+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1urc | |||||||||
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タイトル | Cyclin A binding groove inhibitor Ace-Arg-Lys-Leu-Phe-Gly | |||||||||
要素 |
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キーワード | TRANSFERASE/INHIBITOR / TRANSFERASE-INHIBITOR COMPLEX / INHIBITOR / LIGAND EXCHANGE / DRUG DESIGN / PEPTIDOMIMETICS | |||||||||
機能・相同性 | 機能・相同性情報 Phosphorylation of proteins involved in the G2/M transition by Cyclin A:Cdc2 complexes / cyclin A2-CDK1 complex / cell cycle G1/S phase transition / cellular response to luteinizing hormone stimulus / mitotic cell cycle phase transition / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / cellular response to leptin stimulus / male pronucleus / female pronucleus / cellular response to cocaine ...Phosphorylation of proteins involved in the G2/M transition by Cyclin A:Cdc2 complexes / cyclin A2-CDK1 complex / cell cycle G1/S phase transition / cellular response to luteinizing hormone stimulus / mitotic cell cycle phase transition / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / cellular response to leptin stimulus / male pronucleus / female pronucleus / cellular response to cocaine / response to glucagon / cyclin-dependent protein serine/threonine kinase regulator activity / cellular response to insulin-like growth factor stimulus / positive regulation of DNA biosynthetic process / cochlea development / cyclin A1-CDK2 complex / cyclin E2-CDK2 complex / cyclin E1-CDK2 complex / cellular response to platelet-derived growth factor stimulus / cyclin A2-CDK2 complex / positive regulation of DNA-templated DNA replication initiation / G2 Phase / cyclin-dependent protein kinase activity / Y chromosome / Phosphorylation of proteins involved in G1/S transition by active Cyclin E:Cdk2 complexes / positive regulation of heterochromatin formation / p53-Dependent G1 DNA Damage Response / X chromosome / PTK6 Regulates Cell Cycle / regulation of DNA replication / regulation of anaphase-promoting complex-dependent catabolic process / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / centriole replication / Regulation of APC/C activators between G1/S and early anaphase / centrosome duplication / Telomere Extension By Telomerase / G0 and Early G1 / Activation of the pre-replicative complex / cellular response to nitric oxide / cyclin-dependent protein kinase holoenzyme complex / cyclin-dependent kinase / animal organ regeneration / cyclin-dependent protein serine/threonine kinase activity / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / Activation of ATR in response to replication stress / Cyclin E associated events during G1/S transition / Cyclin A/B1/B2 associated events during G2/M transition / Cajal body / Cyclin A:Cdk2-associated events at S phase entry / condensed chromosome / mitotic G1 DNA damage checkpoint signaling / regulation of mitotic cell cycle / regulation of G2/M transition of mitotic cell cycle / cyclin binding / post-translational protein modification / : / meiotic cell cycle / positive regulation of DNA replication / male germ cell nucleus / cellular response to estradiol stimulus / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / potassium ion transport / DNA Damage/Telomere Stress Induced Senescence / CDK-mediated phosphorylation and removal of Cdc6 / Meiotic recombination / SCF(Skp2)-mediated degradation of p27/p21 / Orc1 removal from chromatin / G1/S transition of mitotic cell cycle / Transcriptional regulation of granulopoiesis / G2/M transition of mitotic cell cycle / Cyclin D associated events in G1 / cellular senescence / positive regulation of fibroblast proliferation / Regulation of TP53 Degradation / nuclear envelope / Factors involved in megakaryocyte development and platelet production / Processing of DNA double-strand break ends / cellular response to hypoxia / Senescence-Associated Secretory Phenotype (SASP) / regulation of gene expression / peptidyl-serine phosphorylation / DNA replication / Regulation of TP53 Activity through Phosphorylation / transcription regulator complex / Ras protein signal transduction / chromosome, telomeric region / Ub-specific processing proteases / endosome / chromatin remodeling / protein domain specific binding / cell division / protein phosphorylation / DNA repair / protein serine kinase activity / protein serine/threonine kinase activity / DNA-templated transcription / centrosome / positive regulation of cell population proliferation / protein kinase binding / positive regulation of DNA-templated transcription 類似検索 - 分子機能 | |||||||||
