+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1bmk | ||||||
---|---|---|---|---|---|---|---|
タイトル | THE COMPLEX STRUCTURE OF THE MAP KINASE P38/SB218655 | ||||||
要素 | PROTEIN (MAP KINASE P38) | ||||||
キーワード | TRANSFERASE / INHIBITORS / MAP KINASE / SERINE/ THREONINE-PROTEIN KINASE / P38 | ||||||
機能・相同性 | 機能・相同性情報 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 | Homo sapiens (ヒト) | ||||||
手法 | X線回折 / 分子置換 / 解像度: 2.4 Å | ||||||
データ登録者 | Wang, Z. / Canagarajah, B. / Boehm, J.C. / Kassis, S. / Cobb, M.H. / Young, P.R. / Abdel-Meguid, S. / Adams, J.L. / Goldsmith, E.J. | ||||||
引用 | ジャーナル: Structure / 年: 1998 タイトル: Structural basis of inhibitor selectivity in MAP kinases. 著者: Wang, Z. / Canagarajah, B.J. / Boehm, J.C. / Kassisa, S. / Cobb, M.H. / Young, P.R. / Abdel-Meguid, S. / Adams, J.L. / Goldsmith, E.J. #1: ジャーナル: J.Biol.Chem. / 年: 1995 タイトル: Pro-Inflammatory Cytokines and Environmental Stress Cause P38 Mitogen- Activated Protein Kinase Activation by Dual Phosphorylation on Tyrosine and Threonine 著者: Raingeaud, J. / Gupta, S. / Rogers, J.S. / Dickens, M. / Han, J. / Ulevitch, R.J. / Davis, R.J. #2: ジャーナル: Science / 年: 1994 タイトル: A Map Kinase Targeted by Endotoxin and Hyperosmolarity in Mammalian Cells 著者: Han, J. / Lee, J.D. / Bibbs, L. / Ulevitch, R.J. #3: ジャーナル: Nature / 年: 1994 タイトル: A Protein Kinase Involved in the Regulation of Inflammatory Cytokine Biosynthesis 著者: Lee, J.C. / Laydon, J.T. / Mcdonnell, P.C. / Gallagher, T.F. / Kumar, S. / Green, D. / Mcnulty, D. / Blumenthal, M.J. / Heys, J.R. / Landvatter, S.W. / Strickler, J.E. / Mclaughlin, M.M. / ...著者: Lee, J.C. / Laydon, J.T. / Mcdonnell, P.C. / Gallagher, T.F. / Kumar, S. / Green, D. / Mcnulty, D. / Blumenthal, M.J. / Heys, J.R. / Landvatter, S.W. / Strickler, J.E. / Mclaughlin, M.M. / Siemens, I.R. / Fisher, S.M. / Livi, G.P. / White, J.R. / Adams, J.L. / Young, P.R. | ||||||
履歴 |
|
-構造の表示
構造ビューア | 分子: MolmilJmol/JSmol |
---|
-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 1bmk.cif.gz | 86.3 KB | 表示 | PDBx/mmCIF形式 |
---|---|---|---|---|
PDB形式 | pdb1bmk.ent.gz | 64.6 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1bmk.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/bm/1bmk ftp://data.pdbj.org/pub/pdb/validation_reports/bm/1bmk | HTTPS FTP |
---|
-関連構造データ
-リンク
-集合体
登録構造単位 |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
単位格子 |
|
-要素
#1: タンパク質 | 分子量: 43378.312 Da / 分子数: 1 / 変異: 19 RESIDUES INSERTED AT N-TERMINUS / 由来タイプ: 組換発現 / 詳細: SB218655 PYRIDINYLIMIDAZOLE / 由来: (組換発現) Homo sapiens (ヒト) / 株: BL21 (DE3) / 解説: YES / プラスミド: PET15B / 生物種 (発現宿主): Escherichia coli / 細胞株 (発現宿主): BL21(DE3) / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 株 (発現宿主): BL21 (DE3) / 参照: UniProt: Q16539 |
---|---|
#2: 化合物 | ChemComp-SB5 / |
#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 |
---|
-試料調製
結晶 | マシュー密度: 2.92 Å3/Da / 溶媒含有率: 58 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
結晶化 | pH: 7.4 詳細: 18% PEG 8000, 0.2M MG(OAC)2, 0.1M HEPES, PH7.0, pH 7.4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
結晶化 | *PLUS 手法: 蒸気拡散法詳細: Wang, Z., (1997) Proc. Natl. Acad. Sci. USA, 94, 2327. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
溶液の組成 | *PLUS
|
-データ収集
回折 | 平均測定温度: 100 K |
---|---|
放射光源 | 由来: 回転陽極 / タイプ: RIGAKU RU300 / 波長: 1.54 |
検出器 | タイプ: RIGAKU RAXIS IIC / 検出器: IMAGE PLATE / 日付: 1997年3月3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: 1.54 Å / 相対比: 1 |
反射 | 解像度: 2.4→35.1 Å / Num. obs: 19500 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / 冗長度: 10.3 % / Rsym value: 0.05 / Net I/σ(I): 22.6 |
反射 シェル | 解像度: 2.4→2.49 Å / Mean I/σ(I) obs: 6.9 / Rsym value: 0.201 / % possible all: 96 |
反射 | *PLUS Num. measured all: 200387 / Rmerge(I) obs: 0.05 |
-解析
ソフトウェア |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
精密化 | 構造決定の手法: 分子置換 開始モデル: MAP KINASE P38 解像度: 2.4→20 Å / σ(F): 2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 41.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 2.4→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
拘束条件 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ソフトウェア | *PLUS 名称: X-PLOR / 分類: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化 | *PLUS 最高解像度: 2.4 Å / σ(F): 2 / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
溶媒の処理 | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | *PLUS Biso mean: 41.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
拘束条件 | *PLUS
|