+
データを開く
-
基本情報
登録情報 | データベース: PDB / ID: 2oow | ||||||
---|---|---|---|---|---|---|---|
タイトル | MIF Bound to a Fluorinated OXIM Derivative | ||||||
![]() | Macrophage migration inhibitory factor | ||||||
![]() | ISOMERASE / alternative ligand-binding modes | ||||||
機能・相同性 | ![]() positive regulation of prostaglandin secretion involved in immune response / positive regulation of myeloid leukocyte cytokine production involved in immune response / phenylpyruvate tautomerase / L-dopachrome isomerase / dopachrome isomerase activity / phenylpyruvate tautomerase activity / positive regulation of lipopolysaccharide-mediated signaling pathway / cytokine receptor binding / positive regulation of arachidonic acid secretion / negative regulation of myeloid cell apoptotic process ...positive regulation of prostaglandin secretion involved in immune response / positive regulation of myeloid leukocyte cytokine production involved in immune response / phenylpyruvate tautomerase / L-dopachrome isomerase / dopachrome isomerase activity / phenylpyruvate tautomerase activity / positive regulation of lipopolysaccharide-mediated signaling pathway / cytokine receptor binding / positive regulation of arachidonic acid secretion / negative regulation of myeloid cell apoptotic process / negative regulation of macrophage chemotaxis / negative regulation of mature B cell apoptotic process / carboxylic acid metabolic process / positive regulation of chemokine (C-X-C motif) ligand 2 production / prostaglandin biosynthetic process / negative regulation of protein metabolic process / regulation of macrophage activation / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / chemoattractant activity / positive regulation of protein kinase A signaling / protein homotrimerization / negative regulation of cellular senescence / negative regulation of DNA damage response, signal transduction by p53 class mediator / DNA damage response, signal transduction by p53 class mediator / positive regulation of phosphorylation / positive regulation of B cell proliferation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / negative regulation of cell migration / positive regulation of cytokine production / cytokine activity / Cell surface interactions at the vascular wall / positive regulation of tumor necrosis factor production / positive regulation of peptidyl-tyrosine phosphorylation / cellular senescence / positive regulation of fibroblast proliferation / positive regulation of peptidyl-serine phosphorylation / secretory granule lumen / protease binding / vesicle / ficolin-1-rich granule lumen / cell surface receptor signaling pathway / positive regulation of ERK1 and ERK2 cascade / inflammatory response / negative regulation of gene expression / innate immune response / positive regulation of cell population proliferation / Neutrophil degranulation / negative regulation of apoptotic process / cell surface / extracellular space / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / plasma membrane / cytoplasm / cytosol 類似検索 - 分子機能 | ||||||
生物種 | ![]() | ||||||
手法 | ![]() ![]() | ||||||
![]() | Crichlow, G.V. / Al-Abed, Y. / Lolis, E. | ||||||
![]() | ![]() タイトル: Alternative chemical modifications reverse the binding orientation of a pharmacophore scaffold in the active site of macrophage migration inhibitory factor. 著者: Crichlow, G.V. / Cheng, K.F. / Dabideen, D. / Ochani, M. / Aljabari, B. / Pavlov, V.A. / Miller, E.J. / Lolis, E. / Al-Abed, Y. | ||||||
履歴 |
|
-
構造の表示
構造ビューア | 分子: ![]() ![]() |
---|
-
ダウンロードとリンク
-
ダウンロード
PDBx/mmCIF形式 | ![]() | 88.4 KB | 表示 | ![]() |
---|---|---|---|---|
PDB形式 | ![]() | 65.7 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 | ![]() | 1 MB | 表示 | ![]() |
