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データを開く
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基本情報
登録情報 | データベース: PDB / ID: 5fpt | ||||||
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タイトル | Structure of hepatitis C virus (HCV) full-length NS3 complex with small-molecule ligand 2-(1-methyl-1H-indol-3-yl)acetic acid (AT3437) in an alternate binding site. | ||||||
![]() | HEPATITIS C VIRUS FULL-LENGTH NS3 COMPLEX | ||||||
![]() | HYDROLASE / HEPATITIS C VIRUS / HCV / NS3 COMPLEX / PROTEASE-HELICASE / PROTEIN-LIGAND COMPLEX / FRAGMENT SCREENING / ALTERNATE BINDING SITE / AT3437. | ||||||
機能・相同性 | ![]() hepacivirin / host cell mitochondrial membrane / host cell lipid droplet / symbiont-mediated suppression of host TRAF-mediated signal transduction / transformation of host cell by virus / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / SH3 domain binding / nucleoside-triphosphate phosphatase ...hepacivirin / host cell mitochondrial membrane / host cell lipid droplet / symbiont-mediated suppression of host TRAF-mediated signal transduction / transformation of host cell by virus / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / SH3 domain binding / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / viral nucleocapsid / clathrin-dependent endocytosis of virus by host cell / 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 / RNA helicase activity / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / ribonucleoprotein complex / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / serine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / host cell nucleus / virion attachment to host cell / host cell plasma membrane / structural molecule activity / virion membrane / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane 類似検索 - 分子機能 | ||||||
生物種 | ![]() | ||||||
手法 | ![]() ![]() ![]() | ||||||
![]() | Jhoti, H. / Ludlow, R.F. / Saini, H.K. / Tickle, I.J. / Verdonk, M. / Pathuri, P. / Williams, P.A. | ||||||
![]() | ![]() タイトル: Detection of Secondary Binding Sites in Proteins Using Fragment Screening. 著者: Ludlow, R.F. / Verdonk, M.L. / Saini, H.K. / Tickle, I.J. / Jhoti, H. #1: ![]() タイトル: Molecular Views of Viral Polyprotein Processing Revealed by the Crystal Structure of the Hepatitis C Virus Bifunctional Protease-Helicase. 著者: Yao, N. / Reichert, P. / Taremi, S.S. / Prosise, W.W. / Weber, P.C. #2: ![]() タイトル: Discovery of an Allosteric Mechanism for the Regulation of Hcv Ns3 Protein Function. 著者: Saalau-Bethell, S.M. / Woodhead, A.J. / Chessari, G. / Carr, M.G. / Coyle, J. / Graham, B. / Hiscock, S.D. / Murray, C.W. / Pathuri, P. / Rich, S.J. / Richardson, C.J. / Williams, P.A. / Jhoti, H. | ||||||
履歴 |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
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構造の表示
構造ビューア | 分子: ![]() ![]() |
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ダウンロードとリンク
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ダウンロード
PDBx/mmCIF形式 | ![]() | 480.1 KB | 表示 | ![]() |
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PDB形式 | ![]() | 393.9 KB | 表示 | ![]() |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
その他 | ![]() |
-検証レポート
文書・要旨 | ![]() | 463.2 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 473.3 KB | 表示 | |
XML形式データ | ![]() | 48.2 KB | 表示 | |
CIF形式データ | ![]() | 69.2 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
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リンク
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集合体
登録構造単位 | ![]()
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単位格子 |
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非結晶学的対称性 (NCS) | NCS oper: (Code: given Matrix: (-0.91125, 0.41157, -0.01519), ベクター: |
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要素
#1: タンパク質 | 分子量: 70869.391 Da / 分子数: 2 / 由来タイプ: 組換発現 由来: (組換発現) ![]() 株: GENOTYPE 1B / プラスミド: PET17 / 発現宿主: ![]() ![]() 参照: UniProt: P26663, 加水分解酵素; プロテアーゼ; ペプチド結合加水分解酵素; セリンエンドペプチターゼ #2: 化合物 | #3: 水 | ChemComp-HOH / | 非ポリマーの詳細 | 2-(1-METHYL-1H-INDOL-3-YL)ACETIC ACID (3VY): ASTEX COMPOUND REGISTRY AT3437. | 配列の詳細 | N-TERM HIS TAG (37). DELETION 1-2. DELETION 632-686. | |
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-実験情報
-実験
実験 | 手法: ![]() |
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試料調製
結晶 | マシュー密度: 2.66 Å3/Da / 溶媒含有率: 53.33 % / 解説: NONE |
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結晶化 | pH: 6.6 詳細: 0.2 M 2-(N-MORPHOLINO)ETHANESULFONIC ACID (MES)-NAOH, 18% W/V POLYETHYLENE GLYCOL (PEG) 6000, 10% W/V 2-METHYL-2, 4-PENTANDIOL (MPD). PROTEIN CONC. = 7.5 MG/ML., pH 6.6 |
-データ収集
回折 | 平均測定温度: 93 K |
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放射光源 | 由来: ![]() ![]() ![]() |
検出器 | タイプ: ADSC QUANTUM 315 / 検出器: CCD / 日付: 2010年8月27日 / 詳細: MIRRORS |
放射 | 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: 0.9724 Å / 相対比: 1 |
反射 | 解像度: 2.72→70.55 Å / Num. obs: 39316 / % possible obs: 99 % / Observed criterion σ(I): -3.7 / 冗長度: 3.2 % / Biso Wilson estimate: 61.95 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 10.6 |
反射 シェル | 解像度: 2.72→2.83 Å / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 2 / % possible all: 99.8 |
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解析
ソフトウェア |
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精密化 | 構造決定の手法: ![]() 開始モデル: PDB ENTRY 5FPS 解像度: 2.72→70.55 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.889 / Rfactor Rfree error: 0 / 交差検証法: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.348
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原子変位パラメータ | Biso mean: 47.16 Å2
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Refine analyze | Luzzati coordinate error obs: 0.27 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 2.72→70.55 Å
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拘束条件 |
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精密化 TLS | 手法: refined / Refine-ID: X-RAY DIFFRACTION
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精密化 TLSグループ |
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