+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1bbr | ||||||
---|---|---|---|---|---|---|---|
タイトル | THE STRUCTURE OF RESIDUES 7-16 OF THE A ALPHA CHAIN OF HUMAN FIBRINOGEN BOUND TO BOVINE THROMBIN AT 2.3 ANGSTROMS RESOLUTION | ||||||
要素 |
| ||||||
キーワード | SERINE PROTEASE (セリンプロテアーゼ) | ||||||
機能・相同性 | 機能・相同性情報 blood coagulation, common pathway / induction of bacterial agglutination / fibrinogen complex / Regulation of TLR by endogenous ligand / fibrinogen binding / blood coagulation, fibrin clot formation / Α顆粒 / MyD88 deficiency (TLR2/4) / positive regulation of heterotypic cell-cell adhesion / IRAK4 deficiency (TLR2/4) ...blood coagulation, common pathway / induction of bacterial agglutination / fibrinogen complex / Regulation of TLR by endogenous ligand / fibrinogen binding / blood coagulation, fibrin clot formation / Α顆粒 / MyD88 deficiency (TLR2/4) / positive regulation of heterotypic cell-cell adhesion / IRAK4 deficiency (TLR2/4) / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / extracellular matrix structural constituent / plasminogen activation / p130Cas linkage to MAPK signaling for integrins / トロンビン / positive regulation of peptide hormone secretion / positive regulation of exocytosis / GRB2:SOS provides linkage to MAPK signaling for Integrins / protein polymerization / Integrin cell surface interactions / positive regulation of blood coagulation / negative regulation of endothelial cell apoptotic process / Common Pathway of Fibrin Clot Formation / positive regulation of substrate adhesion-dependent cell spreading / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of vasoconstriction / fibrinolysis / Integrin signaling / cell-matrix adhesion / platelet alpha granule lumen / Post-translational protein phosphorylation / acute-phase response / positive regulation of protein secretion / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / 血小板 / 凝固・線溶系 / 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 / extracellular vesicle / 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 / ER-Phagosome pathway / protein-containing complex assembly / collagen-containing extracellular matrix / blood microparticle / 獲得免疫系 / positive regulation of ERK1 and ERK2 cascade / Amyloid fiber formation / 小胞体 / external side of plasma membrane / signaling receptor binding / serine-type endopeptidase activity / 自然免疫系 / calcium ion binding / structural molecule activity / 細胞膜 / 小胞体 / タンパク質分解 / extracellular space / extracellular exosome / extracellular region / metal ion binding / 細胞膜 類似検索 - 分子機能 | ||||||
生物種 | Bos taurus (ウシ) Homo sapiens (ヒト) | ||||||
手法 | X線回折 / 解像度: 2.3 Å | ||||||
データ登録者 | Martin, P. / Edwards, B. | ||||||
引用 | ジャーナル: J.Biol.Chem. / 年: 1992 タイトル: The structure of residues 7-16 of the A alpha-chain of human fibrinogen bound to bovine thrombin at 2.3-A resolution. 著者: Martin, P.D. / Robertson, W. / Turk, D. / Huber, R. / Bode, W. / Edwards, B.F. | ||||||
履歴 |
|
-構造の表示
構造ビューア | 分子: MolmilJmol/JSmol |
---|
-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 1bbr.cif.gz | 205.8 KB | 表示 | PDBx/mmCIF形式 |
---|---|---|---|---|
PDB形式 | pdb1bbr.ent.gz | 168.8 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1bbr.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