---|---|---|---|---|
文書・詳細版 | ![]() | 1 MB | 表示 | |
XML形式データ | ![]() | 19.7 KB | 表示 | |
CIF形式データ | ![]() | 26.9 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
-
リンク
-
集合体
登録構造単位 | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
単位格子 |
| ||||||||||||
非結晶学的対称性 (NCS) | NCS oper:
| ||||||||||||
詳細 | The asymmetric unit contains one homotrimer of MIF, which is presumed to be the physiologically active entity |
-
要素
-タンパク質 , 1種, 3分子 ABC
#1: タンパク質 | 分子量: 12355.056 Da / 分子数: 3 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() |
---|
-非ポリマー , 5種, 276分子 ![](data/chem/img/SO4.gif)
![](data/chem/img/OX4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/IPA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/OX4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/IPA.gif)
![](data/chem/img/HOH.gif)
#2: 化合物 | ChemComp-SO4 / #3: 化合物 | #4: 化合物 | ChemComp-GOL / #5: 化合物 | #6: 水 | ChemComp-HOH / | |
---|
-実験情報
-実験
実験 | 手法: ![]() |
---|
-
試料調製
結晶 | マシュー密度: 2.7 Å3/Da / 溶媒含有率: 54.37 % |
---|---|
結晶化 | 温度: 296 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 7.5 詳細: 50% saturated ammonium sulfate, 4% isopropanol, 0.1 M tris(hydroxymethyl)aminomethan; mixed with protein:inhibitor complex in a 1:1 ratio, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K |
-データ収集
回折 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
放射光源 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
検出器 | タイプ: RIGAKU RAXIS IV / 検出器: IMAGE PLATE / 日付: 2006年10月16日 / 詳細: mirrors | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
放射 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
放射波長 | 波長: 1.5418 Å / 相対比: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
反射 | 解像度: 1.75→100 Å / Num. obs: 41057 / % possible obs: 100 % / Observed criterion σ(I): -3 / 冗長度: 4.7 % / Rmerge(I) obs: 0.06 / Χ2: 1.287 / Net I/σ(I): 19.4 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
反射 シェル |
|
-位相決定
Phasing MR | Rfactor: 0.333 / Cor.coef. Fo:Fc: 0.735 / Cor.coef. Io to Ic: 0.686
|
---|
-
解析
ソフトウェア |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
精密化 | 構造決定の手法: ![]() 開始モデル: PDB entry 2OOH 解像度: 1.75→100 Å / FOM work R set: 0.881 / Isotropic thermal model: isotropic / 交差検証法: THROUGHOUT / σ(F): 0 / 立体化学のターゲット値: Engh & Huber 詳細: THE STATISTICS LISTED BY RESOLUTION SHELL ARE FROM THE LAST ROUND OF CNS REFINEMENT. MINOR MANUAL ADJUSTEMENTS WERE PERFORMED AFTERWARDS. THE OVERALL STATISTICS REPRESENT THE FINAL MODEL. ...詳細: THE STATISTICS LISTED BY RESOLUTION SHELL ARE FROM THE LAST ROUND OF CNS REFINEMENT. MINOR MANUAL ADJUSTEMENTS WERE PERFORMED AFTERWARDS. THE OVERALL STATISTICS REPRESENT THE FINAL MODEL. INHIBITOR MOLECULES WERE MODELLED WITH PARTIAL OCCUPANCIES. GLYCEROL MOLECULES MODELLED IN THE SAME ACTIVE SITES AS INHIBITOR HAVE OCCUPANCIES WERE MODLLED AS HAVING OCCUPANCIES EQUAL TO 1-(INHIBITOR OCCUPANCY FOR THAT ACTIVE SITE). THE RATIO OF INHIBITOR : GLYCEROL OCCUPANCY FOR EACH ACTIVE SITE WAS DETERMINED BY OCCUPANCY REFINEMENT IN CNS. THE AROMATIC RING OF EACH INHIBITOR AND THE NEARBY SIDE CHAIN OF LYS 32 SEEM TO SHOW SOME DISORDER (ESPECIALLY THE INHIBITOR AROMATIC RING). THE COORDINATES INDICATE TOO SHORT A DISTANCE BETWEEN LYS 32 IN CHAIN C AND THE AROMATIC RING OF THE NEARBY INHIBITOR. HOWEVER, THEIR AVERAGE POSITIONS DO NOT NECESSARILY REFLECT THEIR PROXIMITY AT ANY GIVEN TIME, DUE TO THIS DISORDER.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 23.844 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 1.75→100 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
拘束条件 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS精密化 シェル | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16
|