+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 3pd1 | ||||||
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タイトル | Caspase-3 K242A | ||||||
要素 |
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キーワード | HYDROLASE/HYDROLASE INHIBITOR / Salt Bridge / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
機能・相同性 | 機能・相同性情報 caspase-3 / Stimulation of the cell death response by PAK-2p34 / phospholipase A2 activator activity / anterior neural tube closure / intrinsic apoptotic signaling pathway in response to osmotic stress / leukocyte apoptotic process / positive regulation of pyroptotic inflammatory response / glial cell apoptotic process / NADE modulates death signalling / luteolysis ...caspase-3 / Stimulation of the cell death response by PAK-2p34 / phospholipase A2 activator activity / anterior neural tube closure / intrinsic apoptotic signaling pathway in response to osmotic stress / leukocyte apoptotic process / positive regulation of pyroptotic inflammatory response / glial cell apoptotic process / NADE modulates death signalling / luteolysis / response to cobalt ion / cysteine-type endopeptidase activity involved in apoptotic signaling pathway / death-inducing signaling complex / cellular response to staurosporine / cyclin-dependent protein serine/threonine kinase inhibitor activity / Apoptosis induced DNA fragmentation / cysteine-type endopeptidase activity involved in execution phase of apoptosis / Caspase activation via Dependence Receptors in the absence of ligand / Apoptotic cleavage of cell adhesion proteins / death receptor binding / SMAC, XIAP-regulated apoptotic response / Activation of caspases through apoptosome-mediated cleavage / axonal fasciculation / Signaling by Hippo / cysteine-type endopeptidase activity involved in apoptotic process / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / fibroblast apoptotic process / negative regulation of cytokine production / epithelial cell apoptotic process / platelet formation / execution phase of apoptosis / Other interleukin signaling / positive regulation of amyloid-beta formation / Apoptotic cleavage of cellular proteins / pyroptotic inflammatory response / negative regulation of B cell proliferation / T cell homeostasis / negative regulation of activated T cell proliferation / B cell homeostasis / neurotrophin TRK receptor signaling pathway / protein maturation / negative regulation of cell cycle / response to X-ray / response to amino acid / Caspase-mediated cleavage of cytoskeletal proteins / cell fate commitment / regulation of macroautophagy / response to tumor necrosis factor / Pyroptosis / response to glucose / response to UV / response to glucocorticoid / keratinocyte differentiation / enzyme activator activity / striated muscle cell differentiation / Degradation of the extracellular matrix / intrinsic apoptotic signaling pathway / erythrocyte differentiation / hippocampus development / apoptotic signaling pathway / sensory perception of sound / response to nicotine / regulation of protein stability / protein catabolic process / response to hydrogen peroxide / neuron differentiation / protein processing / response to wounding / positive regulation of neuron apoptotic process / response to estradiol / heart development / peptidase activity / protease binding / neuron apoptotic process / response to lipopolysaccharide / aspartic-type endopeptidase activity / learning or memory / response to hypoxia / response to xenobiotic stimulus / cysteine-type endopeptidase activity / neuronal cell body / DNA damage response / protein-containing complex binding / apoptotic process / proteolysis / nucleoplasm / nucleus / cytosol / cytoplasm 類似検索 - 分子機能 | ||||||
生物種 | Homo sapiens (ヒト) | ||||||
手法 | X線回折 / シンクロトロン / 解像度: 1.62 Å | ||||||
データ登録者 | Walters, J. / Swartz, P. / Mattos, C. / Clark, A.C. | ||||||
引用 | ジャーナル: Arch.Biochem.Biophys. / 年: 2011 タイトル: Thermodynamic, enzymatic and structural effects of removing a salt bridge at the base of loop 4 in (pro)caspase-3. 著者: Walters, J. / Swartz, P. / Mattos, C. / Clark, A.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 | 3pd1.cif.gz | 63.6 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb3pd1.ent.gz | 50.4 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 3pd1.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/pd/3pd1 ftp://data.pdbj.org/pub/pdb/validation_reports/pd/3pd1 | HTTPS FTP |
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-関連構造データ
-リンク
-集合体
登録構造単位 |
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1 |
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2 |
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3 |
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単位格子 |
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Components on special symmetry positions |
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-要素
#1: タンパク質 | 分子量: 28612.570 Da / 分子数: 1 / 断片: UNP residues 29-277 / 変異: K242A / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: CASP3, CPP32 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3) LysS / 参照: UniProt: P42574, caspase-3 |
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#2: タンパク質・ペプチド | |
#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 |
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-試料調製
結晶 | マシュー密度: 2.4 Å3/Da / 溶媒含有率: 48.65 % |
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結晶化 | 温度: 291 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 8.5 詳細: Inhibitor, Ac-DEVD-CMK, reconstituted in DMSO, was added at a 5:1 inhibitor:protein ratio (w/w). Final buffer consisted of 10 mM Tris-HCl (pH 8.5), 10 mM DTT, 3 mM NaN3., VAPOR DIFFUSION, ...詳細: Inhibitor, Ac-DEVD-CMK, reconstituted in DMSO, was added at a 5:1 inhibitor:protein ratio (w/w). Final buffer consisted of 10 mM Tris-HCl (pH 8.5), 10 mM DTT, 3 mM NaN3., VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-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: シンクロトロン / サイト: APS / ビームライン: 22-ID / 波長: 1 Å |
検出器 | タイプ: MAR scanner 300 mm plate / 検出器: IMAGE PLATE / 日付: 2005年2月3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 Å / 相対比: 1 |
反射 | 解像度: 1.62→50 Å / Num. all: 34489 / Num. obs: 34489 / % possible obs: 95.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 |
反射 シェル | 解像度: 1.62→1.68 Å / % possible all: 99 |
-解析
ソフトウェア |
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精密化 | 解像度: 1.62→33.71 Å / Occupancy max: 1 / Occupancy min: 0.05 / σ(F): 0
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溶媒の処理 | Bsol: 23.8611 Å2 | ||||||||||||||||||||||||||||
原子変位パラメータ | Biso max: 54.86 Å2 / Biso mean: 18.6835 Å2 / Biso min: 7.93 Å2
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精密化ステップ | サイクル: LAST / 解像度: 1.62→33.71 Å
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拘束条件 |
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