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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: 2c0i | ||||||
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タイトル | Src family kinase Hck with bound inhibitor A-420983 | ||||||
![]() | TYROSINE-PROTEIN KINASE HCK | ||||||
![]() | TRANSFERASE / TYROSINE-PROTEIN KINASE / ATP-BINDING / KINASE / LIPOPROTEIN / MYRISTATE / NUCLEOTIDE-BINDING / PALMITATE / PHOSPHORYLATION / SH2 DOMAIN / SH3 DOMAIN | ||||||
機能・相同性 | ![]() leukocyte degranulation / respiratory burst after phagocytosis / innate immune response-activating signaling pathway / leukocyte migration involved in immune response / regulation of podosome assembly / regulation of phagocytosis / FLT3 signaling through SRC family kinases / Nef and signal transduction / regulation of DNA-binding transcription factor activity / positive regulation of actin filament polymerization ...leukocyte degranulation / respiratory burst after phagocytosis / innate immune response-activating signaling pathway / leukocyte migration involved in immune response / regulation of podosome assembly / regulation of phagocytosis / FLT3 signaling through SRC family kinases / Nef and signal transduction / regulation of DNA-binding transcription factor activity / positive regulation of actin filament polymerization / Fc-gamma receptor signaling pathway involved in phagocytosis / mesoderm development / FCGR activation / localization / type II interferon-mediated signaling pathway / Signaling by CSF3 (G-CSF) / lipopolysaccharide-mediated signaling pathway / transport vesicle / extrinsic component of cytoplasmic side of plasma membrane / negative regulation of inflammatory response to antigenic stimulus / cell surface receptor protein tyrosine kinase signaling pathway / phosphotyrosine residue binding / FCGR3A-mediated IL10 synthesis / caveola / cell projection / integrin-mediated signaling pathway / Regulation of signaling by CBL / regulation of actin cytoskeleton organization / FCGR3A-mediated phagocytosis / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / Inactivation of CSF3 (G-CSF) signaling / cytoplasmic side of plasma membrane / cytokine-mediated signaling pathway / peptidyl-tyrosine phosphorylation / Signaling by CSF1 (M-CSF) in myeloid cells / regulation of cell shape / regulation of inflammatory response / protein tyrosine kinase activity / protein autophosphorylation / lysosome / cell differentiation / cytoskeleton / cell adhesion / intracellular signal transduction / inflammatory response / protein phosphorylation / intracellular membrane-bounded organelle / innate immune response / focal adhesion / signaling receptor binding / lipid binding / positive regulation of cell population proliferation / negative regulation of apoptotic process / Golgi apparatus / ATP binding / nucleus / plasma membrane / cytosol 類似検索 - 分子機能 | ||||||
生物種 | ![]() | ||||||
手法 | ![]() ![]() ![]() | ||||||
![]() | Borhani, D.W. / Burchat, A. / Calderwood, D.J. / Hirst, G.C. / Li, B. / Loew, A. | ||||||
![]() | ![]() タイトル: Discovery of A-770041, a Src-Family Selective Orally Active Lck Inhibitor that Prevents Organ Allograft Rejection. 著者: Burchat, A. / Borhani, D.W. / Calderwood, D.J. / Hirst, G.C. / Li, B. / Stachlewitz, R.F. #1: ジャーナル: Bioorg.Med.Chem.Lett. / 年: 2004 タイトル: A-420983: A Potent, Orally Active Inhibitor of Lck with Efficacy in a Model of Transplant Rejection 著者: Borhani, D.W. / Calderwood, D.J. / Friedman, M.M. / Hirst, G.C. / Li, B. / Leung, A.K.W. / Mcrae, B. / Ratnofsky, S. / Ritter, K. / Waegell, W. | ||||||
履歴 |
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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 | ![]() | 196.7 KB | 表示 | ![]() |
