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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: 4h3x | ||||||
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タイトル | Crystal structure of an MMP broad spectrum hydroxamate based inhibitor CC27 in complex with the MMP-9 catalytic domain | ||||||
![]() | Matrix metalloproteinase-9 | ||||||
![]() | HYDROLASE/HYDROLASE Inhibitor / HYDROLASE/HYDROXAMATE INHIBITOR / Zincin-like / Gelatinase / Collagenase (Catalytic Domain) / HYDROLASE-HYDROLASE Inhibitor complex | ||||||
機能・相同性 | ![]() gelatinase B / negative regulation of epithelial cell differentiation involved in kidney development / negative regulation of cation channel activity / negative regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / cellular response to UV-A / positive regulation of keratinocyte migration / regulation of neuroinflammatory response / positive regulation of epidermal growth factor receptor signaling pathway / Assembly of collagen fibrils and other multimeric structures / positive regulation of DNA binding ...gelatinase B / negative regulation of epithelial cell differentiation involved in kidney development / negative regulation of cation channel activity / negative regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / cellular response to UV-A / positive regulation of keratinocyte migration / regulation of neuroinflammatory response / positive regulation of epidermal growth factor receptor signaling pathway / Assembly of collagen fibrils and other multimeric structures / positive regulation of DNA binding / Activation of Matrix Metalloproteinases / endodermal cell differentiation / positive regulation of release of cytochrome c from mitochondria / response to amyloid-beta / macrophage differentiation / Collagen degradation / collagen catabolic process / extracellular matrix disassembly / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / negative regulation of intrinsic apoptotic signaling pathway / positive regulation of vascular associated smooth muscle cell proliferation / collagen binding / cellular response to cadmium ion / embryo implantation / Degradation of the extracellular matrix / extracellular matrix organization / positive regulation of receptor binding / skeletal system development / Signaling by SCF-KIT / metalloendopeptidase activity / cellular response to reactive oxygen species / metallopeptidase activity / cell migration / tertiary granule lumen / peptidase activity / cellular response to lipopolysaccharide / Interleukin-4 and Interleukin-13 signaling / collagen-containing extracellular matrix / endopeptidase activity / ficolin-1-rich granule lumen / Extra-nuclear estrogen signaling / positive regulation of protein phosphorylation / positive regulation of apoptotic process / serine-type endopeptidase activity / Neutrophil degranulation / negative regulation of apoptotic process / apoptotic process / proteolysis / extracellular space / extracellular exosome / zinc ion binding / extracellular region / identical protein binding 類似検索 - 分子機能 | ||||||
生物種 | ![]() | ||||||
手法 | ![]() ![]() ![]() | ||||||
![]() | Stura, E.A. / Vera, L. / Cassar-Lajeunesse, E. / Nuti, E. / Dive, V. / Rossello, A. | ||||||
![]() | ![]() タイトル: Crystallization of bi-functional ligand protein complexes. 著者: Antoni, C. / Vera, L. / Devel, L. / Catalani, M.P. / Czarny, B. / Cassar-Lajeunesse, E. / Nuti, E. / Rossello, A. / Dive, V. / Stura, E.A. #1: ![]() タイトル: Crystallization of bi-functional ligand protein complexes. 著者: Antoni, C. / Vera, L. / Devel, L. / Catalani, M.P. / Czarny, B. / Cassar-Lajeunesse, E. / Nuti, E. / Rossello, A. / Dive, V. / Stura, E.A. | ||||||
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 | ![]() | 98.1 KB | 表示 | ![]() |
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PDB形式 | ![]() | 73 KB | 表示 | ![]() |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
その他 | ![]() |
-検証レポート
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
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-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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要素
-タンパク質 , 1種, 2分子 AB
#1: タンパク質 | 分子量: 18338.318 Da / 分子数: 2 断片: human wild-type MMP-9 catalytic domain unp residues 107-215/391-443 変異: E402Q,E402Q / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() |
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-非ポリマー , 7種, 402分子 ![](data/chem/img/ZN.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/10B.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PGO.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/10B.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PGO.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
#2: 化合物 | ChemComp-ZN / #3: 化合物 | ChemComp-CA / #4: 化合物 | #5: 化合物 | ChemComp-GOL / #6: 化合物 | ChemComp-PGO / | #7: 化合物 | #8: 水 | ChemComp-HOH / | |
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-詳細
配列の詳細 | THE CRYSTALLIZED SEQUENCE CORRESPONDS TO A CHIMERIC CONSTRUCT OBTAINED BY DELETING THE DOMAIN ...THE 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: 2.29 Å3/Da / 溶媒含有率: 46.34 % |
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結晶化 | 温度: 293 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 7 詳細: protein: hMMP-9-WT 5.5 mg/mL 120 milli-M acetohydroxamic acid. Reservoir: 10% PEG 20,000, 60mM MES pH 5.5 + 18% MPEG 5,000, 0.08 M imidazole piperidine; pH 8.5, 0.05 M NaCl. Cryoprotectant: ...詳細: protein: hMMP-9-WT 5.5 mg/mL 120 milli-M acetohydroxamic acid. Reservoir: 10% PEG 20,000, 60mM MES pH 5.5 + 18% MPEG 5,000, 0.08 M imidazole piperidine; pH 8.5, 0.05 M NaCl. Cryoprotectant: 10% Di-ethylene glycol, 10% 1.2-propanediol, 10% glycerol, 10% PEG 10K, 10% PCTP 50/50, 200mM NaCl , VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-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: ADSC QUANTUM 315r / 検出器: CCD / 日付: 2011年1月31日 / 詳細: bent cylindrical mirror | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
放射 | モノクロメーター: horizontally diffracting Si (111) monochromator and Pt coated mirrors in Kirkpatrick-Baez geometry for focusing 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: 0.8726 Å / 相対比: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
反射 | 解像度: 1.76→50 Å / Num. all: 32612 / Num. obs: 31957 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / 冗長度: 4.23 % / Biso Wilson estimate: 24.441 Å2 / Rmerge(I) obs: 0.136 / Rsym value: 0.119 / Net I/σ(I): 8.41 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
反射 シェル | Diffraction-ID: 1
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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: 4H2E 解像度: 1.764→42.806 Å / SU ML: 0.23 / Isotropic thermal model: Isotropic / 交差検証法: THROUGHOUT / σ(F): 2 / σ(I): -3 / 位相誤差: 25.49 / 立体化学のターゲット値: ML
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溶媒の処理 | 減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 1.764→42.806 Å
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拘束条件 |
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LS精密化 シェル | Refine-ID: X-RAY DIFFRACTION
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