- PDB-1gi4: A NOVEL SERINE PROTEASE INHIBITION MOTIF INVOLVING A MULTI-CENTER... -
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基本情報
登録情報
データベース: PDB / ID: 1gi4
タイトル
A NOVEL SERINE PROTEASE INHIBITION MOTIF INVOLVING A MULTI-CENTERED SHORT HYDROGEN BONDING NETWORK AT THE ACTIVE SITE
要素
BETA-TRYPSIN
キーワード
HYDROLASE / three-centered / very short hydrogen bond / oxyanion hole water / shift of pKa of His57 / structure-based drug design / specificity / urokinase / trypsin / thrombin / Zn+2-mediated inhibition
機能・相同性
機能・相同性情報
trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / endopeptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding 類似検索 - 分子機能
: / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin ...: / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta 類似検索 - ドメイン・相同性
解像度: 1.37→1.43 Å / Rmerge(I) obs: 0.248 / Num. unique all: 2480 / % possible all: 34.3
反射
*PLUS
Num. measured all: 191096
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解析
ソフトウェア
名称
バージョン
分類
bioteX
データ収集
bioteX
データ削減
X-PLOR
3.851
精密化
bioteX
データスケーリング
精密化
構造決定の手法: フーリエ合成 / 解像度: 1.37→7 Å / σ(F): 1.8 / 立体化学のターゲット値: X-PLOR force field 詳細: Bulk solvent terms included in Fob file created with standard X-PLOR script. Residues simultaneously refined in two or more conformations are: Val53, Leu66, Ser86, Lys87, Leu99, Ser113, ...詳細: Bulk solvent terms included in Fob file created with standard X-PLOR script. Residues simultaneously refined in two or more conformations are: Val53, Leu66, Ser86, Lys87, Leu99, Ser113, Ser130, Gln135, Asp165, Ser166, Ser170, Gln175, Ser217, Lys230, Ser236 Disordered waters are: HOH271 which is close to HOH272; HOH349 which is close to HOH350; HOH756 which is close to Lys230 in conformation 1, but makes an H-bond to Lys230 in conformation 2. His40 and HIS91 are MONOPROTONATED ON THE EPSILON NITROGEN. His57 is doubly protonatd.
Rfactor
反射数
%反射
Rfree
0.214
4932
10 %
Rwork
0.193
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obs
0.192
48722
83 %
all
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58701
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精密化ステップ
サイクル: LAST / 解像度: 1.37→7 Å
タンパク質
核酸
リガンド
溶媒
全体
原子数
3366
0
38
828
4232
拘束条件
Refine-ID
タイプ
Dev ideal
X-RAY DIFFRACTION
x_bond_d
0.016
X-RAY DIFFRACTION
x_angle_deg
3.7
ソフトウェア
*PLUS
名称: X-PLOR / バージョン: 3.851 / 分類: refinement
精密化
*PLUS
最低解像度: 7 Å / σ(F): 1.8 / % reflection Rfree: 10 %
溶媒の処理
*PLUS
原子変位パラメータ
*PLUS
拘束条件
*PLUS
Refine-ID
タイプ
Dev ideal
X-RAY DIFFRACTION
x_angle_deg
3.7
X-RAY DIFFRACTION
x_dihedral_angle_d
X-RAY DIFFRACTION
x_dihedral_angle_deg
26.3
LS精密化 シェル
*PLUS
最高解像度: 1.37 Å / 最低解像度: 1.43 Å / Rfactor Rfree: 0.214 / Rfactor obs: 0.193