- PDB-7oet: C-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH 1,5-dimethyl-N-(2-(meth... -
+
データを開く
IDまたはキーワード:
読み込み中...
-
基本情報
登録情報
データベース: PDB / ID: 7oet
タイトル
C-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH 1,5-dimethyl-N-(2-(methylamino)-2-oxo-1-(tetrahydro-2H-pyran-4-yl)ethyl)-6-oxo-N-(2-phenyl-2-(pyridin-2-yl)ethyl)-1,6-dihydropyridine-3-carboxamide
要素
Bromodomain-containing protein 2
キーワード
NUCLEAR PROTEIN / INHIBITOR / HISTONE / EPIGENETIC READER / BROMODOMAIN / BRD2 / BROMODOMAIN CONTAINING PROTEIN 2 / ANTAGONIST
機能・相同性
機能・相同性情報
acetylation-dependent protein binding / chromatin looping / RUNX3 regulates p14-ARF / positive regulation of T-helper 17 cell lineage commitment / protein localization to chromatin / neural tube closure / lysine-acetylated histone binding / nucleosome assembly / spermatogenesis / nuclear speck ...acetylation-dependent protein binding / chromatin looping / RUNX3 regulates p14-ARF / positive regulation of T-helper 17 cell lineage commitment / protein localization to chromatin / neural tube closure / lysine-acetylated histone binding / nucleosome assembly / spermatogenesis / nuclear speck / protein serine/threonine kinase activity / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytoplasm 類似検索 - 分子機能
NET domain superfamily / NET domain profile. / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / : / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain, conserved site / Bromodomain signature. / Bromodomain ...NET domain superfamily / NET domain profile. / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / : / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily 類似検索 - ドメイン・相同性
Chem-80Z / Bromodomain-containing protein 2 類似検索 - 構成要素
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: 0.966 Å / 相対比: 1
反射
解像度: 1.41→42.29 Å / Num. obs: 23909 / % possible obs: 99.3 % / 冗長度: 4.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.037 / Net I/σ(I): 17.4
反射 シェル
解像度: 1.41→1.43 Å / 冗長度: 4.5 % / Rmerge(I) obs: 0.656 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1157 / CC1/2: 0.718 / % possible all: 99.6
-
解析
ソフトウェア
名称
バージョン
分類
REFMAC
5.8.0258
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: フーリエ合成 開始モデル: in house structure 解像度: 1.41→15.696 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.217 / SU ML: 0.046 / 交差検証法: FREE R-VALUE / ESU R: 0.063 / ESU R Free: 0.062 / 詳細: Hydrogens have been added in their riding positions
Rfactor
反射数
%反射
Rfree
0.1959
1204
5.074 %
Rwork
0.18
22527
-
all
0.181
-
-
obs
-
23731
99.226 %
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 PLUS MASK
原子変位パラメータ
Biso mean: 28.07 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.824 Å2
-0 Å2
-0 Å2
2-
-
0.177 Å2
-0 Å2
3-
-
-
0.647 Å2
精密化ステップ
サイクル: LAST / 解像度: 1.41→15.696 Å
タンパク質
核酸
リガンド
溶媒
全体
原子数
921
0
73
83
1077
拘束条件
Refine-ID
タイプ
Dev ideal
Dev ideal target
数
X-RAY DIFFRACTION
r_bond_refined_d
0.004
0.013
1027
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.017
953
X-RAY DIFFRACTION
r_angle_refined_deg
1.128
1.644
1371
X-RAY DIFFRACTION
r_angle_other_deg
1.254
1.637
2216
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
4.625
5
113
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
31.036
22.182
55
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
11.743
15
170
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
16.238
15
6
X-RAY DIFFRACTION
r_chiral_restr
0.063
0.2
117
X-RAY DIFFRACTION
r_gen_planes_refined
0.004
0.02
1210
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
220
X-RAY DIFFRACTION
r_nbd_refined
0.195
0.2
211
X-RAY DIFFRACTION
r_symmetry_nbd_other
0.165
0.2
799
X-RAY DIFFRACTION
r_nbtor_refined
0.171
0.2
489
X-RAY DIFFRACTION
r_symmetry_nbtor_other
0.081
0.2
375
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.109
0.2
63
X-RAY DIFFRACTION
r_symmetry_nbd_refined
0.152
0.2
6
X-RAY DIFFRACTION
r_nbd_other
0.137
0.2
53
X-RAY DIFFRACTION
r_symmetry_xyhbond_nbd_refined
0.103
0.2
12
X-RAY DIFFRACTION
r_mcbond_it
1.578
3.487
453
X-RAY DIFFRACTION
r_mcbond_other
1.564
3.471
451
X-RAY DIFFRACTION
r_mcangle_it
2.579
7.807
566
X-RAY DIFFRACTION
r_mcangle_other
2.577
7.824
566
X-RAY DIFFRACTION
r_scbond_it
2.305
4.029
573
X-RAY DIFFRACTION
r_scbond_other
2.303
4.038
574
X-RAY DIFFRACTION
r_scangle_it
3.807
8.68
805
X-RAY DIFFRACTION
r_scangle_other
3.805
8.695
806
X-RAY DIFFRACTION
r_lrange_it
5.622
32.061
1157
X-RAY DIFFRACTION
r_lrange_other
5.579
31.769
1143
LS精密化 シェル
Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20