- PDB-8ufm: Crystal Structure of L516C/Y647C Mutant of SARS-Unique Domain (SU... -
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基本情報
登録情報
データベース: PDB / ID: 8ufm
タイトル
Crystal Structure of L516C/Y647C Mutant of SARS-Unique Domain (SUD) from SARS-CoV-2
要素
Papain-like protease nsp3
キーワード
VIRAL PROTEIN (ウイルスタンパク質) / Structural Genomics (構造ゲノミクス) / Center for Structural Genomics of Infectious Diseases / CSGID / SUD / Sars unique domain / Center for Structural Biology of Infectious Diseases / CSBID
機能・相同性
機能・相同性情報
viral genome replication / methyltransferase activity / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / ISG15-specific peptidase activity / Transcription of SARS-CoV-2 sgRNAs / メチル化 / Translation of Replicase and Assembly of the Replication Transcription Complex / Replication of the SARS-CoV-2 genome / double membrane vesicle viral factory outer membrane ...viral genome replication / methyltransferase activity / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / ISG15-specific peptidase activity / Transcription of SARS-CoV-2 sgRNAs / メチル化 / Translation of Replicase and Assembly of the Replication Transcription Complex / Replication of the SARS-CoV-2 genome / double membrane vesicle viral factory outer membrane / 3C様プロテアーゼ / host cell endosome / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / SARS-CoV-2 modulates host translation machinery / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / host cell Golgi apparatus / symbiont-mediated perturbation of host ubiquitin-like protein modification / endonuclease activity / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / 加水分解酵素; プロテアーゼ; ペプチド結合加水分解酵素; システインプロテアーゼ / single-stranded RNA binding / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / viral protein processing / induction by virus of host autophagy / symbiont-mediated suppression of host gene expression / cysteine-type endopeptidase activity / lipid binding / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / SARS-CoV-2 activates/modulates innate and adaptive immune responses / タンパク質分解 / zinc ion binding / 生体膜 類似検索 - 分子機能
解像度: 1.65→1.68 Å / 冗長度: 14.4 % / Mean I/σ(I) obs: 2 / Num. unique obs: 1971 / CC1/2: 0.772 / CC star: 0.933 / Rpim(I) all: 0.437 / Χ2: 1.007 / % possible all: 99.7
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解析
ソフトウェア
名称
バージョン
分類
REFMAC
5.8.0267
精密化
PDB_EXTRACT
3.27
データ抽出
HKL-3000
データ削減
HKL-3000
データスケーリング
MOLREP
位相決定
精密化
構造決定の手法: 分子置換 / 解像度: 1.65→28.26 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.959 / SU B: 4.329 / SU ML: 0.07 / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.085 / ESU R Free: 0.084 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
Rfactor
反射数
%反射
Selection details
Rfree
0.2079
1997
5 %
RANDOM
Rwork
0.1848
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obs
0.186
37981
99.81 %
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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: MASK