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PDB形式 | ![]() | 155.6 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 | ![]() | 874.8 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 892.8 KB | 表示 | |
XML形式データ | ![]() | 36.2 KB | 表示 | |
CIF形式データ | ![]() | 51.2 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ドメイン:
NCSドメイン領域: Component-ID: 1
NCSアンサンブル:
NCS oper: (Code: given Matrix: (0.944154, 0.025026, -0.328552), ベクター: |
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要素
#1: タンパク質 | 分子量: 52000.227 Da / 分子数: 2 / 断片: SH3-SH2-SH1, RESIDUES 80-525 / 変異: YES / 由来タイプ: 組換発現 詳細: SRC NUMBERING USED. ADD 20 TO THE RESIDUE NUMBERS IN THIS ENTRY TO OBTAIN ACTUAL HUMAN HCK RESIDUE NUMBERS. RESIDUE Y501 (HCK Y521) IS PHOSPHORYLATED 由来: (組換発現) ![]() 発現宿主: ![]() ![]() 参照: UniProt: P08631, EC: 2.7.1.112 #2: 化合物 | #3: 化合物 | #4: 水 | ChemComp-HOH / | 構成要素の詳細 | ENGINEERED RESIDUE IN CHAIN A, GLN 502 TO GLU ENGINEERED RESIDUE IN CHAIN A, GLN 503 TO GLU ...ENGINEERED | 配列の詳細 | THE PROTEIN CRYSTALLIZED INCLUDED EIGHT NON-NATIVE N-TERMINAL RESIDUES: GLY-ALA-MET-GLY-SER-GLY-ILE- ...THE PROTEIN CRYSTALLIZ | |
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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: 3.1 Å3/Da / 溶媒含有率: 59.9 % |
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結晶化 | 温度: 277 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 8 詳細: HCK (10 MG/ML IN 150 MM NACL, 20 MM TRIS.HCL PH 8.0) WAS MIXED WITH A-420983 [100 MM STOCK SOLUTION OF THE BIS-MALEIC ACID SALT IN DMSO) TO GIVE A FINAL A-420983 CONCENTRATION OF 1 MM. HCK/A- ...詳細: HCK (10 MG/ML IN 150 MM NACL, 20 MM TRIS.HCL PH 8.0) WAS MIXED WITH A-420983 [100 MM STOCK SOLUTION OF THE BIS-MALEIC ACID SALT IN DMSO) TO GIVE A FINAL A-420983 CONCENTRATION OF 1 MM. HCK/A-420983 WAS THEN MIXED WITH RESERVOIR SOLUTION (12% PEG 6000, 3% 1, 5-DIAMINOPENTANE, 20% GLYCEROL, 200 MM CA(OAC)2, 100 MM TRIS.HCL PH 8.0) AND EQUILBRATED AGAINST THE RESERVOIR SOLUTION BY VAPOR DIFFUSION (SITTING DROPS) AT 277 K. |
-データ収集
回折 | 平均測定温度: 100 K |
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放射光源 | 由来: ![]() ![]() ![]() |
検出器 | タイプ: MARRESEARCH / 検出器: CCD / 日付: 2002年2月7日 |
放射 | モノクロメーター: SI(111) DOUBLE MONOCHROMATOR / 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: 1.0332 Å / 相対比: 1 |
反射 | 解像度: 2.3→15 Å / Num. obs: 50423 / % possible obs: 88.9 % / Observed criterion σ(I): 0 / 冗長度: 2.5 % / Biso Wilson estimate: 54.7 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.8 |
反射 シェル | 解像度: 2.3→2.38 Å / 冗長度: 2.1 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 3.3 / % possible all: 75.5 |
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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 1AD5 解像度: 2.3→19.96 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.91 / SU B: 15.259 / SU ML: 0.192 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / ESU R: 0.341 / ESU R Free: 0.261 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE ACTIVATION LOOP (RESIDUES A386-A398 AND B386-B398) IS DISORDERED IN BOTH HCK MOLECULES (CHAINS A AND B). HCK CHAIN A IS SLIGHTLY BETTER ...詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE ACTIVATION LOOP (RESIDUES A386-A398 AND B386-B398) IS DISORDERED IN BOTH HCK MOLECULES (CHAINS A AND B). HCK CHAIN A IS SLIGHTLY BETTER ORDERED THAN CHAIN B. SIMILARLY, THE LIGAND A1506 IS BETTER ORDERED THAN B1506. SEVEN N-TERMINAL RESIDUES (FROM THE EXPRESSION VECTOR, GLY-ALA -MET-GLY-SER-GLY-ILE) ARE DISORDERED IN BOTH CHAINS. RESIDUE ARG-59 IS NON-NATIVE (EXPRESSION VECTOR).
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 50.47 Å2
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精密化ステップ | サイクル: LAST / 解像度: 2.3→19.96 Å
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拘束条件 |
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