gz | 36.9 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 5ip5.json.gz | ツリー表示 | PDBx/mmJSON形式 | |
その他 | その他のダウンロード |
-検証レポート
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/ip/5ip5 ftp://data.pdbj.org/pub/pdb/validation_reports/ip/5ip5 | HTTPS FTP |
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-関連構造データ
関連構造データ | 3bweS S: 精密化の開始モデル |
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類似構造データ |
-リンク
-集合体
登録構造単位 |
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1 |
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単位格子 |
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-要素
#1: タンパク質 | 分子量: 20151.525 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: PARK7 / 発現宿主: Escherichia coli (大腸菌) 参照: UniProt: Q99497, 加水分解酵素; エステル加水分解酵素; 3価のアルコールのエステル加水分解酵素, 加水分解酵素; ...参照: UniProt: Q99497, 加水分解酵素; エステル加水分解酵素; 3価のアルコールのエステル加水分解酵素, 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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#2: 化合物 | ChemComp-TLA / |
#3: 水 | ChemComp-HOH / |
-実験情報
-実験
実験 | 手法: X線回折 / 使用した結晶の数: 1 |
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-試料調製
結晶 | マシュー密度: 3.07 Å3/Da / 溶媒含有率: 59.99 % |
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結晶化 | 温度: 295 K / 手法: マイクロバッチ法 / pH: 6.5 詳細: 1.5 M sodium potassium tartrate, 3.5 M ammonium sulfate, 0.1 M Na-Cacodylate |
-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: シンクロトロン / サイト: PAL/PLS / ビームライン: 7A (6B, 6C1) / 波長: 1.127 Å |
検出器 | タイプ: ADSC QUANTUM 270 / 検出器: CCD / 日付: 2012年7月10日 |
放射 | モノクロメーター: osmic mirror / 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: 1.127 Å / 相対比: 1 |
反射 | 解像度: 1.66→30 Å / Num. obs: 29365 / % possible obs: 99.8 % / 冗長度: 2.1 % / Net I/σ(I): 54.3 |
反射 シェル | 解像度: 1.66→1.72 Å / 冗長度: 1.6 % / % possible all: 100 |
-解析
ソフトウェア |
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精密化 | 構造決定の手法: 分子置換 開始モデル: 3BWE 解像度: 1.66→20 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.955 / SU B: 0.941 / SU ML: 0.033 / 交差検証法: THROUGHOUT / ESU R: 0.065 / ESU R Free: 0.066 / 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: 13.826 Å2
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精密化ステップ | サイクル: 1 / 解像度: 1.66→20 Å
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拘束条件 |
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