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基本情報
登録情報 | データベース: PDB / ID: 1rdq | ||||||
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タイトル | Hydrolysis of ATP in the crystal of Y204A mutant of cAMP-dependent protein kinase | ||||||
![]() | (cAMP-dependent protein ...) x 2 | ||||||
![]() | TRANSFERASE/TRANSFERASE INHIBITOR / cAMP-dependent protein kinase / catalytic mechanism / ATP hydrolysis / two nucleotide states / TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX | ||||||
機能・相同性 | ![]() spontaneous exocytosis of neurotransmitter / PKA activation in glucagon signalling / CREB1 phosphorylation through the activation of Adenylate Cyclase / negative regulation of meiotic cell cycle / HDL assembly / DARPP-32 events / Rap1 signalling / PKA activation / Vasopressin regulates renal water homeostasis via Aquaporins / Regulation of insulin secretion ...spontaneous exocytosis of neurotransmitter / PKA activation in glucagon signalling / CREB1 phosphorylation through the activation of Adenylate Cyclase / negative regulation of meiotic cell cycle / HDL assembly / DARPP-32 events / Rap1 signalling / PKA activation / Vasopressin regulates renal water homeostasis via Aquaporins / Regulation of insulin secretion / GPER1 signaling / Hedgehog 'off' state / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / MAPK6/MAPK4 signaling / GLI3 is processed to GLI3R by the proteasome / Factors involved in megakaryocyte development and platelet production / Regulation of PLK1 Activity at G2/M Transition / Interleukin-3, Interleukin-5 and GM-CSF signaling / CD209 (DC-SIGN) signaling / Mitochondrial protein degradation / RET signaling / Ion homeostasis / VEGFA-VEGFR2 Pathway / regulation of cellular respiration / regulation of protein processing / protein localization to lipid droplet / regulation of bicellular tight junction assembly / cellular response to parathyroid hormone stimulus / cAMP-dependent protein kinase / cellular response to cold / regulation of osteoblast differentiation / sperm capacitation / cAMP-dependent protein kinase activity / ciliary base / negative regulation of glycolytic process through fructose-6-phosphate / cAMP-dependent protein kinase complex / AMP-activated protein kinase activity / postsynaptic modulation of chemical synaptic transmission / cellular response to glucagon stimulus / protein kinase A regulatory subunit binding / plasma membrane raft / axoneme / mesoderm formation / sperm flagellum / regulation of proteasomal protein catabolic process / negative regulation of smoothened signaling pathway / positive regulation of gluconeogenesis / sperm midpiece / negative regulation of TORC1 signaling / regulation of synaptic transmission, glutamatergic / protein kinase A signaling / protein serine/threonine/tyrosine kinase activity / protein export from nucleus / acrosomal vesicle / positive regulation of protein export from nucleus / neural tube closure / cellular response to glucose stimulus / modulation of chemical synaptic transmission / neuromuscular junction / positive regulation of insulin secretion / adenylate cyclase-activating G protein-coupled receptor signaling pathway / small GTPase binding / mRNA processing / presynapse / manganese ion binding / cellular response to heat / peptidyl-serine phosphorylation / postsynapse / dendritic spine / regulation of cell cycle / protein kinase activity / nuclear speck / protein domain specific binding / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / glutamatergic synapse / ubiquitin protein ligase binding / positive regulation of cell population proliferation / protein-containing complex binding / protein kinase binding / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / magnesium ion binding / protein-containing complex / mitochondrion / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm 類似検索 - 分子機能 | ||||||
生物種 | ![]() ![]() | ||||||
手法 | ![]() ![]() ![]() | ||||||
![]() | Yang, J. / Ten Eyck, L.F. / Xuong, N.H. / Taylor, S.S. | ||||||
