- PDB-4bti: factor Xa in complex with the dual thrombin-FXa inhibitor 58. -
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IDまたはキーワード:
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基本情報
登録情報
データベース: PDB / ID: 4bti
タイトル
factor Xa in complex with the dual thrombin-FXa inhibitor 58.
要素
COAGULATION FACTOR X HEAVY CHAIN
COAGULATION FACTOR X LIGHT CHAIN
キーワード
HYDROLASE / SAR107375 / FACTOR XA INHIBITOR / THROMBIN INHIBITOR / CHLOROTHIOPHENE P1 FRAGMENT / S3 SUBSITE / MICROSOMES STABILITY / ORAL ANTITHROMBOTIC / DUAL INHIBITOR / IV ANTITHROMBOTIC
機能・相同性
機能・相同性情報
coagulation factor Xa / Defective factor IX causes thrombophilia / Defective cofactor function of FVIIIa variant / Defective F9 variant does not activate FX / Extrinsic Pathway of Fibrin Clot Formation / positive regulation of leukocyte chemotaxis / positive regulation of TOR signaling / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Common Pathway of Fibrin Clot Formation ...coagulation factor Xa / Defective factor IX causes thrombophilia / Defective cofactor function of FVIIIa variant / Defective F9 variant does not activate FX / Extrinsic Pathway of Fibrin Clot Formation / positive regulation of leukocyte chemotaxis / positive regulation of TOR signaling / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins / Intrinsic Pathway of Fibrin Clot Formation / phospholipid binding / Golgi lumen / blood coagulation / positive regulation of cell migration / endoplasmic reticulum lumen / external side of plasma membrane / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space / extracellular region / plasma membrane 類似検索 - 分子機能
SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "FB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.
手法: 蒸気拡散法, ハンギングドロップ法 / pH: 5.7 詳細: PROTEIN SOLUTION: 8 MG/ML DESGLA FACTOR XA, 5 MM MES (PH 6.0), 5 MM CACL2, 100 MM BENZAMIDINE. RESERVOIR SOLUTION: 18-20% PEG600, 50 MM MES (PH 5.7). HANGING DROP SETUP.
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
Reflection twin
Crystal-ID
ID
Operator
Domain-ID
Fraction
1
1
H, K, L
1
0.619
1
1
K, H, -L
2
0.381
反射
解像度: 2.29→47.98 Å / Num. obs: 26327 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / 冗長度: 2.9 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 6.7
反射 シェル
解像度: 2.29→2.36 Å / 冗長度: 2.5 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.6 / % possible all: 94.7
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解析
ソフトウェア
名称
バージョン
分類
REFMAC
5.7.0029
精密化
XDS
データ削減
XSCALE
データスケーリング
精密化
構造決定の手法: 分子置換 開始モデル: IN-HOUSE FACTOR XA STRUCTURE 解像度: 2.3→36.99 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.9 / SU B: 8.394 / SU ML: 0.134 / 交差検証法: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.051 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD / 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
反射数
%反射
Selection details
Rfree
0.22434
1207
4.6 %
RANDOM
Rwork
0.166
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-
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obs
0.16862
25117
98.46 %
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溶媒の処理
イオンプローブ半径: 0.7 Å / 減衰半径: 0.7 Å / VDWプローブ半径: 1 Å / 溶媒モデル: MASK