- PDB-4tz4: Crystal Structure of Human Cereblon in Complex with DDB1 and Lena... -
+
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: 4tz4
タイトル
Crystal Structure of Human Cereblon in Complex with DDB1 and Lenalidomide
要素
DNA damage-binding protein 1
Protein cereblon
キーワード
DNA Binding Protein/Ligase / DCAF / DNA Binding Protein-Ligase complex
機能・相同性
機能・相同性情報
negative regulation of monoatomic ion transmembrane transport / positive regulation by virus of viral protein levels in host cell / spindle assembly involved in female meiosis / epigenetic programming in the zygotic pronuclei / Cul4-RING E3 ubiquitin ligase complex / UV-damage excision repair / biological process involved in interaction with symbiont / regulation of mitotic cell cycle phase transition / WD40-repeat domain binding / Cul4A-RING E3 ubiquitin ligase complex ...negative regulation of monoatomic ion transmembrane transport / positive regulation by virus of viral protein levels in host cell / spindle assembly involved in female meiosis / epigenetic programming in the zygotic pronuclei / Cul4-RING E3 ubiquitin ligase complex / UV-damage excision repair / biological process involved in interaction with symbiont / regulation of mitotic cell cycle phase transition / WD40-repeat domain binding / Cul4A-RING E3 ubiquitin ligase complex / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / negative regulation of reproductive process / negative regulation of developmental process / locomotory exploration behavior / cullin family protein binding / viral release from host cell / positive regulation of Wnt signaling pathway / ectopic germ cell programmed cell death / negative regulation of protein-containing complex assembly / positive regulation of viral genome replication / proteasomal protein catabolic process / positive regulation of gluconeogenesis / nucleotide-excision repair / positive regulation of protein-containing complex assembly / Recognition of DNA damage by PCNA-containing replication complex / regulation of circadian rhythm / DNA Damage Recognition in GG-NER / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Formation of Incision Complex in GG-NER / Wnt signaling pathway / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / positive regulation of protein catabolic process / cellular response to UV / rhythmic process / site of double-strand break / Neddylation / ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / proteasome-mediated ubiquitin-dependent protein catabolic process / Potential therapeutics for SARS / transmembrane transporter binding / damaged DNA binding / chromosome, telomeric region / protein ubiquitination / DNA repair / apoptotic process / DNA damage response / negative regulation of apoptotic process / protein-containing complex binding / nucleolus / perinuclear region of cytoplasm / protein-containing complex / DNA binding / extracellular space / extracellular exosome / nucleoplasm / metal ion binding / nucleus / membrane / cytosol / cytoplasm 類似検索 - 分子機能
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: 1 Å / 相対比: 1
反射
解像度: 3.01→50 Å / Num. obs: 37313 / % possible obs: 98.5 % / 冗長度: 6.1 % / Rmerge(I) obs: 0.181 / Χ2: 1.058 / Net I/av σ(I): 10.061 / Net I/σ(I): 5.9 / Num. measured all: 228575
反射 シェル
Diffraction-ID: 1 / Rejects: _
解像度 (Å)
冗長度 (%)
Rmerge(I) obs
Num. unique all
Χ2
% possible all
3.01-3.12
5.8
0.723
3184
1.02
85.8
3.12-3.24
6.3
0.584
3703
1.082
99.9
3.24-3.39
6.3
0.392
3731
1.08
100
3.39-3.57
6.3
0.294
3739
1.054
100
3.57-3.79
6.3
0.23
3768
1.045
100
3.79-4.08
6.2
0.187
3745
1.045
99.9
4.08-4.5
6.2
0.147
3795
1.034
100
4.5-5.15
6.1
0.121
3796
1.088
99.9
5.15-6.48
6.1
0.136
3835
1.087
99.9
6.48-50
5.6
0.082
4017
1.036
99.5
-
解析
ソフトウェア
名称
バージョン
分類
REFMAC
5.6.0117
精密化
HKL-3000
データ削減
PDB_EXTRACT
3.14
データ抽出
Coot
モデル構築
精密化
構造決定の手法: 分子置換 開始モデル: DDB1 解像度: 3.01→50 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.873 / SU B: 38.571 / SU ML: 0.328 / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R Free: 0.465 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD 詳細: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : RESIDUAL ONLY
Rfactor
反射数
%反射
Selection details
Rfree
0.2706
1857
5 %
RANDOM
Rwork
0.2015
35396
-
-
obs
0.2049
37253
99.4 %
-
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: MASK