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データを開く
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基本情報
登録情報 | データベース: PDB / ID: 3rak | ||||||
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タイトル | CDK2 in complex with inhibitor RC-2-32 | ||||||
![]() | Cyclin-dependent kinase 2 | ||||||
![]() | TRANSFERASE/TRANSFERASE INHIBITOR / protein kinase / inhibitor / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
機能・相同性 | ![]() cyclin A1-CDK2 complex / cyclin E2-CDK2 complex / cyclin E1-CDK2 complex / cyclin A2-CDK2 complex / positive regulation of DNA-templated DNA replication initiation / G2 Phase / cyclin-dependent protein kinase activity / Y chromosome / Phosphorylation of proteins involved in G1/S transition by active Cyclin E:Cdk2 complexes / positive regulation of heterochromatin formation ...cyclin A1-CDK2 complex / cyclin E2-CDK2 complex / cyclin E1-CDK2 complex / cyclin A2-CDK2 complex / positive regulation of DNA-templated DNA replication initiation / G2 Phase / cyclin-dependent protein kinase activity / Y chromosome / Phosphorylation of proteins involved in G1/S transition by active Cyclin E:Cdk2 complexes / positive regulation of heterochromatin formation / p53-Dependent G1 DNA Damage Response / X chromosome / PTK6 Regulates Cell Cycle / regulation of anaphase-promoting complex-dependent catabolic process / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / centriole replication / Regulation of APC/C activators between G1/S and early anaphase / centrosome duplication / Telomere Extension By Telomerase / G0 and Early G1 / Activation of the pre-replicative complex / cellular response to nitric oxide / cyclin-dependent protein kinase holoenzyme complex / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / Activation of ATR in response to replication stress / Cyclin E associated events during G1/S transition / Cyclin A/B1/B2 associated events during G2/M transition / Cajal body / Cyclin A:Cdk2-associated events at S phase entry / condensed chromosome / mitotic G1 DNA damage checkpoint signaling / regulation of mitotic cell cycle / regulation of G2/M transition of mitotic cell cycle / cyclin binding / post-translational protein modification / : / meiotic cell cycle / positive regulation of DNA replication / male germ cell nucleus / potassium ion transport / DNA Damage/Telomere Stress Induced Senescence / CDK-mediated phosphorylation and removal of Cdc6 / SCF(Skp2)-mediated degradation of p27/p21 / Meiotic recombination / Orc1 removal from chromatin / G1/S transition of mitotic cell cycle / Transcriptional regulation of granulopoiesis / G2/M transition of mitotic cell cycle / Cyclin D associated events in G1 / cellular senescence / Regulation of TP53 Degradation / nuclear envelope / Factors involved in megakaryocyte development and platelet production / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / regulation of gene expression / peptidyl-serine phosphorylation / DNA replication / Regulation of TP53 Activity through Phosphorylation / transcription regulator complex / Ras protein signal transduction / chromosome, telomeric region / endosome / chromatin remodeling / protein domain specific binding / cell division / protein phosphorylation / DNA repair / protein serine kinase activity / protein serine/threonine kinase activity / DNA-templated transcription / centrosome / positive regulation of cell population proliferation / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / magnesium ion binding / signal transduction / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol 類似検索 - 分子機能 | ||||||
生物種 | ![]() | ||||||
手法 | ![]() ![]() | ||||||
![]() | Betzi, S. / Alam, R. / Han, H. / Becker, A. / Schonbrunn, E. | ||||||
![]() | ![]() タイトル: Development of highly potent and selective diaminothiazole inhibitors of cyclin-dependent kinases. 著者: Schonbrunn, E. / Betzi, S. / Alam, R. / Martin, M.P. / Becker, A. / Han, H. / Francis, R. / Chakrasali, R. / Jakkaraj, S. / Kazi, A. / Sebti, S.M. / Cubitt, C.L. / Gebhard, A.W. / Hazlehurst, ...著者: Schonbrunn, E. / Betzi, S. / Alam, R. / Martin, M.P. / Becker, A. / Han, H. / Francis, R. / Chakrasali, R. / Jakkaraj, S. / Kazi, A. / Sebti, S.M. / Cubitt, C.L. / Gebhard, A.W. / Hazlehurst, L.A. / Tash, J.S. / Georg, G.I. | ||||||
履歴 |
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構造の表示
構造ビューア | 分子: ![]() ![]() |
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ダウンロードとリンク
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ダウンロード
PDBx/mmCIF形式 | ![]() | 76.1 KB | 表示 | ![]() |
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PDB形式 | ![]() | 55.3 KB | 表示 | ![]() |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
その他 | ![]() |
-検証レポート
文書・要旨 | ![]() | 725.2 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 731.4 KB | 表示 | |
XML形式データ | ![]() | 15 KB | 表示 | |
CIF形式データ | ![]() | 21.4 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
関連構造データ | ![]() 3qqkC ![]() 3qtqC ![]() 3qtrC ![]() 3qtsC ![]() 3qtuC ![]() 3qtwC ![]() 3qtxC ![]() 3qtzC ![]() 3qu0C ![]() 3qxpC ![]() 3r8uC ![]() 3r8vC ![]() 3r8zC ![]() 3r9dC ![]() 3r9hC ![]() 3r9nC ![]() 3r9oC ![]() 3rahC ![]() 3ralC ![]() 3rjcC ![]() 3rk5C ![]() 3rk7C ![]() 3rk9C ![]() 3rkbC ![]() 3rmfC ![]() 3rniC ![]() 3rprC ![]() 3rpvC ![]() 3rpyC ![]() 3rzbC ![]() 3s00C ![]() 3s0oC ![]() 3s1hC ![]() 3sqqC ![]() 4gcjC ![]() 1pw2S C: 同じ文献を引用 ( 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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要素
#1: タンパク質 | 分子量: 34761.348 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() |
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#2: 化合物 | ChemComp-03Z / |
#3: 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 Å3/Da / 溶媒含有率: 38.63 % |
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結晶化 | 温度: 291 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 7.5 詳細: 5 mg/mL CDK2 protein, 3 mM inhibitor, 15% v/v PEG3350, 50 mM HEPES/NaOH, 50 mM Na/K phosphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-データ収集
回折 | 平均測定温度: 93 K |
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放射光源 | 由来: ![]() |
検出器 | タイプ: RIGAKU SATURN 944+ / 検出器: CCD / 日付: 2008年6月16日 / 詳細: MIRRORS |
放射 | モノクロメーター: MIRRORS / 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: 1.54178 Å / 相対比: 1 |
反射 | 解像度: 1.75→20 Å / Num. all: 27433 / Num. obs: 27433 / % possible obs: 95.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / 冗長度: 6.77 % / Biso Wilson estimate: 17.2 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 27.96 |
反射 シェル | 解像度: 1.75→1.8 Å / 冗長度: 6.84 % / Rmerge(I) obs: 0.187 / Mean I/σ(I) obs: 10.01 / Num. unique all: 2141 / % possible all: 92.4 |
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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 1PW2 解像度: 1.75→18.79 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1461961.54 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / 交差検証法: THROUGHOUT / σ(F): 0 / 立体化学のターゲット値: Engh & Huber / 詳細: BULK SOLVENT MODEL USED
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溶媒の処理 | 溶媒モデル: FLAT MODEL / Bsol: 49.962 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 24.9 Å2
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Refine analyze |
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精密化ステップ | サイクル: LAST / 解像度: 1.75→18.79 Å
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拘束条件 |
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Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS精密化 シェル | 解像度: 1.75→1.86 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Xplor file |
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