![]() | ![]() タイトル: Crystal Structure of a cAMP-dependent Protein Kinase Mutant at 1.26A: New Insights into the Catalytic Mechanism. 著者: Yang, J. / Ten Eyck, L.F. / Xuong, N.H. / Taylor, S.S. #1: ![]() タイトル: Crystal structure of a transition state mimic of the catalytic subunit of cAMP-dependent protein kinase 著者: Madhusudan / Akamine, P. / Xuong, N.H. / Taylor, S.S. #2: ![]() タイトル: Crystal structure of the catalytic subunit of cAMP-dependent protein kinase complexed with MgATP and peptide inhibitor 著者: Zheng, J. / Knighton, D.R. / Ten Eyck, L.F. / Karlsson, R. / Xuong, N.H. / Taylor, S.S. / M., Sowadski J. #3: ![]() タイトル: Dynamic features of cAMP-dependent protein kinase revealed by apoenzyme crystal structure 著者: Akamine, P. / Madhusudan / Wu, J. / Xuong, N.H. / Ten Eyck, L.F. / Taylor, S.S. | ||||||
履歴 |
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構造の表示
構造ビューア | 分子: ![]() ![]() |
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PDBx/mmCIF形式 | ![]() | 185.8 KB | 表示 | ![]() |
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PDB形式 | ![]() | 142.6 KB | 表示 | ![]() |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
その他 | ![]() |
-検証レポート
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
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-関連構造データ
関連構造データ | ![]() 1apmS S: 精密化の開始モデル |
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類似構造データ |
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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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詳細 | the biological assembly is a monomer |
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要素
-CAMP-dependent protein ... , 2種, 2分子 EI
#1: タンパク質 | 分子量: 40565.223 Da / 分子数: 1 / 変異: Y204A / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() ![]() ![]() |
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#2: タンパク質・ペプチド | 分子量: 2226.411 Da / 分子数: 1 / Fragment: residues 5-24 / 由来タイプ: 合成 詳細: THE PROTEIN WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THE PROTEIN IS NATURALLY FOUND IN Mus musculus (mouse) |
-非ポリマー , 7種, 446分子 ![](data/chem/img/PO4.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/ATP.gif)
![](data/chem/img/MRD.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/ATP.gif)
![](data/chem/img/MRD.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#3: 化合物 | ChemComp-PO4 / | ||||||||||
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#4: 化合物 | #5: 化合物 | ChemComp-ADP / | #6: 化合物 | ChemComp-ATP / | #7: 化合物 | ChemComp-MRD / ( | #8: 化合物 | ChemComp-GOL / | #9: 水 | ChemComp-HOH / | |
-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: 53.08 % |
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結晶化 | 温度: 277 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 8 詳細: MPD, Bicine, ammonium acetate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K |
-データ収集
回折 | 平均測定温度: 110 K |
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放射光源 | 由来: ![]() ![]() ![]() |
検出器 | タイプ: MARRESEARCH / 検出器: IMAGE PLATE / 日付: 2001年4月1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: 1.08 Å / 相対比: 1 |
反射 | 解像度: 1.26→100 Å / Num. all: 122234 / Num. obs: 114998 / % possible obs: 94.1 % / Observed criterion σ(I): 2 / 冗長度: 4.8 % / Biso Wilson estimate: 13.2 Å2 / Rsym value: 0.05 / Net I/σ(I): 19.4 |
反射 シェル | 解像度: 1.26→1.28 Å / 冗長度: 2 % / Mean I/σ(I) obs: 3.4 / Num. unique all: 3827 / Rsym value: 0.253 / % possible all: 61 |
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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: PDB entry 1APM 解像度: 1.26→50 Å / Isotropic thermal model: isotropic / 交差検証法: THROUGHOUT / σ(F): 0 / σ(I): 0 / 立体化学のターゲット値: Engh & Huber 詳細: used cns solve 1.0, then shelxl97 for anisotropic refinement. The R factor values used for refinement shell are isotropic B
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原子変位パラメータ | Biso mean: 14.7 Å2 | |||||||||||||||||||||||||
Refine analyze |
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精密化ステップ | サイクル: LAST / 解像度: 1.26→50 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 1.26→1.34 Å / Rfactor Rfree error: 0.01
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