+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1ppg | ||||||||||||
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タイトル | The refined 2.3 angstroms crystal structure of human leukocyte elastase in a complex with a valine chloromethyl ketone inhibitor | ||||||||||||
要素 |
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キーワード | HYDROLASE/HYDROLASE INHIBITOR / SERINE PROTEINASE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||||||||
機能・相同性 | 機能・相同性情報 leukocyte elastase / biosynthetic process of antibacterial peptides active against Gram-negative bacteria / neutrophil-mediated killing of fungus / negative regulation of chemotaxis / acute inflammatory response to antigenic stimulus / positive regulation of leukocyte tethering or rolling / response to yeast / leukocyte migration involved in inflammatory response / negative regulation of interleukin-8 production / negative regulation of chemokine production ...leukocyte elastase / biosynthetic process of antibacterial peptides active against Gram-negative bacteria / neutrophil-mediated killing of fungus / negative regulation of chemotaxis / acute inflammatory response to antigenic stimulus / positive regulation of leukocyte tethering or rolling / response to yeast / leukocyte migration involved in inflammatory response / negative regulation of interleukin-8 production / negative regulation of chemokine production / Antimicrobial peptides / cytokine binding / pyroptotic inflammatory response / Activation of Matrix Metalloproteinases / neutrophil-mediated killing of gram-negative bacterium / Collagen degradation / extracellular matrix disassembly / Pyroptosis / phagocytosis / response to UV / transcription repressor complex / phagocytic vesicle / Degradation of the extracellular matrix / secretory granule / Regulation of Complement cascade / positive regulation of interleukin-8 production / positive regulation of smooth muscle cell proliferation / positive regulation of MAP kinase activity / protein catabolic process / negative regulation of inflammatory response / intracellular calcium ion homeostasis / specific granule lumen / transcription corepressor activity / azurophil granule lumen / positive regulation of immune response / peptidase activity / heparin binding / collagen-containing extracellular matrix / endopeptidase activity / protease binding / response to lipopolysaccharide / defense response to bacterium / serine-type endopeptidase activity / Neutrophil degranulation / negative regulation of transcription by RNA polymerase II / cell surface / proteolysis / extracellular space / extracellular exosome / extracellular region / cytoplasm / cytosol 類似検索 - 分子機能 | ||||||||||||
生物種 | HOMO SAPIENS (ヒト) | ||||||||||||
手法 | X線回折 / 解像度: 2.3 Å | ||||||||||||
データ登録者 | Bode, W. / Wei, A-Z. | ||||||||||||
引用 | ジャーナル: FEBS Lett. / 年: 1988 タイトル: The refined 2.3 A crystal structure of human leukocyte elastase in a complex with a valine chloromethyl ketone inhibitor. 著者: Wei, A.Z. / Mayr, I. / Bode, W. #1: ジャーナル: Embo J. / 年: 1986 タイトル: X-Ray Crystal Structure of the Complex of Human Leukocyte Elastase (Pmn Elastase) and the Third Domain of the Turkey Ovomucoid Inhibitor 著者: Bode, W. / Wei, A.-Z. / Huber, R. / Meyer, E. / Travis, J. / Neumann, S. | ||||||||||||
履歴 |
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Remark 700 | SHEET THE SHEETS PRESENTED AS *B1* AND *B2* ON SHEET RECORDS BELOW ARE ACTUALLY SIX-STRANDED BETA- ...SHEET THE SHEETS PRESENTED AS *B1* AND *B2* ON SHEET RECORDS BELOW ARE ACTUALLY SIX-STRANDED BETA-BARRELS. THESE ARE REPRESENTED BY SEVEN-STRANDED SHEETS IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-構造の表示
構造ビューア | 分子: MolmilJmol/JSmol |
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-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 1ppg.cif.gz | 65.1 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb1ppg.ent.gz | 46.3 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1ppg.json.gz | ツリー表示 | PDBx/mmJSON形式 | |
その他 | その他のダウンロード |
-検証レポート
文書・要旨 | 1ppg_validation.pdf.gz | 573.5 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 1ppg_full_validation.pdf.gz | 592.7 KB | 表示 | |
XML形式データ | 1ppg_validation.xml.gz | 10.5 KB | 表示 | |
CIF形式データ | 1ppg_validation.cif.gz | 15.3 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/pp/1ppg ftp://data.pdbj.org/pub/pdb/validation_reports/pp/1ppg | HTTPS FTP |
-関連構造データ
-リンク
-集合体
登録構造単位 |
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2 |
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単位格子 |
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-要素
#1: タンパク質 | 分子量: 23318.982 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) HOMO SAPIENS (ヒト) / 参照: UniProt: P08246, leukocyte elastase |
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#2: タンパク質・ペプチド | |
#3: 多糖 | beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose- ...beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose |
#4: 多糖 | alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-2)-beta-D-mannopyranose-(1- ...alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-2)-beta-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose |
#5: 水 | ChemComp-HOH / |
構成要素の詳細 | THE UNBOUND FORM OF THE INHIBITOR IS MEO-SUCCINYL-ALA-ALA-PRO-VAL CHLOROMETHYLKETONE. UPON REACTION ...THE UNBOUND FORM OF THE INHIBITOR IS MEO-SUCCINYL-ALA-ALA-PRO-VAL CHLOROMETH |
-実験情報
-実験
実験 | 手法: X線回折 |
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-試料調製
結晶 | マシュー密度: 2.36 Å3/Da / 溶媒含有率: 47.86 % | |||||||||||||||
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結晶化 | *PLUS 温度: 20 ℃ / pH: 9 / 手法: 蒸気拡散法, ハンギングドロップ法 | |||||||||||||||
溶液の組成 | *PLUS
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-データ収集
放射 | 散乱光タイプ: x-ray |
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放射波長 | 相対比: 1 |
反射 | *PLUS 最高解像度: 2.3 Å / Num. obs: 7390 / % possible obs: 75 % / Num. measured all: 20260 / Rmerge(I) obs: 0.081 |
-解析
ソフトウェア | 名称: EREF / 分類: 精密化 | ||||||||||||
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精密化 | 解像度: 2.3→8 Å / Rfactor Rwork: 0.145 | ||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 2.3→8 Å
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ソフトウェア | *PLUS 名称: EREF / 分類: refinement | ||||||||||||
精密化 | *PLUS 最高解像度: 2.3 Å / 最低解像度: 8 Å / Num. reflection obs: 7104 / σ(I): 2 / Rfactor obs: 0.145 | ||||||||||||
溶媒の処理 | *PLUS | ||||||||||||
原子変位パラメータ | *PLUS | ||||||||||||
拘束条件 | *PLUS
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