+
データを開く
-
基本情報
登録情報 | データベース: PDB / ID: 6rki | ||||||
---|---|---|---|---|---|---|---|
タイトル | Fragment AZ-023 binding at the p53pT387/14-3-3 sigma interface | ||||||
![]() |
| ||||||
![]() | PEPTIDE BINDING PROTEIN / protein protein interaction / fragment soaking / stabilization | ||||||
機能・相同性 | ![]() Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / signal transduction by p53 class mediator / negative regulation of G1 to G0 transition / negative regulation of glucose catabolic process to lactate via pyruvate / Transcriptional activation of cell cycle inhibitor p21 / regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Activation of NOXA and translocation to mitochondria / negative regulation of pentose-phosphate shunt / ATP-dependent DNA/DNA annealing activity ...Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / signal transduction by p53 class mediator / negative regulation of G1 to G0 transition / negative regulation of glucose catabolic process to lactate via pyruvate / Transcriptional activation of cell cycle inhibitor p21 / regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Activation of NOXA and translocation to mitochondria / negative regulation of pentose-phosphate shunt / ATP-dependent DNA/DNA annealing activity / negative regulation of helicase activity / regulation of cell cycle G2/M phase transition / intrinsic apoptotic signaling pathway in response to hypoxia / regulation of fibroblast apoptotic process / oxidative stress-induced premature senescence / oligodendrocyte apoptotic process / negative regulation of miRNA processing / positive regulation of thymocyte apoptotic process / glucose catabolic process to lactate via pyruvate / regulation of tissue remodeling / positive regulation of mitochondrial membrane permeability / negative regulation of mitophagy / positive regulation of programmed necrotic cell death / mRNA transcription / bone marrow development / circadian behavior / histone deacetylase regulator activity / RUNX3 regulates CDKN1A transcription / germ cell nucleus / regulation of mitochondrial membrane permeability involved in apoptotic process / regulation of DNA damage response, signal transduction by p53 class mediator / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / negative regulation of glial cell proliferation / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / negative regulation of neuroblast proliferation / Regulation of TP53 Activity through Association with Co-factors / mitochondrial DNA repair / T cell lineage commitment / negative regulation of DNA replication / ER overload response / regulation of epidermal cell division / protein kinase C inhibitor activity / B cell lineage commitment / positive regulation of cardiac muscle cell apoptotic process / thymocyte apoptotic process / positive regulation of epidermal cell differentiation / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / keratinocyte development / keratinization / TP53 Regulates Transcription of Caspase Activators and Caspases / cardiac septum morphogenesis / positive regulation of execution phase of apoptosis / entrainment of circadian clock by photoperiod / PI5P Regulates TP53 Acetylation / Association of TriC/CCT with target proteins during biosynthesis / Zygotic genome activation (ZGA) / necroptotic process / positive regulation of release of cytochrome c from mitochondria / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / rRNA transcription / TFIID-class transcription factor complex binding / mitophagy / SUMOylation of transcription factors / negative regulation of telomere maintenance via telomerase / Regulation of localization of FOXO transcription factors / intrinsic apoptotic signaling pathway by p53 class mediator / general transcription initiation factor binding / keratinocyte proliferation / Transcriptional Regulation by VENTX / DNA damage response, signal transduction by p53 class mediator / response to X-ray / replicative senescence / phosphoserine residue binding / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / neuroblast proliferation / cellular response to UV-C / : / Activation of BAD and translocation to mitochondria / hematopoietic stem cell differentiation / negative regulation of reactive oxygen species metabolic process / chromosome