+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1w1g | ||||||
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タイトル | Crystal Structure of the PDK1 Pleckstrin Homology (PH) domain bound to DiC4-phosphatidylinositol (3,4,5)-trisphosphate | ||||||
要素 | 3-PHOSPHOINOSITIDE DEPENDENT PROTEIN KINASE-1 | ||||||
キーワード | TRANSFERASE (転移酵素) / PDK1 / PHOSPHOINOSITIDE DEPENDENT PROTEIN KINASE 1 / PKB / PLECKSTRIN HOMOLOGY DOMAIN / INOSITOL PHOSPHATE (イノシトールリン酸) / PHOSPHOINOSITIDE (ホスファチジルイノシトール) / SIGNAL TRANSDUCTION (シグナル伝達) / PI3-KINASE / PIP3 SERINE/THREONINE PROTEIN KINASE | ||||||
機能・相同性 | 機能・相同性情報 3-phosphoinositide-dependent protein kinase activity / Activation of AKT2 / regulation of mast cell degranulation / negative regulation of toll-like receptor signaling pathway / type B pancreatic cell development / positive regulation of phospholipase activity / RSK activation / hyperosmotic response / regulation of canonical NF-kappaB signal transduction / positive regulation of vascular endothelial cell proliferation ...3-phosphoinositide-dependent protein kinase activity / Activation of AKT2 / regulation of mast cell degranulation / negative regulation of toll-like receptor signaling pathway / type B pancreatic cell development / positive regulation of phospholipase activity / RSK activation / hyperosmotic response / regulation of canonical NF-kappaB signal transduction / positive regulation of vascular endothelial cell proliferation / negative regulation of cardiac muscle cell apoptotic process / phospholipase activator activity / positive regulation of sprouting angiogenesis / Constitutive Signaling by AKT1 E17K in Cancer / CD28 dependent PI3K/Akt signaling / phospholipase binding / positive regulation of blood vessel endothelial cell migration / Role of LAT2/NTAL/LAB on calcium mobilization / Estrogen-stimulated signaling through PRKCZ / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / negative regulation of endothelial cell apoptotic process / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / extrinsic apoptotic signaling pathway / RHO GTPases activate PKNs / GPVI-mediated activation cascade / cellular response to epidermal growth factor stimulus / T cell costimulation / activation of protein kinase B activity / Integrin signaling / insulin-like growth factor receptor signaling pathway / positive regulation of release of sequestered calcium ion into cytosol / VEGFR2 mediated vascular permeability / VEGFR2 mediated cell proliferation / cell projection / calcium-mediated signaling / positive regulation of protein localization to plasma membrane / negative regulation of transforming growth factor beta receptor signaling pathway / peptidyl-threonine phosphorylation / negative regulation of protein kinase activity / epidermal growth factor receptor signaling pathway / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / G beta:gamma signalling through PI3Kgamma / cellular response to insulin stimulus / positive regulation of angiogenesis / Regulation of TP53 Degradation / 遊走 / Downstream TCR signaling / PIP3 activates AKT signaling / insulin receptor signaling pathway / cytoplasmic vesicle / actin cytoskeleton organization / protein autophosphorylation / postsynaptic density / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / non-specific serine/threonine protein kinase / intracellular signal transduction / protein phosphorylation / protein serine kinase activity / focal adhesion / protein serine/threonine kinase activity / ATP binding / 細胞核 / 細胞膜 / 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: 1.45 Å | ||||||
データ登録者 | Komander, D. / Deak, M. / Alessi, D.R. / Van Aalten, D.M.F. | ||||||
引用 | ジャーナル: Embo J. / 年: 2004 タイトル: Structural Insights Into the Regulation of Pdk1 by Phosphoinositides and Inositol Phosphates 著者: Komander, D. / Fairservice, A. / Deak, M. / Kular, G.S. / Prescott, A.R. / Downes, C.P. / Safrany, S.T. / Alessi, D.R. / Van Aalten, D.M.F. | ||||||
履歴 |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-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 | 1w1g.cif.gz | 82.3 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb1w1g.ent.gz | 62.1 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1w1g.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/w1/1w1g ftp://data.pdbj.org/pub/pdb/validation_reports/w1/1w1g | 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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-要素
#1: タンパク質 | 分子量: 17816.186 Da / 分子数: 1 / 断片: PLECKSTRIN HOMOLOGY DOMAIN, RESIDUES 409-556 / 由来タイプ: 組換発現 / 由来: (組換発現) HOMO SAPIENS (ヒト) / プラスミド: PGEX / 発現宿主: ESCHERICHIA COLI (大腸菌) / 株 (発現宿主): BL21 / 参照: UniProt: O15530, EC: 2.7.1.37 |
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#2: 化合物 | ChemComp-4PT / ( |
#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: 2.1 Å3/Da / 溶媒含有率: 0.41 % |
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結晶化 | pH: 4.2 詳細: 25 % PEG 4000, 0.1 M SODIUM ACETATE [PH 4.2], 0.3 M AMMONIUM ACETATE |
-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: 回転陽極 / タイプ: RIGAKU MICROMAX-007 / 波長: 1.5418 |
検出器 | タイプ: RIGAKU RAXIS 4 / 検出器: IMAGE PLATE / 日付: 2003年9月15日 / 詳細: MIRRORS |
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: 1.5418 Å / 相対比: 1 |
反射 | 解像度: 1.45→30 Å / Num. obs: 25810 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / 冗長度: 2.9 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 8.8 |
反射 シェル | 解像度: 1.45→1.5 Å / 冗長度: 2.7 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.5 / % 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: PDK1PH INSP4 MODEL 解像度: 1.45→25 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.956 / SU B: 4.471 / SU ML: 0.073 / 交差検証法: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.081 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE SIDE CHAINS OF SOME DISORDERED RESIDUES WERE REFINED EITHER WITH THE OCCUPANCY SET TO 0.02, OR THE RESIDUE WAS MUTATED TO ALA. THE ACYL- ...詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE SIDE CHAINS OF SOME DISORDERED RESIDUES WERE REFINED EITHER WITH THE OCCUPANCY SET TO 0.02, OR THE RESIDUE WAS MUTATED TO ALA. THE ACYL-CHAINS OF THE LIGAND WERE 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 26.94 Å2
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精密化ステップ | サイクル: LAST / 解像度: 1.45→25 Å
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拘束条件 |
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