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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: 1fzc | ||||||||||||
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タイトル | CRYSTAL STRUCTURE OF FRAGMENT DOUBLE-D FROM HUMAN FIBRIN WITH TWO DIFFERENT BOUND LIGANDS | ||||||||||||
![]() | (FIBRIN) x 5 | ||||||||||||
![]() | BLOOD COAGULATION / PLASMA PROTEIN / CROSSLINKING | ||||||||||||
機能・相同性 | ![]() blood coagulation, common pathway / induction of bacterial agglutination / fibrinogen complex / Regulation of TLR by endogenous ligand / platelet alpha granule / blood coagulation, fibrin clot formation / cellular response to leptin stimulus / positive regulation of heterotypic cell-cell adhesion / MyD88 deficiency (TLR2/4) / IRAK4 deficiency (TLR2/4) ...blood coagulation, common pathway / induction of bacterial agglutination / fibrinogen complex / Regulation of TLR by endogenous ligand / platelet alpha granule / blood coagulation, fibrin clot formation / cellular response to leptin stimulus / positive regulation of heterotypic cell-cell adhesion / MyD88 deficiency (TLR2/4) / IRAK4 deficiency (TLR2/4) / extracellular matrix structural constituent / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / plasminogen activation / p130Cas linkage to MAPK signaling for integrins / positive regulation of peptide hormone secretion / GRB2:SOS provides linkage to MAPK signaling for Integrins / positive regulation of exocytosis / protein secretion / cellular response to interleukin-1 / protein polymerization / Integrin cell surface interactions / Common Pathway of Fibrin Clot Formation / negative regulation of endothelial cell apoptotic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of vasoconstriction / fibrinolysis / cell adhesion molecule binding / Integrin signaling / positive regulation of substrate adhesion-dependent cell spreading / platelet alpha granule lumen / cell-matrix adhesion / positive regulation of protein secretion / Post-translational protein phosphorylation / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / platelet aggregation / response to calcium ion / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Signaling by BRAF and RAF1 fusions / Platelet degranulation / extracellular vesicle / protein-folding chaperone binding / ER-Phagosome pathway / protein-containing complex assembly / cell cortex / : / protein-macromolecule adaptor activity / blood microparticle / adaptive immune response / positive regulation of ERK1 and ERK2 cascade / Amyloid fiber formation / endoplasmic reticulum lumen / external side of plasma membrane / signaling receptor binding / innate immune response / synapse / structural molecule activity / cell surface / endoplasmic reticulum / extracellular space / extracellular exosome / extracellular region / metal ion binding / plasma membrane 類似検索 - 分子機能 | ||||||||||||
生物種 | ![]() | ||||||||||||
手法 | ![]() ![]() ![]() | ||||||||||||
![]() | Everse, S.J. / Spraggon, G. / Veerapandian, L. / Riley, M. / Doolittle, R.F. | ||||||||||||
![]() | ![]() タイトル: Crystal structure of fragment double-D from human fibrin with two different bound ligands. 著者: Everse, S.J. / Spraggon, G. / Veerapandian, L. / Riley, M. / Doolittle, R.F. #1: ![]() タイトル: Crystal Structures of Fragment D from Human Fibrinogen and its Crosslinked Counterpart from Fibrin 著者: Spraggon, G. / Everse, S.J. / Doolittle, R.F. #2: ![]() タイトル: Erratum. Crystal Structures of Fragment D from Human Fibrinogen and its Crosslinked Counterpart from Fibrin 著者: Spraggon, G. / Everse, S.J. / Doolittle, R.F. | ||||||||||||
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 | ![]() | 304.6 KB | 表示 | ![]() |
