+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 2ws6 | ||||||
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タイトル | Semi-synthetic analogue of human insulin NMeTyrB26-insulin in hexamer form | ||||||
要素 |
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キーワード | HORMONE / CARBOHYDRATE METABOLISM / GLUCOSE METABOLISM / ANALOGUE / DIABETES MELLITUS | ||||||
機能・相同性 | 機能・相同性情報 negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / positive regulation of nitric oxide mediated signal transduction / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / Signaling by Insulin receptor / IRS activation / Insulin processing / regulation of protein secretion / positive regulation of peptide hormone secretion ...negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / positive regulation of nitric oxide mediated signal transduction / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / Signaling by Insulin receptor / IRS activation / Insulin processing / regulation of protein secretion / positive regulation of peptide hormone secretion / positive regulation of respiratory burst / negative regulation of acute inflammatory response / Regulation of gene expression in beta cells / alpha-beta T cell activation / regulation of amino acid metabolic process / negative regulation of respiratory burst involved in inflammatory response / negative regulation of protein secretion / positive regulation of dendritic spine maintenance / positive regulation of glycogen biosynthetic process / Synthesis, secretion, and deacylation of Ghrelin / regulation of protein localization to plasma membrane / fatty acid homeostasis / negative regulation of gluconeogenesis / negative regulation of lipid catabolic process / Signal attenuation / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / COPI-mediated anterograde transport / positive regulation of lipid biosynthetic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / positive regulation of insulin receptor signaling pathway / nitric oxide-cGMP-mediated signaling / negative regulation of reactive oxygen species biosynthetic process / positive regulation of protein autophosphorylation / Insulin receptor recycling / transport vesicle / insulin-like growth factor receptor binding / neuron projection maintenance / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of brown fat cell differentiation / positive regulation of protein metabolic process / NPAS4 regulates expression of target genes / activation of protein kinase B activity / positive regulation of glycolytic process / Insulin receptor signalling cascade / positive regulation of mitotic nuclear division / positive regulation of nitric-oxide synthase activity / positive regulation of cytokine production / positive regulation of long-term synaptic potentiation / acute-phase response / endosome lumen / Regulation of insulin secretion / positive regulation of D-glucose import / positive regulation of protein secretion / negative regulation of proteolysis / positive regulation of cell differentiation / regulation of transmembrane transporter activity / insulin receptor binding / wound healing / regulation of synaptic plasticity / negative regulation of protein catabolic process / hormone activity / positive regulation of neuron projection development / cognition / positive regulation of protein localization to nucleus / Golgi lumen / vasodilation / glucose metabolic process / cell-cell signaling / insulin receptor signaling pathway / glucose homeostasis / regulation of protein localization / positive regulation of NF-kappaB transcription factor activity / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of cell growth / protease binding / secretory granule lumen / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of cell migration / G protein-coupled receptor signaling pathway / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / negative regulation of gene expression / positive regulation of cell population proliferation / regulation of DNA-templated transcription / positive regulation of gene expression / extracellular space / extracellular region / identical protein 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: 1.5 Å | ||||||
データ登録者 | Brzozowski, A.M. / Jiracek, J. / Zakova, L. / Antolikova, E. / Watson, C.J. / Turkenburg, J.P. / Dodson, G.G. | ||||||
引用 | ジャーナル: Proc.Natl.Acad.Sci.USA / 年: 2010 タイトル: Implications for the Active Form of Human Insulin Based on the Structural Convergence of Highly Active Hormone Analogues. 著者: Jiracek, J. / Zakova, L. / Antolikova, E. / Watson, C.J. / Turkenburg, J.P. / Dodson, G.G. / Brzozowski, A.M. | ||||||
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 | 2ws6.cif.gz | 149.6 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb2ws6.ent.gz | 121.1 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 2ws6.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
文書・要旨 | 2ws6_validation.pdf.gz | 549.2 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 2ws6_full_validation.pdf.gz | 558.6 KB | 表示 | |
XML形式データ | 2ws6_validation.xml.gz | 18.3 KB | 表示 | |
CIF形式データ | 2ws6_validation.cif.gz | 26.2 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/ws/2ws6 ftp://data.pdbj.org/pub/pdb/validation_reports/ws/2ws6 | HTTPS FTP |
-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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-要素
-タンパク質・ペプチド , 3種, 12分子 ACEGIKBDFHJL
#1: タンパク質・ペプチド | 分子量: 2383.698 Da / 分子数: 6 / 由来タイプ: 合成 / 詳細: A CHAIN OF HUMAN INSULIN / 由来: (合成) HOMO SAPIENS (ヒト) / 参照: UniProt: P01308 #2: タンパク質・ペプチド | 分子量: 3433.953 Da / 分子数: 2 / 由来タイプ: 合成 / 由来: (合成) HOMO SAPIENS (ヒト) / 参照: UniProt: P01308 #3: タンパク質・ペプチド | 分子量: 3447.979 Da / 分子数: 4 / 由来タイプ: 合成 詳細: METHYLATION OF TYROSINE RESIDUE 26 NITROGEN ATOM OF HUMAN INSULIN 由来: (合成) HOMO SAPIENS (ヒト) / 参照: UniProt: P01308 |
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-非ポリマー , 5種, 255分子
#4: 化合物 | ChemComp-IPH / #5: 化合物 | #6: 化合物 | #7: 化合物 | ChemComp-GOL / | #8: 水 | ChemComp-HOH / | |
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-詳細
非ポリマーの詳細 | ZINC (ZN): ZINC CATION CHLORINE (CL): CHLORINE ANION |
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配列の詳細 | N ATOM OF 26Y PEPTIDE IS METHYLATED |
-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: 2.43 Å3/Da / 溶媒含有率: 49 % / 解説: NONE |
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結晶化 | pH: 8.2 詳細: 6% TRIS PH 8.2, 0.1 M NA CITRATE, 0.02% ZN ACETATE, 0.06% PHENOL |
-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: ESRF / ビームライン: ID14-1 / 波長: 0.934 |
検出器 | タイプ: ADSC CCD / 検出器: CCD / 日付: 2008年1月30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: 0.934 Å / 相対比: 1 |
反射 | 解像度: 1.5→40 Å / Num. obs: 50473 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / 冗長度: 3.9 % / Biso Wilson estimate: 17.1 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 11.7 |
反射 シェル | 解像度: 1.5→1.55 Å / 冗長度: 3 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 5 / % possible all: 99.9 |
-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 1MSO 解像度: 1.5→40 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.533 / SU ML: 0.043 / 交差検証法: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.073 / 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 RESIDUAL ONLY. A14, B21, C4, D1, I4, I14, L1 SIDE CHAINS OCCUPANCIES ARE SET TO ZERO DUE TO HIGH MOBILITY OF THESE SIDE CHAINS. B27- ...詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES RESIDUAL ONLY. A14, B21, C4, D1, I4, I14, L1 SIDE CHAINS OCCUPANCIES ARE SET TO ZERO DUE TO HIGH MOBILITY OF THESE SIDE CHAINS. B27-B30, D28-D30 F30, H28-H30, L28-L30 ARE NOT MODELLED DUE TO DISORDER.
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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 mean: 18.661 Å2
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精密化ステップ | サイクル: LAST / 解像度: 1.5→40 Å
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拘束条件 |
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