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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: 3fmn | ||||||
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タイトル | P38 kinase crystal structure in complex with RO2530 | ||||||
![]() | Mitogen-activated protein kinase 14 | ||||||
![]() | SIGNALING PROTEIN / TRANSFERASE / P38 / MAP KINASE / SERINE/THREONINE KINASE / ATP-binding / Kinase / Nucleotide-binding / Nucleus / Phosphoprotein / Serine/threonine-protein kinase | ||||||
機能・相同性 | ![]() positive regulation of cyclase activity / stress-activated protein kinase signaling cascade / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / CD163 mediating an anti-inflammatory response / regulation of synaptic membrane adhesion / stress-induced premature senescence / cell surface receptor protein serine/threonine kinase signaling pathway / 3'-UTR-mediated mRNA stabilization / KSRP (KHSRP) binds and destabilizes mRNA / cartilage condensation ...positive regulation of cyclase activity / stress-activated protein kinase signaling cascade / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / CD163 mediating an anti-inflammatory response / regulation of synaptic membrane adhesion / stress-induced premature senescence / cell surface receptor protein serine/threonine kinase signaling pathway / 3'-UTR-mediated mRNA stabilization / KSRP (KHSRP) binds and destabilizes mRNA / cartilage condensation / positive regulation of myoblast fusion / cellular response to UV-B / Platelet sensitization by LDL / mitogen-activated protein kinase p38 binding / positive regulation of muscle cell differentiation / positive regulation of myotube differentiation / NFAT protein binding / Myogenesis / glucose import / Activation of the AP-1 family of transcription factors / negative regulation of hippo signaling / ERK/MAPK targets / regulation of cytokine production involved in inflammatory response / p38MAPK cascade / fatty acid oxidation / cellular response to lipoteichoic acid / MAP kinase kinase activity / response to muramyl dipeptide / response to dietary excess / RHO GTPases Activate NADPH Oxidases / MAP kinase activity / regulation of ossification / cellular response to vascular endothelial growth factor stimulus / mitogen-activated protein kinase / signal transduction in response to DNA damage / positive regulation of myoblast differentiation / chondrocyte differentiation / vascular endothelial growth factor receptor signaling pathway / stress-activated MAPK cascade / skeletal muscle tissue development / positive regulation of cardiac muscle cell proliferation / lipopolysaccharide-mediated signaling pathway / negative regulation of inflammatory response to antigenic stimulus / p38MAPK events / striated muscle cell differentiation / response to muscle stretch / positive regulation of interleukin-12 production / positive regulation of brown fat cell differentiation / osteoclast differentiation / positive regulation of erythrocyte differentiation / DNA damage checkpoint signaling / activated TAK1 mediates p38 MAPK activation / positive regulation of glucose import / stem cell differentiation / cellular response to ionizing radiation / NOD1/2 Signaling Pathway / response to insulin / bone development / negative regulation of canonical Wnt signaling pathway / cell morphogenesis / placenta development / platelet activation / cellular response to virus / spindle pole / VEGFA-VEGFR2 Pathway / positive regulation of protein import into nucleus / osteoblast differentiation / ADP signalling through P2Y purinoceptor 1 / glucose metabolic process / chemotaxis / positive regulation of reactive oxygen species metabolic process / cellular senescence / cellular response to tumor necrosis factor / peptidyl-serine phosphorylation / cellular response to lipopolysaccharide / protein phosphatase binding / angiogenesis / secretory granule lumen / Oxidative Stress Induced Senescence / Regulation of TP53 Activity through Phosphorylation / ficolin-1-rich granule lumen / transcription by RNA polymerase II / cell surface receptor signaling pathway / intracellular signal transduction / nuclear speck / protein serine kinase activity / protein serine/threonine kinase activity / glutamatergic synapse / Neutrophil degranulation / positive regulation of gene expression / apoptotic process / regulation of transcription by RNA polymerase II / enzyme binding / signal transduction / positive regulation of transcription by RNA polymerase II / mitochondrion / extracellular region / nucleoplasm / ATP binding / nucleus 類似検索 - 分子機能 | ||||||
生物種 | ![]() | ||||||
手法 | ![]() ![]() ![]() | ||||||
![]() | Kuglstatter, A. / Ghate, M. | ||||||
![]() | ![]() タイトル: P38 kinase crystal structure in complex with RO2530 著者: Soth, M. / Kuglstatter, A. / Gabriel, T. | ||||||
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 | ![]() | 92.3 KB | 表示 | ![]() |
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PDB形式 | ![]() | 68.2 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 | ![]() 1p38 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 asymmetric unit of the crystal structure contains one biological unit. |
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要素
#1: タンパク質 | 分子量: 42748.715 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-530 / |
#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: 2.9 Å3/Da / 溶媒含有率: 57.54 % |
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結晶化 | 温度: 290 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 7.6 詳細: 50 mM Hepes pH 7.6, 50 mM CaCl2, 17% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
-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: ADSC QUANTUM 210 / 検出器: CCD |
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 Å / 相対比: 1 |
反射 | 解像度: 1.9→50 Å / Num. obs: 39535 / % possible obs: 98.8 % / 冗長度: 4.6 % / Biso Wilson estimate: 29.4 Å2 / Rsym value: 0.047 |
反射 シェル | 解像度: 1.9→1.97 Å / 冗長度: 3.6 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 3731 / Rsym value: 0.496 / % possible all: 94.9 |
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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 1P38 ![]() 1p38 解像度: 1.9→43.27 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.931 / SU B: 6.929 / SU ML: 0.092 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.137 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD
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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: 30.923 Å2
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精密化ステップ | サイクル: LAST / 解像度: 1.9→43.27 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 1.9→1.949 Å / Total num. of bins used: 20
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精密化 TLS | 手法: refined / Origin x: 21.3266 Å / Origin y: 17.1823 Å / Origin z: 21.4917 Å
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精密化 TLSグループ |
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