+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1pgt | ||||||
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タイトル | CRYSTAL STRUCTURE OF HUMAN GLUTATHIONE S-TRANSFERASE P1-1[V104] COMPLEXED WITH S-HEXYLGLUTATHIONE | ||||||
要素 | GLUTATHIONE S-TRANSFERASEグルタチオン-S-トランスフェラーゼ | ||||||
キーワード | TRANSFERASE (転移酵素) / PI CLASS / HGSTP1-1[V104] / DETOXIFICATION | ||||||
機能・相同性 | 機能・相同性情報 nitric oxide storage / S-nitrosoglutathione binding / kinase regulator activity / negative regulation of biosynthetic process / TRAF2-GSTP1 complex / dinitrosyl-iron complex binding / common myeloid progenitor cell proliferation / hepoxilin biosynthetic process / glutathione derivative biosynthetic process / negative regulation of nitric-oxide synthase biosynthetic process ...nitric oxide storage / S-nitrosoglutathione binding / kinase regulator activity / negative regulation of biosynthetic process / TRAF2-GSTP1 complex / dinitrosyl-iron complex binding / common myeloid progenitor cell proliferation / hepoxilin biosynthetic process / glutathione derivative biosynthetic process / negative regulation of nitric-oxide synthase biosynthetic process / negative regulation of JUN kinase activity / nitric oxide binding / linoleic acid metabolic process / negative regulation of leukocyte proliferation / 薬物代謝 / negative regulation of monocyte chemotactic protein-1 production / Paracetamol ADME / JUN kinase binding / glutathione peroxidase activity / negative regulation of stress-activated MAPK cascade / negative regulation of interleukin-1 beta production / regulation of stress-activated MAPK cascade / prostaglandin metabolic process / negative regulation of MAPK cascade / Detoxification of Reactive Oxygen Species / グルタチオン-S-トランスフェラーゼ / negative regulation of acute inflammatory response / glutathione transferase activity / negative regulation of tumor necrosis factor production / negative regulation of tumor necrosis factor-mediated signaling pathway / glutathione metabolic process / negative regulation of canonical NF-kappaB signal transduction / negative regulation of fibroblast proliferation / xenobiotic metabolic process / regulation of ERK1 and ERK2 cascade / response to reactive oxygen species / positive regulation of superoxide anion generation / negative regulation of MAP kinase activity / central nervous system development / fatty acid binding / negative regulation of extrinsic apoptotic signaling pathway / negative regulation of protein kinase activity / negative regulation of ERK1 and ERK2 cascade / secretory granule lumen / cellular response to lipopolysaccharide / vesicle / ficolin-1-rich granule lumen / Neutrophil degranulation / negative regulation of apoptotic process / ミトコンドリア / extracellular space / extracellular exosome / extracellular region / 細胞核 / 細胞質基質 / 細胞質 類似検索 - 分子機能 | ||||||
生物種 | Homo sapiens (ヒト) | ||||||
手法 | X線回折 / 分子置換 / 解像度: 1.8 Å | ||||||
データ登録者 | Ji, X. | ||||||
引用 | ジャーナル: Biochemistry / 年: 1997 タイトル: Structure and function of the xenobiotic substrate-binding site and location of a potential non-substrate-binding site in a class pi glutathione S-transferase. 著者: Ji, X. / Tordova, M. / O'Donnell, R. / Parsons, J.F. / Hayden, J.B. / Gilliland, G.L. / Zimniak, P. #1: ジャーナル: Biochemistry / 年: 1994 タイトル: Structure and Function of the Xenobiotic Substrate Binding Site of a Glutathione S-Transferase as Revealed by X-Ray Crystallographic Analysis of Product Complexes with the Diastereomers ...タイトル: Structure and Function of the Xenobiotic Substrate Binding Site of a Glutathione S-Transferase as Revealed by X-Ray Crystallographic Analysis of Product Complexes with the Diastereomers of 9-(S-Glutathionyl)-10-Hydroxy-9,10-Dihydrophenanthrene 著者: Ji, X. / Johnson, W.W. / Sesay, M.A. / Dickert, L. / Prasad, S.M. / Ammon, H.L. / Armstrong, R.N. / Gilliland, G.L. #2: ジャーナル: Eur.J.Biochem. / 年: 1994 タイトル: Naturally Occurring Human Glutathione S-Transferase Gstp1-1 Isoforms with Isoleucine and Valine in Position 104 Differ in Enzymic Properties 著者: Zimniak, P. / Nanduri, B. / Pikula, S. / Bandorowicz-Pikula, J. / Singhal, S.S. / Srivastava, S.K. / Awasthi, S. / Awasthi, Y.C. #3: ジャーナル: J.Mol.Biol. / 年: 1992 タイトル: Three-Dimensional Structure of Class Pi Glutathione S-Transferase from Human Placenta in Complex with S-Hexylglutathione at 2.8 A Resolution 著者: Reinemer, P. / Dirr, H.W. / Ladenstein, R. / Huber, R. / Lo Bello, M. / Federici, G. / Parker, M.W. | ||||||
