+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 6e2b | |||||||||
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タイトル | Ubiquitin in complex with Pt(2-phenilpyridine)(PPh3) | |||||||||
要素 | Ubiquitinユビキチン | |||||||||
キーワード | PROTEIN BINDING (タンパク質) / cyclometallated platinum (II) complex / ubiquitin (ユビキチン) / platinum coordination | |||||||||
機能・相同性 | 機能・相同性情報 Translesion synthesis by REV1 / Recognition of DNA damage by PCNA-containing replication complex / Translesion Synthesis by POLH / Downregulation of ERBB4 signaling / Spry regulation of FGF signaling / Downregulation of ERBB2:ERBB3 signaling / NOD1/2 Signaling Pathway / APC/C:Cdc20 mediated degradation of Cyclin B / SCF-beta-TrCP mediated degradation of Emi1 / APC-Cdc20 mediated degradation of Nek2A ...Translesion synthesis by REV1 / Recognition of DNA damage by PCNA-containing replication complex / Translesion Synthesis by POLH / Downregulation of ERBB4 signaling / Spry regulation of FGF signaling / Downregulation of ERBB2:ERBB3 signaling / NOD1/2 Signaling Pathway / APC/C:Cdc20 mediated degradation of Cyclin B / SCF-beta-TrCP mediated degradation of Emi1 / APC-Cdc20 mediated degradation of Nek2A / EGFR downregulation / TCF dependent signaling in response to WNT / NRIF signals cell death from the nucleus / p75NTR recruits signalling complexes / NF-kB is activated and signals survival / Activated NOTCH1 Transmits Signal to the Nucleus / Downregulation of TGF-beta receptor signaling / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / Downregulation of SMAD2/3:SMAD4 transcriptional activity / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Senescence-Associated Secretory Phenotype (SASP) / Regulation of innate immune responses to cytosolic DNA / activated TAK1 mediates p38 MAPK activation / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Regulation of FZD by ubiquitination / PINK1-PRKN Mediated Mitophagy / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Regulation of TNFR1 signaling / TNFR1-induced NF-kappa-B signaling pathway / Translesion synthesis by POLK / Translesion synthesis by POLI / Regulation of necroptotic cell death / MAP3K8 (TPL2)-dependent MAPK1/3 activation / HDR through Homologous Recombination (HRR) / Josephin domain DUBs / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / DNA Damage Recognition in GG-NER / Formation of Incision Complex in GG-NER / Gap-filling DNA repair synthesis and ligation in GG-NER / Dual Incision in GG-NER / Fanconi Anemia Pathway / Regulation of TP53 Activity through Phosphorylation / Regulation of TP53 Degradation / Regulation of TP53 Activity through Methylation / Negative regulation of MET activity / Cyclin D associated events in G1 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Downregulation of ERBB2 signaling / E3 ubiquitin ligases ubiquitinate target proteins / Regulation of PTEN localization / ER Quality Control Compartment (ERQC) / Regulation of expression of SLITs and ROBOs / Interferon alpha/beta signaling / Endosomal Sorting Complex Required For Transport (ESCRT) / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / IKK complex recruitment mediated by RIP1 / IRAK2 mediated activation of TAK1 complex / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Alpha-protein kinase 1 signaling pathway / RAS processing / Pexophagy / Inactivation of CSF3 (G-CSF) signaling / Negative regulation of FLT3 / Regulation of BACH1 activity / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Regulation of NF-kappa B signaling / Termination of translesion DNA synthesis / Ovarian tumor domain proteases / Negative regulators of DDX58/IFIH1 signaling / Negative regulation of FGFR1 signaling / Negative regulation of FGFR2 signaling / Negative regulation of FGFR3 signaling / Negative regulation of FGFR4 signaling / Negative regulation of MAPK pathway / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Iron