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基本情報
登録情報 | データベース: PDB / ID: 5n9n | |||||||||
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タイトル | Crystal structure of human Protein kinase CK2 catalytic subunit in complex with the ATP-competitive, tight-binding dibenzofuran inhibitor TF85 (4a) | |||||||||
![]() | Casein kinase II subunit alpha | |||||||||
![]() | TRANSFERASE / Protein kinase / CK2 / Casein kinase 2 / Protein phosphorylation / ATP-competitive inhititors / dibenzofuran derivatives / TIGHT-BINDING INHIBITORS | |||||||||
機能・相同性 | ![]() regulation of chromosome separation / positive regulation of aggrephagy / WNT mediated activation of DVL / Condensation of Prometaphase Chromosomes / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body / Receptor Mediated Mitophagy / Sin3-type complex / Synthesis of PC / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known ...regulation of chromosome separation / positive regulation of aggrephagy / WNT mediated activation of DVL / Condensation of Prometaphase Chromosomes / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body / Receptor Mediated Mitophagy / Sin3-type complex / Synthesis of PC / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / Maturation of hRSV A proteins / negative regulation of apoptotic signaling pathway / positive regulation of Wnt signaling pathway / negative regulation of double-strand break repair via homologous recombination / chaperone-mediated protein folding / negative regulation of ubiquitin-dependent protein catabolic process / Signal transduction by L1 / peptidyl-threonine phosphorylation / Hsp90 protein binding / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / PML body / Wnt signaling pathway / Regulation of PTEN stability and activity / positive regulation of protein catabolic process / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / KEAP1-NFE2L2 pathway / double-strand break repair / rhythmic process / kinase activity / positive regulation of cell growth / peptidyl-serine phosphorylation / Regulation of TP53 Activity through Phosphorylation / protein stabilization / negative regulation of translation / non-specific serine/threonine protein kinase / regulation of cell cycle / cell cycle / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / DNA damage response / positive regulation of cell population proliferation / signal transduction / nucleoplasm / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol 類似検索 - 分子機能 | |||||||||
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手法 | ![]() ![]() ![]() | |||||||||
![]() | Schnitzler, A. / Gratz, A. / Bollacke, A. / Weyrich, M. / Kucklaender, U. / Wuensch, B. / Goetz, C. / Niefind, K. / Jose, J. | |||||||||
![]() | ![]() タイトル: A pi-Halogen Bond of Dibenzofuranones with the Gatekeeper Phe113 in Human Protein Kinase CK2 Leads to Potent Tight Binding Inhibitors. 著者: Schnitzler, A. / Gratz, A. / Bollacke, A. / Weyrich, M. / Kucklander, U. / Wunsch, B. / Gotz, C. / Niefind, K. / Jose, J. #1: ![]() タイトル: Crystal structure of a C-terminal deletion mutant of human protein kinase CK2 catalytic subunit. 著者: Ermakova, I. / Boldyreff, B. / Issinger, O.G. / Niefind, K. #2: ![]() タイトル: Inclining the purine base binding plane in protein kinase CK2 by exchanging the flanking side-chains generates a preference for ATP as a cosubstrate. 著者: Yde, C.W. / Ermakova, I. / Issinger, O.G. / Niefind, K. #3: ![]() タイトル: Structural Hypervariability of the Two Human Protein Kinase CK2 Catalytic Subunit Paralogs Revealed by Complex Structures with a Flavonol- and a Thieno[2,3-d]pyrimidine-Based Inhibitor. 著者: Niefind, K. / Bischoff, N. / Golub, A.G. / Bdzhola, V.G. / Balanda, A.O. / Prykhod'ko, A.O. / Yarmoluk, S.M. #4: ジャーナル: Biochim. Biophys. Acta / 年: 2012 タイトル: TF--a novel cell-permeable and selective inhibitor of human protein kinase CK2 induces apoptosis in the prostate cancer cell line LNCaP. 著者: Goetz, C. / Gratz, A. / Kucklaender, U. / Jose, J. | |||||||||
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 | ![]() | 161.8 KB | 表示 | ![]() |
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PDB形式 | ![]() | 127.2 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 | ![]() | 716.1 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 719.2 KB | 表示 | |
XML形式データ | ![]() | 16.3 KB | 表示 | |
CIF形式データ | ![]() | 23 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
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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: 40066.742 Da / 分子数: 1 / 断片: UNP residues 1-335 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() 参照: UniProt: P68400, non-specific serine/threonine protein kinase | ||||
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#2: 化合物 | ChemComp-KC5 / ( | ||||
#3: 化合物 | ChemComp-ACT / #4: 化合物 | ChemComp-GOL / #5: 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: 1.93 Å3/Da / 溶媒含有率: 36.43 % |
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結晶化 | 温度: 293 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 5.6 詳細: Prior to the crystallization the Inhibitor TF85 was solubilized in 100 % DMSO in a concentration of 10 mM. This TF85 stock solution was mixed with human CK2alpha (construct 1-335; Protein ...詳細: Prior to the crystallization the Inhibitor TF85 was solubilized in 100 % DMSO in a concentration of 10 mM. This TF85 stock solution was mixed with human CK2alpha (construct 1-335; Protein concentration 8-10 mg/ml in 500 mM sodium chloride, 25 mM Tris/HCl pH 8.5) in a ratio of 1:10. After a short time of incubation, this mixture was mixed with reservoir solution [32 % (w/v) PEG4000, 0.2 M ammonium acetate, 0.1 M citrate pH 5.6] in a ratio of 5:2. 3.5 microliter of these mixtures were then equilibrated against the reservoir solution. The crystal growth was induced by seeding with 150 nanoliter seeding suspension after an equilibration time of two days. |
-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: ![]() ![]() ![]() |
検出器 | タイプ: DECTRIS PILATUS 2M / 検出器: PIXEL / 日付: 2012年10月12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: 0.99987 Å / 相対比: 1 |
反射 | 解像度: 1.84→45.51 Å / Num. obs: 25795 / % possible obs: 96.4 % / 冗長度: 3.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Net I/σ(I): 12.6 |
反射 シェル | 解像度: 1.84→1.88 Å / 冗長度: 3 % / Rmerge(I) obs: 0.75 / Num. unique obs: 1395 / CC1/2: 0.644 / Rsym value: 0.75 / % possible all: 84.2 |
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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: 2pvr 解像度: 1.841→34.165 Å / SU ML: 0.19 / 交差検証法: FREE R-VALUE / σ(F): 1.36 / 位相誤差: 21.35
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溶媒の処理 | 減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 1.841→34.165 Å
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拘束条件 |
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LS精密化 シェル |
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精密化 TLS | 手法: refined / Refine-ID: X-RAY DIFFRACTION
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精密化 TLSグループ |
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