+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 2k4l | ||||||||||||||||||
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タイトル | Solution structure of a 2:1C2-(2-naphthyl)pyrrolo[2,1-c][1,4]benzodiazepine (PBD) DNA adduct: molecular basis for unexpectedly high DNA helix stabilization. | ||||||||||||||||||
要素 | 5'-D(*キーワード | DNA / pyrrolo[2 / 1-c][1 / 4]benzodiazepine / PBD / DNA Adduct | 機能・相同性 | Chem-PZD / DNA / DNA (> 10) | 機能・相同性情報 手法 | 溶液NMR / simulated annealing | データ登録者 | Antonow, D. / Barata, T. / Jenkins, T.C. / Parkinson, G.N. / Howard, P.W. / Thurston, D.E. / Zloh, M. | 引用 | ジャーナル: Biochemistry / 年: 2008 タイトル: Solution structure of a 2:1 C2-(2-naphthyl) pyrrolo[2,1-c][1,4]benzodiazepine DNA adduct: molecular basis for unexpectedly high DNA helix stabilization. 著者: Antonow, D. / Barata, T. / Jenkins, T.C. / Parkinson, G.N. / Howard, P.W. / Thurston, D.E. / Zloh, M. #1: ジャーナル: J.Comb.Chem. / 年: 2007 タイトル: Parallel Synthesis of a Novel C2-Aryl Pyrrolo[2,1-c][1,4]benzodiazepine (PBD) Library 著者: Antonow, D. / Cooper, N. / Howard, P.W. / Thurston, D.E. 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 | 2k4l.cif.gz | 200.6 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb2k4l.ent.gz | 165.9 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 2k4l.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 | 2k4l_validation.pdf.gz | 458.4 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 2k4l_full_validation.pdf.gz | 518.1 KB | 表示 | |
XML形式データ | 2k4l_validation.xml.gz | 13.8 KB | 表示 | |
CIF形式データ | 2k4l_validation.cif.gz | 21 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/k4/2k4l ftp://data.pdbj.org/pub/pdb/validation_reports/k4/2k4l | HTTPS FTP |
-関連構造データ
類似構造データ | |
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その他のデータベース |
-リンク
-集合体
登録構造単位 |
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1 |
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NMR アンサンブル |
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-要素
#1: DNA鎖 | 分子量: 4277.827 Da / 分子数: 2 / 由来タイプ: 合成 詳細: THE 14-MER NUCLEOTIDE SEQUENCE AATCTTTAAAGATT WAS SYNTHESISED USING AN APPLIED BIOSYSTEMS DNA SYNTHESIZER. THE DNA SEQUENCE WAS PURIFIED BY REVERSED-PHASE HPLC AT ROOM TEMPERATURE. THE DUPLEX ...詳細: THE 14-MER NUCLEOTIDE SEQUENCE AATCTTTAAAGATT WAS SYNTHESISED USING AN APPLIED BIOSYSTEMS DNA SYNTHESIZER. THE DNA SEQUENCE WAS PURIFIED BY REVERSED-PHASE HPLC AT ROOM TEMPERATURE. THE DUPLEX WAS FORMED BY ANNEALING IN PHOSPHATE BUFFER. #2: 化合物 | |
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-実験情報
-実験
実験 | 手法: 溶液NMR | ||||||||||||||||
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NMR実験 |
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-試料調製
詳細 | 内容: 0.68 mM DNA (5'-D(*(DA)P*(DA)P*(DT)P*(DC)P*(DT)P*(DT)P*(DT)P*(DA)P*(DA)P*(DA)P*(DG)P*(DA)P*(DT)P*(DT))-3'), 90% H2O/10% D2O 溶媒系: 90% H2O/10% D2O |
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試料 | 濃度: 0.68 mM / 構成要素: DNA |
試料状態 | イオン強度: 130 / pH: 6.85 / 圧: ambient / 温度: 298 K |
-NMR測定
NMRスペクトロメーター | タイプ: Bruker Avance / 製造業者: Bruker / モデル: AVANCE / 磁場強度: 500 MHz |
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-解析
NMR software |
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精密化 | 手法: simulated annealing / ソフトェア番号: 1 詳細: DISTANCES RESTRAINTS WERE CALCULATED FROM THREE-DIMENSIONAL NOESY PEAK VOLUMES BY COMPARING TO REFERENCE VOLUME OF CYTOSINE (2.45 A BETWEEN H5 AND H6). ALL DISTANCE CONSTRAINTS WERE ...詳細: DISTANCES RESTRAINTS WERE CALCULATED FROM THREE-DIMENSIONAL NOESY PEAK VOLUMES BY COMPARING TO REFERENCE VOLUME OF CYTOSINE (2.45 A BETWEEN H5 AND H6). ALL DISTANCE CONSTRAINTS WERE CLASSIFIED ACCORDING TO CROSSPEAK INTENSITIES AS (S) STRONG (1.80 TO 2.90), (M) MEDIUM (1.80 TO 4.00) AND (W) WEAK (D = 4.0, -2.2/+1.0 ). DISTANCE CONSTRAINS WITH METHYL PROTONS WERE CONSIDERED SEPARATELY (D = 4.0 , -2.2/+1.5 ). THE SIMULATED ANNEALING APPROACH WAS USED TO GENERATE 200 STRUCTURES. THE 10 LOWEST ENERGY STRUCTURES WERE CHOSEN AND THE ROOT MEAN SQUARE DEVIATION VALUES CALCULATED. | ||||||||||||||||||||||||
NMR constraints | NOE constraints total: 374 / NOE intraresidue total count: 174 / NOE long range total count: 40 / NOE medium range total count: 18 / NOE sequential total count: 102 | ||||||||||||||||||||||||
代表構造 | 選択基準: lowest energy | ||||||||||||||||||||||||
NMRアンサンブル | コンフォーマー選択の基準: structures with the lowest energy 計算したコンフォーマーの数: 200 / 登録したコンフォーマーの数: 10 / Maximum lower distance constraint violation: 0 Å / Maximum upper distance constraint violation: 0 Å | ||||||||||||||||||||||||
NMR ensemble rms | Distance rms dev: 0 Å / Distance rms dev error: 0 Å |