uptake and transport / Deactivation of the beta-catenin transactivating complex / Metalloprotease DUBs / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / Activation of NF-kappaB in B cells / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / SCF(Skp2)-mediated degradation of p27/p21 / FCERI mediated NF-kB activation / Autodegradation of the E3 ubiquitin ligase COP1 / Asymmetric localization of PCP proteins / Degradation of AXIN / Degradation of DVL / Hedgehog ligand biogenesis / Dectin-1 mediated noncanonical NF-kB signaling / CLEC7A (Dectin-1) signaling / Degradation of GLI1 by the proteasome / Hedgehog 'on' state / TNFR2 non-canonical NF-kB pathway / NIK-->noncanonical NF-kB signaling / Assembly of the pre-replicative complex 類似検索 - 分子機能 | |||||||||
生物種 | Bos taurus (ウシ) | |||||||||
手法 | X線回折 / シンクロトロン / 分子置換 / 解像度: 1.45 Å | |||||||||
データ登録者 | Zhemkov, V.A. / Kim, M. | |||||||||
資金援助 | ロシア, 2件
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引用 | ジャーナル: Inorg Chem / 年: 2019 タイトル: Reactions of Cyclometalated Platinum(II) [Pt(N∧C)(PR3)Cl] Complexes with Imidazole and Imidazole-Containing Biomolecules: Fine-Tuning of Reactivity and Photophysical Properties via Ligand Design. 著者: Solomatina, A.I. / Chelushkin, P.S. / Abakumova, T.O. / Zhemkov, V.A. / Kim, M. / Bezprozvanny, I. / Gurzhiy, V.V. / Melnikov, A.S. / Anufrikov, Y.A. / Koshevoy, I.O. / Su, S.H. / Chou, P.T. / Tunik, S.P. | |||||||||
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 | 6e2b.cif.gz | 222.4 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb6e2b.ent.gz | 179.5 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 6e2b.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/e2/6e2b ftp://data.pdbj.org/pub/pdb/validation_reports/e2/6e2b | HTTPS FTP |
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-関連構造データ
関連構造データ | 1ubqS 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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単位格子 |
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-要素
#1: タンパク質 | 分子量: 8576.831 Da / 分子数: 6 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / Cell: erythrocytes / 参照: UniProt: P62992 #2: 化合物 | ChemComp-SO4 / #3: 化合物 | ChemComp-GOL / #4: 化合物 | #5: 水 | ChemComp-HOH / | |
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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: 2.99 Å3/Da / 溶媒含有率: 58.85 % / 解説: prism |
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結晶化 | 温度: 289 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 5.5 詳細: 3M ammonium sulfate, 0.1M sodium citrate buffer, pH 5.5 |
-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: シンクロトロン / サイト: APS / ビームライン: 19-ID / 波長: 0.987 Å |
検出器 | タイプ: ADSC QUANTUM 315r / 検出器: CCD / 日付: 2017年3月25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: 0.987 Å / 相対比: 1 |
反射 | 解像度: 1.45→99.26 Å / Num. obs: 110120 / % possible obs: 98.99 % / 冗長度: 12.9 % / CC1/2: 0.476 / Rmerge(I) obs: 0.16 / Rpim(I) all: 0.069 / Rrim(I) all: 0.168 / Rsym value: 0.112 / Χ2: 0.866 / Net I/σ(I): 13.8 |
反射 シェル | 解像度: 1.45→1.48 Å / 冗長度: 10.8 % / Mean I/σ(I) obs: 1.58 / Num. unique obs: 5428 / CC1/2: 0.476 / Rpim(I) all: 0.566 / Χ2: 0.953 / % possible all: 36.7 |
-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: 1UBQ 解像度: 1.45→99.26 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.89 / SU ML: 0.049 / 交差検証法: THROUGHOUT / ESU R: 0.065 / ESU R Free: 0.067 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD / 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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溶媒の処理 | イオンプローブ半径: 1 Å / 減衰半径: 1 Å / VDWプローブ半径: 1.5 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 19.681 Å2
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精密化ステップ | サイクル: 1 / 解像度: 1.45→99.26 Å
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拘束条件 |
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