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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: 6vbx | ||||||
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タイトル | Crystal structure of Mcl-1 in complex with 138E12 peptide, Lys-covalent antagonist | ||||||
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![]() | APOPTOSIS / MCL-1 / 138E12 peptide / Lys-covalent antagonists | ||||||
機能・相同性 | ![]() BIM-BCL-xl complex / BIM-BCL-2 complex / regulation of developmental pigmentation / RUNX3 regulates BCL2L11 (BIM) transcription / positive regulation of mitochondrial membrane permeability involved in apoptotic process / developmental pigmentation / Activation of BIM and translocation to mitochondria / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / positive regulation of fibroblast apoptotic process / apoptotic process involved in embryonic digit morphogenesis ...BIM-BCL-xl complex / BIM-BCL-2 complex / regulation of developmental pigmentation / RUNX3 regulates BCL2L11 (BIM) transcription / positive regulation of mitochondrial membrane permeability involved in apoptotic process / developmental pigmentation / Activation of BIM and translocation to mitochondria / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / positive regulation of fibroblast apoptotic process / apoptotic process involved in embryonic digit morphogenesis / ear development / meiosis I / positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / mammary gland development / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / cell fate determination / cellular homeostasis / positive regulation of T cell apoptotic process / tube formation / regulation of organ growth / cellular response to glucocorticoid stimulus / channel activity / mitochondrial fusion / Bcl-2 family protein complex / myeloid cell homeostasis / BH domain binding / FOXO-mediated transcription of cell death genes / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / NRAGE signals death through JNK / thymocyte apoptotic process / T cell homeostasis / odontogenesis of dentin-containing tooth / BH3 domain binding / positive regulation of IRE1-mediated unfolded protein response / positive regulation of release of cytochrome c from mitochondria / B cell homeostasis / negative regulation of anoikis / protein transmembrane transporter activity / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / endomembrane system / positive regulation of cell cycle / positive regulation of intrinsic apoptotic signaling pathway / extrinsic apoptotic signaling pathway in absence of ligand / spleen development / FLT3 Signaling / response to endoplasmic reticulum stress / negative regulation of autophagy / cell-matrix adhesion / release of cytochrome c from mitochondria / post-embryonic development / thymus development / kidney development / response to cytokine / positive regulation of protein-containing complex assembly / activation of cysteine-type endopeptidase activity involved in apoptotic process / male gonad development / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of neuron apoptotic process / Signaling by BRAF and RAF1 fusions / Signaling by ALK fusions and activated point mutants / spermatogenesis / microtubule binding / Interleukin-4 and Interleukin-13 signaling / regulation of apoptotic process / in utero embryonic development / mitochondrial outer membrane / positive regulation of apoptotic process / protein heterodimerization activity / DNA damage response / negative regulation of apoptotic process / apoptotic process / protein kinase binding / mitochondrion / nucleoplasm / membrane / nucleus / cytosol / cytoplasm 類似検索 - 分子機能 | ||||||
生物種 | ![]() synthetic construct (人工物) | ||||||
手法 | ![]() ![]() ![]() | ||||||
![]() | Pellecchia, M. / Perry, J.J. / Kenjic, N. / Assar, Z. | ||||||
資金援助 | ![]()
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![]() | ![]() タイトル: Design, Synthesis, and Structural Characterization of Lysine Covalent BH3 Peptides Targeting Mcl-1. 著者: Gambini, L. / Udompholkul, P. / Baggio, C. / Muralidharan, A. / Kenjic, N. / Assar, Z. / Perry, J.J.P. / Pellecchia, M. #1: ジャーナル: Meth. Enzymol. / 年: 1997 タイトル: Processing of X-ray diffraction data collected in oscillation mode. 著者: Otwinowski, Z. / Minor, W. #2: ジャーナル: J Appl Crystallogr / 年: 2007 タイトル: Phaser crystallographic software. 著者: McCoy, A.J. / Grosse-Kunstleve, R.W. / Adams, P.D. / Winn, M.D. / Storoni, L.C. / Read, R.J. #3: ジャーナル: Acta Crystallogr. D Biol. Crystallogr. / 年: 2004 タイトル: REFMAC5 dictionary: organization of prior chemical knowledge and guidelines for its use. 著者: Vagin, A.A. / Steiner, R.A. / Lebedev, A.A. / Potterton, L. / McNicholas, S. / Long, F. / Murshudov, G.N. #4: ジャーナル: Acta Crystallogr D Biol Crystallogr / 年: 2004 タイトル: Coot: model-building tools for molecular graphics. 著者: Paul Emsley / Kevin Cowtan / ![]() 要旨: CCP4mg is a project that aims to provide a general-purpose tool for structural biologists, providing tools for X-ray structure solution, structure comparison and analysis, and publication-quality ...CCP4mg is a project that aims to provide a general-purpose tool for structural biologists, providing tools for X-ray structure solution, structure comparison and analysis, and publication-quality graphics. The map-fitting tools are available as a stand-alone package, distributed as 'Coot'. | ||||||
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 | ![]() | 56.3 KB | 表示 | ![]() |
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PDB形式 | ![]() | 31.4 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 | ![]() 2nl9S 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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要素
#1: タンパク質 | 分子量: 17850.330 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: タンパク質・ペプチド | 分子量: 1805.020 Da / 分子数: 1 / 由来タイプ: 合成 詳細: This is a chemically synthesized peptide with unnatural ligand (see ligand section) on the N-terminal end. Ligands is covalently attached to Lys234 of chain A. 由来: (合成) synthetic construct (人工物) / 参照: UniProt: O43521*PLUS |
#3: 水 | ChemComp-HOH / |
研究の焦点であるリガンドがあるか | Y |
-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: 2.18 Å3/Da / 溶媒含有率: 43.55 % |
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結晶化 | 温度: 298 K / 手法: 蒸気拡散法, シッティングドロップ法 詳細: 0.5M Potassium Thiocyanate, 0.1M Sodium Acetate:HCL pH4.6 |
-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: ![]() ![]() ![]() |
検出器 | タイプ: DECTRIS EIGER X 9M / 検出器: PIXEL / 日付: 2019年10月31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: 1.127 Å / 相対比: 1 |
反射 | 解像度: 1.95→34.001 Å / Num. obs: 12721 / % possible obs: 99.75 % / 冗長度: 7.9 % / Biso Wilson estimate: 32.63 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 22 |
反射 シェル | 解像度: 1.955→2.025 Å / 冗長度: 8.4 % / Rmerge(I) obs: 0.276 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1235 / % possible all: 100 |
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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: 2NL9 解像度: 1.95→34 Å / SU ML: 0.2912 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 34.0423 立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
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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 / 溶媒モデル: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 35.58 Å2 | ||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 1.95→34 Å
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拘束条件 |
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LS精密化 シェル |
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