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PDB形式 | ![]() | 239.8 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 | ![]() | 552 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 637.9 KB | 表示 | |
XML形式データ | ![]() | 40.3 KB | 表示 | |
CIF形式データ | ![]() | 60.3 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 oper:
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要素
-タンパク質 , 3種, 6分子 ADBECF
#1: タンパク質 | 分子量: 10244.963 Da / 分子数: 2 / 断片: DOUBLE-D / 由来タイプ: 天然 / 由来: (天然) ![]() #2: タンパク質 | 分子量: 37691.992 Da / 分子数: 2 / 断片: DOUBLE-D / 由来タイプ: 天然 / 由来: (天然) ![]() #3: タンパク質 | 分子量: 36223.281 Da / 分子数: 2 / 断片: DOUBLE-D / 由来タイプ: 天然 / 由来: (天然) ![]() |
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-タンパク質・ペプチド , 2種, 4分子 GHIJ
#4: タンパク質・ペプチド | 分子量: 426.490 Da / 分子数: 2 / 断片: DOUBLE-D / 由来タイプ: 天然 / 由来: (天然) ![]() #5: タンパク質・ペプチド | 分子量: 467.522 Da / 分子数: 2 / 断片: DOUBLE-D / 由来タイプ: 天然 / 由来: (天然) ![]() |
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-糖 , 3種, 4分子 


#6: 多糖 | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose |
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#7: 糖 | ChemComp-MAN / |
#9: 糖 |
-非ポリマー , 2種, 435分子 


#8: 化合物 | ChemComp-CA / #10: 水 | ChemComp-HOH / | |
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-詳細
Has protein modification | Y |
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配列の詳細 | G1-G4: THIS PEPTIDE MIMICS A17-A20 OF THE FIBRIN SEQUENCE WITH PRO G 4 REPLACING VAL A 20 OF THE ...G1-G4: THIS PEPTIDE MIMICS A17-A20 OF THE FIBRIN SEQUENCE WITH PRO G 4 REPLACING VAL A 20 OF THE FIBRIN SEQUENCE. H1-H4: THIS PEPTIDE MIMICS D17-D20 OF THE FIBRIN SEQUENCE WITH PRO H 4 REPLACING VAL D 20 OF THE FIBRIN SEQUENCE. I1-I4: THIS PEPTIDE MIMICS B15-B18 OF THE FIBRIN SEQUENCE. J1-J4: THIS PEPTIDE MIMICS E15-E18 OF THE FIBRIN SEQUENCE. |
-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: 2.66 Å3/Da / 溶媒含有率: 50 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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結晶化 | pH: 7 詳細: 12% PEG 3350, 50 MM TRIS PH 7.0, 5 MM CALCIUM CHLORIDE, 1MM SODIUM AZIDE, 5MM GLY-PRO-ARG-PRO-AMIDE, 5MM GLY-HIS-ARG-PRO-AMIDE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
結晶 | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
結晶化 | *PLUS 手法: 蒸気拡散法, シッティングドロップ法 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
溶液の組成 | *PLUS
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-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 / 検出器: CCD / 日付: 1997年8月1日 |
放射 | 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray |
放射波長 | 波長: 0.91 Å / 相対比: 1 |
反射 | 解像度: 2.3→30 Å / Num. obs: 81010 / % possible obs: 94.5 % / Observed criterion σ(I): 0 / 冗長度: 4.6 % / Rmerge(I) obs: 0.093 |
反射 | *PLUS Num. measured all: 376448 |
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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: FIBRINOGEN FRAGMENT D 解像度: 2.3→20 Å / 交差検証法: THROUGHOUT / σ(F): 0 詳細: X-PLOR WAS ALSO USED IN THE EARLY STAGES OF REFINEMENT. RESIDUES ASN B 364 AND ASN E 364 ARE GLYCOSYLATED BY BIANNTENARY OLIGOSACCHARIDE CHAINS, ONLY THREE RESIDUES OF WHICH WERE VISIBLE IN ...詳細: X-PLOR WAS ALSO USED IN THE EARLY STAGES OF REFINEMENT. RESIDUES ASN B 364 AND ASN E 364 ARE GLYCOSYLATED BY BIANNTENARY OLIGOSACCHARIDE CHAINS, ONLY THREE RESIDUES OF WHICH WERE VISIBLE IN THE ELECTRON DENSITY FOR THE B CHAIN AND TWO FOR THE E CHAIN.
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原子変位パラメータ | Biso mean: 17.8 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 2.3→20 Å
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拘束条件 |
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ソフトウェア | *PLUS 名称: REFMAC / 分類: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化 | *PLUS Rfactor obs: 0.22 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
溶媒の処理 | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | *PLUS |