生物種 | Homo sapiens (ヒト) synthetic construct (人工物) | |||||||||
手法 | X線回折 / シンクロトロン / 分子置換 / 解像度: 2.6 Å | |||||||||
データ登録者 | Kontopidis, G. / Andrews, M. / McInnes, C. / Cowan, A. / Powers, H. / Innes, L. / Plater, A. / Griffiths, G. / Paterson, D. / Zheleva, D. ...Kontopidis, G. / Andrews, M. / McInnes, C. / Cowan, A. / Powers, H. / Innes, L. / Plater, A. / Griffiths, G. / Paterson, D. / Zheleva, D. / Lane, D. / Green, S. / Walkinshaw, M. / Fischer, P. | |||||||||
引用 | ジャーナル: Org. Biomol. Chem. / 年: 2004 タイトル: Design, synthesis, biological activity and structural analysis of cyclic peptide inhibitors targeting the substrate recruitment site of cyclin-dependent kinase complexes. 著者: Andrews, M.J. / McInnes, C. / Kontopidis, G. / Innes, L. / Cowan, A. / Plater, A. / Fischer, P.M. | |||||||||
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 | 1urc.cif.gz | 240.8 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb1urc.ent.gz | 195.2 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1urc.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
文書・要旨 | 1urc_validation.pdf.gz | 442.9 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 1urc_full_validation.pdf.gz | 487.7 KB | 表示 | |
XML形式データ | 1urc_validation.xml.gz | 29 KB | 表示 | |
CIF形式データ | 1urc_validation.cif.gz | 44.2 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/ur/1urc ftp://data.pdbj.org/pub/pdb/validation_reports/ur/1urc | HTTPS FTP |
-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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単位格子 |
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-要素
#1: タンパク質 | 分子量: 33976.488 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) 発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ) 参照: UniProt: P24941, EC: 2.7.1.37, cyclin-dependent kinase #2: タンパク質 | 分子量: 29867.512 Da / 分子数: 2 / Fragment: RESIDUES 173 - 432 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P20248 #3: タンパク質・ペプチド | 分子量: 647.810 Da / 分子数: 2 / 由来タイプ: 合成 詳細: CYCLIN GROOVE-BOUND CYCLIC(2-5) PENTAPEPTIDE AC-ARG-LYS-LEU-PHE-GLY 由来: (合成) synthetic construct (人工物) #4: 水 | ChemComp-HOH / | 構成要素の詳細 | CYCLIN CONTROLS THE CELL CYCLE AT THE G1/S (START) AND THE G2/M (MITOSIS) TRANSITIONS. KINASE ...CYCLIN CONTROLS THE CELL CYCLE AT THE G1/S (START) AND THE G2/M (MITOSIS) TRANSITION | |
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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: 2.7 Å3/Da / 溶媒含有率: 54 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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結晶化 | pH: 7.8 / 詳細: 22% PEG 3350, 0.1M NA3-CIT, pH 7.80 | |||||||||||||||||||||||||||||||||||||||||||||||||
結晶化 | *PLUS 温度: 17 ℃ / pH: 7 / 手法: 蒸気拡散法, ハンギングドロップ法 / 詳細: Kontopidis, G., (2003) Structure, 11, 1537. | |||||||||||||||||||||||||||||||||||||||||||||||||
溶液の組成 | *PLUS
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-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: SRS / ビームライン: PX14.1 / 波長: 1.488 |
検出器 | タイプ: ADSC CCD / 検出器: CCD / 日付: 2002年10月15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: 1.488 Å / 相対比: 1 |
反射 | 解像度: 2.6→17 Å / Num. obs: 39765 / % possible obs: 99.5 % / 冗長度: 14.2 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 5.8 |
反射 シェル | 解像度: 2.6→2.76 Å / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 1 / % possible all: 99.4 |
反射 | *PLUS 最高解像度: 2.6 Å / Num. obs: 46681 / % possible obs: 98.9 % / Num. measured all: 113421 / Rmerge(I) obs: 0.11 |
反射 シェル | *PLUS 最高解像度: 2.6 Å / 最低解像度: 2.74 Å / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 1 |
-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: PDB ENTRY 1FIN 解像度: 2.6→14 Å / SU B: 12.153 / SU ML: 0.25 / 交差検証法: THROUGHOUT / ESU R: 1.013 / ESU R Free: 0.327 / 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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原子変位パラメータ | Biso mean: 42.1 Å2
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精密化ステップ | サイクル: LAST / 解像度: 2.6→14 Å
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精密化 | *PLUS Rfactor Rfree: 0.255 | ||||||||||||||||||||
溶媒の処理 | *PLUS | ||||||||||||||||||||
原子変位パラメータ | *PLUS |