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/bb/1bbr ftp://data.pdbj.org/pub/pdb/validation_reports/bb/1bbr | HTTPS FTP |
---|
-関連構造データ
-リンク
-集合体
登録構造単位 |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
単位格子 |
| ||||||||
Atom site foot note | 1: CIS PROLINE - PRO H 37 / 2: CIS PROLINE - PRO K 37 / 3: CIS PROLINE - PRO N 37 |
-要素
-タンパク質・ペプチド , 2種, 6分子 LJMFGI
#1: タンパク質・ペプチド | 分子量: 5735.240 Da / 分子数: 3 / 由来タイプ: 組換発現 / 由来: (組換発現) Bos taurus (ウシ) / 参照: UniProt: P00735, トロンビン #4: タンパク質・ペプチド | 分子量: 1047.144 Da / 分子数: 3 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 参照: UniProt: P02671 |
---|
-タンパク質 , 3種, 4分子 HEKN
#2: タンパク質 | 分子量: 17525.346 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Bos taurus (ウシ) / 参照: UniProt: P00735, トロンビン |
---|---|
#3: タンパク質 | 分子量: 12265.071 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Bos taurus (ウシ) / 参照: UniProt: P00735, トロンビン |
#5: タンパク質 | 分子量: 29772.422 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Bos taurus (ウシ) / 参照: UniProt: P00735, トロンビン |
-非ポリマー , 1種, 706分子
#6: 水 | ChemComp-HOH / |
---|
-実験情報
-実験
実験 | 手法: X線回折 |
---|
-試料調製
結晶 | マシュー密度: 3.22 Å3/Da / 溶媒含有率: 61.78 % |
---|---|
結晶化 | *PLUS pH: 8 / 手法: 蒸気拡散法, ハンギングドロップ法 |
溶液の組成 | *PLUS 濃度: 40 % / 一般名: ammonium sulfate |
-データ収集
放射 | 散乱光タイプ: x-ray |
---|---|
放射波長 | 相対比: 1 |
反射 | *PLUS 最高解像度: 2.3 Å / 最低解像度: 9999 Å / Num. obs: 47459 / % possible obs: 78.9 % / Num. measured all: 176974 / Rmerge(I) obs: 0.075 |
反射 シェル | *PLUS 最高解像度: 2.3 Å / 最低解像度: 2.4 Å / % possible obs: 39 % |
-解析
ソフトウェア | 名称: PROLSQ / 分類: 精密化 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
精密化 | 解像度: 2.3→7 Å / Rfactor obs: 0.167 / σ(I): 1 詳細: THERE ARE THREE INDEPENDENT COMPLEXES IN THE ASYMMETRIC UNIT. COMPLEX I IS EPSILON THROMBIN (ADDITIONAL CHAIN BREAK BETWEEN RESIDUES 149A AND 149B), AND MOLECULES II AND III ARE ALPHA ...詳細: THERE ARE THREE INDEPENDENT COMPLEXES IN THE ASYMMETRIC UNIT. COMPLEX I IS EPSILON THROMBIN (ADDITIONAL CHAIN BREAK BETWEEN RESIDUES 149A AND 149B), AND MOLECULES II AND III ARE ALPHA THROMBIN. FIBRINOPEPTIDE I HAS AN OCCUPANCY THAT MAKES THE AVERAGE B OF ARG-318 ROUGHLY EQUAL TO THAT IN FIBRINOPEPTIDES II AND III. THE DEPOSITORS DO NOT SEE ANY DENSITY AT ALL FOR THROMBIN RESIDUES 1U - 1I, AND POOR DENSITY FOR THE N AND C TERMINI OF THE LIGHT CHAINS, THE C TERMINUS OF THE HEAVY CHAINS, AND THE FIVE RESIDUES BORDERING 149B IN MOLECULES II AND III. EPSILON THROMBIN IN COMPLEX I HAS BEEN ASSIGNED CHAIN INDICATORS *L*, *H*, AND *E*. THE FIBRINOPEPTIDE IN COMPLEX I HAS BEEN ASSIGNED CHAIN INDICATOR *F*. ALPHA THROMBIN IN COMPLEX II HAS BEEN ASSIGNED CHAIN INDICATORS *J* AND *K*. THE FIBRINOPEPTIDE IN COMPLEX II HAS BEEN ASSIGNED CHAIN INDICATOR *G*. ALPHA THROMBIN IN COMPLEX III HAS BEEN ASSIGNED CHAIN INDICATORS *M* AND *N*. THE FIBRINOPEPTIDE IN COMPLEX III HAS BEEN ASSIGNED CHAIN INDICATOR *I*. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 2.3→7 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
拘束条件 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化 | *PLUS Num. reflection obs: 47459 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
溶媒の処理 | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | *PLUS Biso mean: 33.5 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
拘束条件 | *PLUS
|