organization / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / negative regulation of keratinocyte proliferation / T cell proliferation involved in immune response / glial cell proliferation / establishment of skin barrier / embryonic organ development / positive regulation of RNA polymerase II transcription preinitiation complex assembly / Pyroptosis / cis-regulatory region sequence-specific DNA binding / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / hematopoietic progenitor cell differentiation / cellular response to glucose starvation / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / cellular response to actinomycin D / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / somitogenesis 類似検索 - 分子機能 | ||||||
生物種 | ![]() | ||||||
手法 | ![]() ![]() | ||||||
![]() | Genet, S. / Wolter, M. / Guillory, X. / Somsen, B. / Leysen, S. / Castaldi, P. / Ottmann, C. | ||||||
資金援助 | ![]()
| ||||||
![]() | ![]() タイトル: Fragment-based Differential Targeting of PPI Stabilizer Interfaces. 著者: Guillory, X. / Wolter, M. / Leysen, S. / Neves, J.F. / Kuusk, A. / Genet, S. / Somsen, B. / Morrow, J.K. / Rivers, E. / van Beek, L. / Patel, J. / Goodnow, R. / Schoenherr, H. / Fuller, N. / ...著者: Guillory, X. / Wolter, M. / Leysen, S. / Neves, J.F. / Kuusk, A. / Genet, S. / Somsen, B. / Morrow, J.K. / Rivers, E. / van Beek, L. / Patel, J. / Goodnow, R. / Schoenherr, H. / Fuller, N. / Cao, Q. / Doveston, R.G. / Brunsveld, L. / Arkin, M.R. / Castaldi, P. / Boyd, H. / Landrieu, I. / Chen, H. / Ottmann, C. | ||||||
履歴 |
|
-
構造の表示
構造ビューア | 分子: ![]() ![]() |
---|
-
ダウンロードとリンク
-
ダウンロード
PDBx/mmCIF形式 | ![]() | 75.5 KB | 表示 | ![]() |
---|---|---|---|---|
PDB形式 | ![]() | 52.7 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 | ![]() | 770.1 KB | 表示 | ![]() |
---|---|---|---|---|
文書・詳細版 | ![]() | 771 KB | 表示 | |
XML形式データ | ![]() | 15.7 KB | 表示 | |
CIF形式データ | ![]() | 24.2 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 | ![]() 6r5lC ![]() 6rhcC ![]() 6rjlC ![]() 6rjqC ![]() 6rjzC ![]() 6rk8C ![]() 6rkkC ![]() 6rkmC ![]() 6rl3C ![]() 6rl4C ![]() 6rl6C ![]() 6rm5C ![]() 6rm7C ![]() 6rp6C ![]() 6rwhC ![]() 6rwiC ![]() 6rwsC ![]() 6rwuC ![]() 6rx2C ![]() 6s39C ![]() 6s3cC ![]() 6s40C ![]() 6s9qC ![]() 6sinC ![]() 6sioC ![]() 6sipC ![]() 6siqC ![]() 6slvC ![]() 6slwC ![]() 6slxC ![]() 5mocS S: 精密化の開始モデル C: 同じ文献を引用 ( |
---|---|
類似構造データ |
-
リンク
-
集合体
登録構造単位 | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
単位格子 |
|
-
要素
-タンパク質 / タンパク質・ペプチド , 2種, 2分子 AP
#1: タンパク質 | 分子量: 28210.518 Da / 分子数: 1 / 由来タイプ: 組換発現 / 詳細: Residues -4 to 0 are expression tag / 由来: (組換発現) ![]() ![]() ![]() |
---|---|
#2: タンパク質・ペプチド | 分子量: 1449.520 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) ![]() |
-非ポリマー , 4種, 383分子 ![](data/chem/img/MG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/K6T.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/K6T.gif)
![](data/chem/img/HOH.gif)
#3: 化合物 | #4: 化合物 | ChemComp-CL / | #5: 化合物 | ChemComp-K6T / | #6: 水 | ChemComp-HOH / | |
---|
-実験情報
-実験
実験 | 手法: ![]() |
---|
-
試料調製
結晶 | マシュー密度: 2.59 Å3/Da / 溶媒含有率: 52.44 % |
---|---|
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: 7.5 詳細: 0.1M Hepes, pH7.5, 27%PEG, 5% Glycerol, 0.2M Calcium Chloride, 2mM DTT. |
-データ収集
回折 | 平均測定温度: 100 K / Serial crystal experiment: N |
---|---|
放射光源 | 由来: SEALED TUBE / タイプ: RIGAKU MICROMAX-003 / 波長: 1.54187 Å |
検出器 | タイプ: DECTRIS PILATUS 200K / 検出器: PIXEL / 日付: 2017年8月10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: 1.54187 Å / 相対比: 1 |
反射 | 解像度: 1.88→26.62 Å / Num. all: 144706 / Num. obs: 23804 / % possible obs: 99.8 % / 冗長度: 6.1 % / CC1/2: 0.998 / Rrim(I) all: 0.083 / Net I/σ(I): 15.5 |
反射 シェル | 解像度: 1.88→1.93 Å / 冗長度: 5.7 % / Mean I/σ(I) obs: 6.3 / Num. unique all: 8396 / Num. unique obs: 1454 / CC1/2: 0.969 / Rrim(I) all: 0.228 / % possible all: 98.8 |
-
解析
ソフトウェア |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
精密化 | 構造決定の手法: ![]() 開始モデル: 5MOC 解像度: 1.88→26.62 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.912 / SU B: 2.455 / SU ML: 0.075 / 交差検証法: FREE R-VALUE / ESU R: 0.124 / ESU R Free: 0.128 / 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 12.645 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 1.88→26.62 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
拘束条件 |
|