+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 6slv | ||||||
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タイトル | Fragment AZ-013 binding at the p53pT387/14-3-3 sigma interface | ||||||
要素 |
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キーワード | PEPTIDE BINDING PROTEIN / protein protein interaction / fragment soaking / stabilization | ||||||
機能・相同性 | 機能・相同性情報 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 / germ cell nucleus / regulation of mitochondrial membrane permeability involved in apoptotic process / RUNX3 regulates CDKN1A transcription / 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 / negative regulation of neuroblast proliferation / Regulation of TP53 Activity through Association with Co-factors / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / mitochondrial DNA repair / T cell lineage commitment / ER overload response / regulation of epidermal cell division / protein kinase C inhibitor activity / negative regulation of DNA replication / 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 / negative regulation of telomere maintenance via telomerase / SUMOylation of transcription factors / Regulation of localization of FOXO transcription factors / intrinsic apoptotic signaling pathway by p53 class mediator / general transcription initiation factor binding / keratinocyte proliferation / mitophagy / Transcriptional Regulation by VENTX / DNA damage response, signal transduction by p53 class mediator / response to X-ray / phosphoserine residue binding / replicative senescence / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / neuroblast proliferation / cellular response to UV-C / : / Activation of BAD and translocation to mitochondria / negative regulation of reactive oxygen species metabolic process / hematopoietic stem cell differentiation / chromosome organization / positive regulation of RNA polymerase II transcription preinitiation complex assembly / negative regulation of keratinocyte proliferation / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / T cell proliferation involved in immune response / glial cell proliferation / establishment of skin barrier / Pyroptosis / cis-regulatory region sequence-specific DNA binding / embryonic organ development / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / hematopoietic progenitor cell differentiation / 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 / type II interferon-mediated signaling pathway 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: 1.9 Å | ||||||
データ登録者 | Ottmann, C. / Wolter, M. / Guillory, X. / Leysen, S. / Genet, S. / Somsen, B. / Patel, J. / Castaldi, P. | ||||||
資金援助 | オランダ, 1件
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引用 | ジャーナル: J.Med.Chem. / 年: 2020 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 |
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-構造の表示
構造ビューア | 分子: MolmilJmol/JSmol |
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-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 6slv.cif.gz | 137.5 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb6slv.ent.gz | 86.9 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 6slv.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/sl/6slv ftp://data.pdbj.org/pub/pdb/validation_reports/sl/6slv | HTTPS FTP |
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-関連構造データ
関連構造データ | 6r5lC 6rhcC 6rjlC 6rjqC 6rjzC 6rk8C 6rkiC 6rkkC 6rkmC 6rl3C 6rl4C 6rl6C 6rm5C 6rm7C 6rp6C 6rwhC 6rwiC 6rwsC 6rwuC 6rx2C 6s39C 6s3cC 6s40C 6s9qC 6sinC 6sioC 6sipC 6siqC 6slwC 6slxC 5mocS C: 同じ文献を引用 (文献) S: 精密化の開始モデル |
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類似構造データ |
-リンク
-集合体
登録構造単位 |
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1 |
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単位格子 |
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Components on special symmetry positions |
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-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: 26542.914 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: SFN, HME1 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P31947 |
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#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) Homo sapiens (ヒト) / 参照: UniProt: P04637 |
-非ポリマー , 4種, 284分子
#3: 化合物 | #4: 化合物 | ChemComp-CL / | #5: 化合物 | ChemComp-LJW / | #6: 水 | ChemComp-HOH / | |
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-詳細
研究の焦点であるリガンドがあるか | Y |
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-実験情報
-実験
実験 | 手法: X線回折 / 使用した結晶の数: 1 |
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-試料調製
結晶 | マシュー密度: 2.59 Å3/Da / 溶媒含有率: 52.5 % |
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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 |
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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: 2016年10月14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: 1.9→41.84 Å / Num. obs: 23310 / % possible obs: 99.97 % / 冗長度: 2 % / Biso Wilson estimate: 11.2288685469 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.05203 / Rrim(I) all: 0.07358 / Net I/σ(I): 10.31 |
反射 シェル | 解像度: 1.9→1.968 Å / Rmerge(I) obs: 0.1837 / Mean I/σ(I) obs: 2.98 / Num. unique obs: 2300 / CC1/2: 0.916 / Rrim(I) all: 0.2598 / % possible all: 100 |
-解析
ソフトウェア |
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精密化 | 構造決定の手法: 分子置換 開始モデル: 5MOC 解像度: 1.9→41.84 Å / 交差検証法: FREE R-VALUE
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精密化ステップ | サイクル: LAST / 解像度: 1.9→41.84 Å
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拘束条件 |
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LS精密化 シェル |
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