- PDB-2hym: NMR based Docking Model of the Complex between the Human Type I I... -
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基本情報
登録情報
データベース: PDB / ID: 2hym
タイトル
NMR based Docking Model of the Complex between the Human Type I Interferon Receptor and Human Interferon alpha-2
要素
Interferon alpha-2
Soluble IFN alpha/beta receptor
キーワード
IMMUNE SYSTEM / interferon receptor complex
機能・相同性
機能・相同性情報
type I interferon receptor activity / type I interferon binding / interleukin-22 receptor activity / type I interferon receptor binding / JAK pathway signal transduction adaptor activity / cell surface receptor signaling pathway via STAT / negative regulation of interleukin-5 production / response to interferon-beta / negative regulation of interleukin-13 production / negative regulation of T cell differentiation ...type I interferon receptor activity / type I interferon binding / interleukin-22 receptor activity / type I interferon receptor binding / JAK pathway signal transduction adaptor activity / cell surface receptor signaling pathway via STAT / negative regulation of interleukin-5 production / response to interferon-beta / negative regulation of interleukin-13 production / negative regulation of T cell differentiation / natural killer cell activation involved in immune response / response to interferon-alpha / positive regulation of peptidyl-serine phosphorylation of STAT protein / negative regulation of T-helper 2 cell cytokine production / T cell activation involved in immune response / negative regulation of viral entry into host cell / TRAF6 mediated IRF7 activation / type I interferon-mediated signaling pathway / cytokine binding / response to exogenous dsRNA / B cell proliferation / cell surface receptor signaling pathway via JAK-STAT / humoral immune response / Regulation of IFNA/IFNB signaling / cellular response to interferon-beta / B cell differentiation / cytokine activity / response to virus / Evasion by RSV of host interferon responses / cellular response to virus / cytokine-mediated signaling pathway / Interferon alpha/beta signaling / cell-cell signaling / Factors involved in megakaryocyte development and platelet production / collagen-containing extracellular matrix / defense response to virus / adaptive immune response / Potential therapeutics for SARS / cell surface receptor signaling pathway / inflammatory response / negative regulation of gene expression / negative regulation of DNA-templated transcription / apoptotic process / protein kinase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / extracellular space / extracellular region / plasma membrane 類似検索 - 分子機能
Interferon alpha, beta and delta family signature. / Interferon alpha, beta and delta. / Interferon alpha/beta/delta / Interferon alpha/beta domain / Interferon/interleukin receptor domain / Interferon-alpha/beta receptor, fibronectin type III / Tissue factor / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; ...Interferon alpha, beta and delta family signature. / Interferon alpha, beta and delta. / Interferon alpha/beta/delta / Interferon alpha/beta domain / Interferon/interleukin receptor domain / Interferon-alpha/beta receptor, fibronectin type III / Tissue factor / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulins / Immunoglobulin-like fold / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha 類似検索 - ドメイン・相同性
0.3 mM Interferon-alpha2 (D,15N), 90% D2O, 10% H2O, 20 mM deuterated tris buffer, 0.02% NaN3
90% D2O, 10% H2O
2
0.3 mM Interferon-alpha2 (D,15N, 13C), 5% D2O, 95% H2O, 20 mM deuterated tris buffer, 0.02% NaN3
5% D2O, 95% H2O
3
0.3 mM Interferon-alpha2 (D,15N), 5% D2O, 95% H2O, 20 mM deuterated tris buffer, 0.02% NaN3
5% D2O, 95% H2O
試料状態
イオン強度: 20 mM deuterated tris buffer / pH: 8 / 圧: ambient / 温度: 308 K
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NMR測定
放射
プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M
放射波長
相対比: 1
NMRスペクトロメーター
タイプ
製造業者
モデル
磁場強度 (MHz)
Spectrometer-ID
Bruker DMX
Bruker
DMX
500
1
Bruker DRX
Bruker
DRX
800
2
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解析
NMR software
名称
バージョン
開発者
分類
XwinNMR
3
Bruker
collection
NMRPipe
2.3
Delaglio, Grzesiek, Vuister, Zhu, Pfeifer, Bax
解析
NMRView
5.2.2
Johnson, Blevins
データ解析
HADDOCK
1.3
Dominguez, Boelens, Bonvin
精密化
精密化
手法: Rigid body docking, semi-flexible simulated annealing, refinement using explicit water ソフトェア番号: 1 詳細: 1000 conformers were obtained in the rigid body docking and 200 best conformers were selected for semi-flexible simulated annealing followed by refinement
代表構造
選択基準: closest to the average
NMRアンサンブル
コンフォーマー選択の基準: LOWEST ENERGY STRUCTURES OF LOWEST ENERGY CLUSTER 計算したコンフォーマーの数: 200 / 登録したコンフォーマーの数: 10