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 | 1pgt.cif.gz | 103.9 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb1pgt.ent.gz | 78.7 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1pgt.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/pg/1pgt ftp://data.pdbj.org/pub/pdb/validation_reports/pg/1pgt | HTTPS FTP |
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-関連構造データ
-リンク
-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 oper: (Code: given Matrix: (0.94607, -0.108441, 0.305274), ベクター: |
-要素
#1: タンパク質 | 分子量: 23363.742 Da / 分子数: 2 / 変異: VAL 104 VARIANT / 由来タイプ: 組換発現 詳細: HGSTP1-1[V104] AND HGSTP1-1[I104] ARE NATURALLY OCCURRING VARIANTS OF HGSTP1-1 OBTAINED BY SITE-DIRECTED MUTAGENESIS 由来: (組換発現) Homo sapiens (ヒト) / 細胞株: 293 / 細胞内の位置: CYTOPLASM細胞質 / 遺伝子: GTP_HUMAN / 器官: PLACENTA胎盤 / プラスミド: BL21 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21 (DE3) PLYSS 参照: UniProt: P09211, グルタチオン-S-トランスフェラーゼ #2: 化合物 | #3: 化合物 | #4: 水 | ChemComp-HOH / | |
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-実験情報
-実験
実験 | 手法: X線回折 / 使用した結晶の数: 2 |
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-試料調製
結晶 | マシュー密度: 2.4 Å3/Da / 溶媒含有率: 49 % | |||||||||||||||||||||||||||||||||||
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結晶化 | 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 6.5 詳細: CRYSTALS WERE GROWN IN HANGING DROPS WHICH INITIALLY CONSISTED OF 5.9 MG/ML PROTEIN IN 0.1 M HEPES BUFFER (PH 6.5) CONTAINING 8.3 MM S-HEXYLGLUTATHIONE AND 1.0 M BUFFERED (PH 6.5) AMMONIUM ...詳細: CRYSTALS WERE GROWN IN HANGING DROPS WHICH INITIALLY CONSISTED OF 5.9 MG/ML PROTEIN IN 0.1 M HEPES BUFFER (PH 6.5) CONTAINING 8.3 MM S-HEXYLGLUTATHIONE AND 1.0 M BUFFERED (PH 6.5) AMMONIUM SULFATE. THE DROPS WERE EQUILIBRATED AT 293 K AGAINST WELL SOLUTION CONTAINING BETWEEN 1.9 - 2.0 M AMMONIUM SULFATE IN 0.1 M HEPES BUFFER (PH 6.5)., vapor diffusion - hanging drop | |||||||||||||||||||||||||||||||||||
結晶化 | *PLUS 手法: 蒸気拡散法, ハンギングドロップ法 | |||||||||||||||||||||||||||||||||||
溶液の組成 | *PLUS
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-データ収集
回折 | 平均測定温度: 293 K |
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放射光源 | 由来: 回転陽極 / タイプ: ENRAF-NONIUS FR571 / 波長: 1.5418 |
検出器 | タイプ: MACSCIENCE / 検出器: IMAGE PLATE / 日付: 1996年3月1日 / 詳細: MIRRORS |
放射 | モノクロメーター: NI FILTER / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray |
放射波長 | 波長: 1.5418 Å / 相対比: 1 |
反射 | 解像度: 1.8→30 Å / Num. obs: 43132 / % possible obs: 96 % / Observed criterion σ(I): 0 / 冗長度: 4.2 % / Biso Wilson estimate: 24.48 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 13.92 |
反射 シェル | 解像度: 1.8→1.83 Å / 冗長度: 1.41 % / Rmerge(I) obs: 0.303 / Mean I/σ(I) obs: 1.81 / % possible all: 86.9 |
反射 シェル | *PLUS % possible obs: 86.9 % |
-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: PDB ENTRY 1GSS 解像度: 1.8→6 Å / 交差検証法: THROUGHOUT / σ(F): 2 詳細: X-PLOR IS USED AT EARLY STAGE OF REFINEMENT. GPRLSA IS A MODIFIED VERSION OF PROLSQ BY FUREY, WANG AND SAX (J. APPL. CRYSTALLOGR.,1982,15,160-166). CROSS-VALIDATION INCLUDES GEOMETRY CHECK ...詳細: X-PLOR IS USED AT EARLY STAGE OF REFINEMENT. GPRLSA IS A MODIFIED VERSION OF PROLSQ BY FUREY, WANG AND SAX (J. APPL. CRYSTALLOGR.,1982,15,160-166). CROSS-VALIDATION INCLUDES GEOMETRY CHECK AND R FACTOR CALCULATION FOR ALL DATA.
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原子変位パラメータ | Biso mean: 24.94 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 1.8→6 Å
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拘束条件 |
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ソフトウェア | *PLUS 名称: GPRLSA / 分類: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化 | *PLUS σ(I): 1 / Rfactor obs: 0.182 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
溶媒の処理 | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | *PLUS |