- PDB-1ajy: STRUCTURE AND MOBILITY OF THE PUT3 DIMER: A DNA PINCER, NMR, 13 S... -
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基本情報
登録情報
データベース: PDB / ID: 1ajy
タイトル
STRUCTURE AND MOBILITY OF THE PUT3 DIMER: A DNA PINCER, NMR, 13 STRUCTURES
要素
PUT3
キーワード
TRANSCRIPTION REGULATION / PUT3
機能・相同性
機能・相同性情報
positive regulation of proline catabolic process to glutamate / proline metabolic process / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-templated transcription / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleus 類似検索 - 分子機能
手法: molecular dynamics / ソフトェア番号: 1 詳細: PROGRAMS WRITTEN BY MICHAEL NILGES FOR SYMMETRIC DIMERS WERE USED (NILGES, M. PROTEINS 17, 297-309 (1993)). STRUCTURES WERE STARTED FROM AN EXTENDED MONOMER CONFORMATION AND RANDOM ROTATIONS ...詳細: PROGRAMS WRITTEN BY MICHAEL NILGES FOR SYMMETRIC DIMERS WERE USED (NILGES, M. PROTEINS 17, 297-309 (1993)). STRUCTURES WERE STARTED FROM AN EXTENDED MONOMER CONFORMATION AND RANDOM ROTATIONS WERE MADE AROUND THE PHI-PSI ANGLES. THE MONOMER WAS THEN DUPLICATED AND MOLECULAR DYNAMICS WAS PERFORMED USING NMR DISTANCE RESTRAINTS AND GENERATED SYMMETRY DISTANCE RESTRAINTS. RMSD CALCULATED BY SUPERIMPOSING STRUCTURES ON LOWEST ENERGY STRUCTURE FOR RESIDUES 33-62 OF EACH MONOMER AND 68-98 OF EACH DIMER. RMSD (ANGSTROMS): ATOMS FOR RESIDUES 33-62: 0.55 ATOMS FOR RESIDUES 33-62: 1.1 BACKBONE ATOMS FOR RESIDUES 68-98: 0.7 HEAVY ATOMS FOR RESIDUES 68-98: 1.5
NMRアンサンブル
コンフォーマー選択の基準: NO VIOLATION ABOVE 0.5 ANGSTROMS AND 5 DEGREE DIHEDRAL ANGLE 計算したコンフォーマーの数: 50 / 登録したコンフォーマーの数: 13