+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 107d | ||||||
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タイトル | SOLUTION STRUCTURE OF THE COVALENT DUOCARMYCIN A-DNA DUPLEX COMPLEX | ||||||
要素 |
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キーワード | DNA / DOUBLE HELIX | ||||||
機能・相同性 | Chem-DUO / DNA 機能・相同性情報 | ||||||
手法 | 溶液NMR / MOLECULAR DYNAMICS, MATRIX RELAXATION | ||||||
データ登録者 | Lin, C.H. / Patel, D.J. | ||||||
引用 | ジャーナル: J.Mol.Biol. / 年: 1995 タイトル: Solution structure of the covalent duocarmycin A-DNA duplex complex. 著者: Lin, C.H. / Patel, D.J. | ||||||
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 | 107d.cif.gz | 51.9 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb107d.ent.gz | 40 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 107d.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 | 107d_validation.pdf.gz | 422.3 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 107d_full_validation.pdf.gz | 451.1 KB | 表示 | |
XML形式データ | 107d_validation.xml.gz | 5.9 KB | 表示 | |
CIF形式データ | 107d_validation.cif.gz | 7 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/07/107d ftp://data.pdbj.org/pub/pdb/validation_reports/07/107d | 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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NMR アンサンブル |
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-要素
#1: DNA鎖 | 分子量: 2039.359 Da / 分子数: 1 / 由来タイプ: 合成 / 詳細: CHEMICALLY SYNTHESIZED / キーワード: DEOXYRIBONUCLEIC ACID |
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#2: DNA鎖 | 分子量: 2195.487 Da / 分子数: 1 / 由来タイプ: 合成 / 詳細: CHEMICALLY SYNTHESIZED / キーワード: DEOXYRIBONUCLEIC ACID |
#3: 化合物 | ChemComp-DUO / |
-実験情報
-実験
実験 | 手法: 溶液NMR |
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NMR実験の詳細 | Text: DUOCARMYCIN A WAS PROVIDED BY KYOWA HAKKO KOGYO CO., JAPAN. |
-解析
ソフトウェア |
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NMR software | 名称: X-PLOR / 開発者: BRUNGER / 分類: 精密化 | ||||||||
精密化 | 手法: MOLECULAR DYNAMICS, MATRIX RELAXATION / ソフトェア番号: 1 詳細: TWO STARTING STRUCTURES WERE GENERATED BY MANUALLY DOCKING THE DRUG ONTO A- AND B-FORM DNA USING INSIGHT II AND WERE SUBSEQUENTLY REFINED BY DISTANCE-RESTRAINED MOLECULAR DYNAMICS USING A SET ...詳細: TWO STARTING STRUCTURES WERE GENERATED BY MANUALLY DOCKING THE DRUG ONTO A- AND B-FORM DNA USING INSIGHT II AND WERE SUBSEQUENTLY REFINED BY DISTANCE-RESTRAINED MOLECULAR DYNAMICS USING A SET OF INTER-PROTON DISTANCE RESTRAINTS DERIVED FROM THE 2-D NMR DATA. ONE INITIAL VELOCITY SEED WAS USED FOR EACH STARTING STRUCTURE WHICH YIELDS TWO DISTANCE-REFINED STRUCTURES. THEY WERE REFINED FURTHER WITH TWO INITIAL VELOCITIES USING RELAXATION-MATRIX BASED NOE INTENSITY-RESTRAINED MOLECULAR DYNAMICS TO GENERATE THE FINAL FOUR STRUCTURES. THE FINAL FOUR STRUCTURES WERE OBTAINED BY TAKING THE AVERAGE COORDINATES OF THE LAST 1.0 PS OF THE DYNAMICS DURING RELAXATION MATRIX REFINEMENT AND ENERGY MINIMIZED. THE R(1/6) VALUE WAS USED TO REFINE THE STRUCTURE DURING RELAXATION MATRIX REFINEMENT. THE SUMMATIONS RUN THROUGH ALL OBSERVED, QUANTIFIABLE NOE CROSSPEAKS IN NOESY SPECTRA RECORDED IN D2O AND MIXING TIMES OF 40, 80, 120 AND 160 MS. THE R(1/6) FACTOR AND THE RMS DEVIATIONS FROM IDEAL GEOMETRY FOR THE FOUR FINAL STRUCTURES ARE: MODEL1-MODEL4 R(1/6) FACTOR 0.042-0.045 BOND (ANG) 0.009-0.010 ANGLES (DEG) 3.078-3.780 IMPROPERS (DEG) 0.310-0.321. THE STRUCTURE HAS APPROXIMATE TWO-FOLD SYMMETRY RELATING THE TWO STRANDS OF THE DNA WITH THE SYMMETRY AXIS PERPENDICULAR TO THE HELICAL AXIS. THE TRANSFORMATION MATRIX WAS CALCULATED FOR THE AVERAGED STRUCTURE OF THE FOUR MODELS. | ||||||||
NMRアンサンブル | 登録したコンフォーマーの数: 4 |