- PDB-5a5r: Crystal structure of human ATAD2 bromodomain in complex with 5-5-... -
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基本情報
登録情報
データベース: PDB / ID: 5a5r
タイトル
Crystal structure of human ATAD2 bromodomain in complex with 5-5- methoxypyridin-3-yl-3-methyl-8-piperidin-4-ylamino-1,2-dihydro-1,7- naphthyridin-2-one
要素
ATPASE FAMILY AAA DOMAIN-CONTAINING PROTEIN 2
キーワード
HYDROLASE / INHIBITOR / ATAD2 / BROMODOMAIN / EPIGENETICS / ATPASE FAMILY AAA DOMAIN-CONTAINING PROTEIN 2
機能・相同性
機能・相同性情報
nucleosome disassembly / 加水分解酵素; 酸無水物に作用; リン含有酸無水物に作用 / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / transcription initiation-coupled chromatin remodeling / nucleosome assembly / histone binding / chromatin binding / positive regulation of DNA-templated transcription / ATP hydrolysis activity / extracellular exosome ...nucleosome disassembly / 加水分解酵素; 酸無水物に作用; リン含有酸無水物に作用 / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / transcription initiation-coupled chromatin remodeling / nucleosome assembly / histone binding / chromatin binding / positive regulation of DNA-templated transcription / ATP hydrolysis activity / extracellular exosome / nucleoplasm / ATP binding / nucleus 類似検索 - 分子機能
ATPase family AAA domain-containing protein ATAD2-like / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain ...ATPase family AAA domain-containing protein ATAD2-like / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Mainly Alpha 類似検索 - ドメイン・相同性
Chem-NP8 / ATPase family AAA domain-containing protein 2 類似検索 - 構成要素
ATPASEFAMILYAAADOMAIN-CONTAININGPROTEIN2 / AAA NUCLEAR COREGULATOR CANCER-ASSOCIATED PROTEIN / ANCCA / H UMAN ATPASE FAMILY AAA DOMAIN- ...AAA NUCLEAR COREGULATOR CANCER-ASSOCIATED PROTEIN / ANCCA / H UMAN ATPASE FAMILY AAA DOMAIN-CONTAINING PROTEIN 2
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: 0.9763 Å / 相対比: 1
反射
解像度: 2.01→30.79 Å / Num. obs: 17849 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / 冗長度: 10.1 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.3
反射 シェル
解像度: 2.01→2.06 Å / 冗長度: 9.9 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 3.5 / % possible all: 100
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解析
ソフトウェア
名称
バージョン
分類
REFMAC
5.6.0117
精密化
XDS
データ削減
Aimless
データスケーリング
精密化
構造決定の手法: 分子置換 開始モデル: NONE 解像度: 2.01→30.79 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.955 / SU B: 5.366 / SU ML: 0.079 / 交差検証法: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.116 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD / 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
Rfactor
反射数
%反射
Selection details
Rfree
0.19974
905
5.1 %
RANDOM
Rwork
0.17864
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obs
0.17967
16834
99.53 %
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溶媒の処理
イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.2 Å / 溶媒モデル: BABINET MODEL WITH MASK