+
データを開く
-
基本情報
登録情報 | データベース: PDB / ID: 6gpb | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
タイトル | REFINED CRYSTAL STRUCTURE OF THE PHOSPHORYLASE-HEPTULOSE 2-PHOSPHATE-OLIGOSACCHARIDE-AMP COMPLEX | |||||||||
![]() | GLYCOGEN PHOSPHORYLASE B | |||||||||
![]() | GLYCOGEN PHOSPHORYLASE | |||||||||
機能・相同性 | ![]() glycogen phosphorylase / glycogen phosphorylase activity / linear malto-oligosaccharide phosphorylase activity / SHG alpha-glucan phosphorylase activity / glycogen catabolic process / skeletal muscle myofibril / pyridoxal phosphate binding / nucleotide binding 類似検索 - 分子機能 | |||||||||
生物種 | ![]() ![]() | |||||||||
手法 | ![]() | |||||||||
![]() | Acharya, K.R. / Johnson, L.N. | |||||||||
![]() | ![]() タイトル: Refined crystal structure of the phosphorylase-heptulose 2-phosphate-oligosaccharide-AMP complex. 著者: Johnson, L.N. / Acharya, K.R. / Jordan, M.D. / McLaughlin, P.J. #1: ![]() タイトル: Glycogen Phosphorylase B: Description of the Protein Structure 1 1991 著者: Acharya, K.R. / Stuart, D.I. / Varvill, K.M. / Johnson, L.N. #2: ![]() タイトル: Structural Mechanism for Glycogen Phosphorylase Control by Phosphorylation and AMP 著者: Barford, D. / Hu, S.-H. / Johnson, L.N. #3: ![]() タイトル: Comparison of the Binding of Glucose and Glucose-1-Phosphate Derivatives to T-State Glycogen Phosphorylase B 著者: Martin, J.L. / Johnson, L.N. / Withers, S.G. #4: ![]() タイトル: The Allosteric Transition of Glycogen Phosphorylase 著者: Barford, D. / Johnson, L.N. #5: ![]() タイトル: Structural Changes in Glycogen Phosphorylase Induced by Phosphorylation 著者: Sprang, S.R. / Acharya, K.R. / Goldsmith, E.J. / Stuart, D.I. / Varvill, K. / Fletterick, R.J. / Madsen, N.B. / Johnson, L.N. | |||||||||
履歴 |
|
-
構造の表示
構造ビューア | 分子: ![]() ![]() |
---|
-
ダウンロードとリンク
-
ダウンロード
PDBx/mmCIF形式 | ![]() | 196.3 KB | 表示 | ![]() |
---|---|---|---|---|
PDB形式 | ![]() | 153.4 KB | 表示 | ![]() |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
その他 | ![]() |
-検証レポート
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
---|
-関連構造データ
類似構造データ |
---|
-
リンク
-
集合体
登録構造単位 | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
単位格子 |
| ||||||||
Atom site foot note | 1: RESIDUE 380 IS LEU IN THE SEQUENCE (K.NAKANO,P.K.HWANG, R.J.FLETTERICK, FEBS LETT., V. 204, P. 283, 1986) BUT IT HAS BEEN PRESENTED AS ILE IN THIS ENTRY. THIS ASSIGNMENT WAS MADE IN THE ORIGINAL ...1: RESIDUE 380 IS LEU IN THE SEQUENCE (K.NAKANO,P.K.HWANG, R.J.FLETTERICK, FEBS LETT., V. 204, P. 283, 1986) BUT IT HAS BEEN PRESENTED AS ILE IN THIS ENTRY. THIS ASSIGNMENT WAS MADE IN THE ORIGINAL STRUCTURE DETERMINATION AT 1.9 ANGSTROMS (PRESENTED IN PROTEIN DATA BANK ENTRY 1GPB) AND CARRIED THROUGH TO THE OTHER ENTRIES. ILE IS MORE CONSISTENT WITH THE ELECTRON DENSITY. HOWEVER, THE RESOLUTION AT 1.9 ANGSTROMS DOES NOT ALLOW A DEFINITIVE ASSIGNMENT. |
-
要素
-タンパク質 , 1種, 1分子 A
#1: タンパク質 | 分子量: 97291.203 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() |
---|
-糖 , 2種, 2分子 ![](data/chem/img/H2P.gif)
#2: 多糖 | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D- ...alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltopentaose |
---|---|
#3: 糖 | ChemComp-H2P / |
-非ポリマー , 3種, 611分子 ![](data/chem/img/PLP.gif)
![](data/chem/img/AMP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/AMP.gif)
![](data/chem/img/HOH.gif)
#4: 化合物 | ChemComp-PLP / | ||
---|---|---|---|
#5: 化合物 | #6: 水 | ChemComp-HOH / | |
-詳細
非ポリマーの詳細 | MALTOHEPTAOSE CONSISTS OF SEVEN LINKED GLUCOSES. ONLY FIVE OF THE GLUCOSES WERE LOCATED IN THE ...MALTOHEPTA |
---|---|
配列の詳細 | RESIDUE 380 IS LEU IN THE SEQUENCE (K.NAKANO,P.K.HWANG, R.J.FLETTERICK, FEBS LETT., V. 204, P. 283, ...RESIDUE 380 IS LEU IN THE SEQUENCE (K.NAKANO,P.K.HWANG, R.J.FLETTERICK |
-実験情報
-実験
実験 | 手法: ![]() |
---|
-
試料調製
結晶 | マシュー密度: 2.47 Å3/Da / 溶媒含有率: 50.13 % | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
結晶化 | *PLUS 温度: 16 ℃ / pH: 6.7 / 手法: batch method / 詳細: took Mclaughlin et al., 1984 from original paper | ||||||||||||||||||||
溶液の組成 | *PLUS
|
-データ収集
反射 | *PLUS 最高解像度: 2.86 Å / Num. obs: 18715 / Num. measured all: 88108 / Rmerge(I) obs: 0.063 |
---|
-
解析
ソフトウェア | 名称: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
精密化 | 解像度: 2.86→8 Å 詳細: THE N-TERMINAL RESIDUES 14 - 18 WERE ESTABLISHED TOWARDS THE END OF THE REFINEMENT. THESE RESIDUES ARE NOT WELL ORDERED. THEIR ATTACHMENT TO THE REST OF THE CHAIN CONTAINS SOME BAD ...詳細: THE N-TERMINAL RESIDUES 14 - 18 WERE ESTABLISHED TOWARDS THE END OF THE REFINEMENT. THESE RESIDUES ARE NOT WELL ORDERED. THEIR ATTACHMENT TO THE REST OF THE CHAIN CONTAINS SOME BAD STEREOCHEMISTRY. A MORE CAREFUL AND CORRECT REPOSITIONING OF THESE RESIDUES IS GIVEN IN PROTEIN DATA BANK ENTRY 2GPB, THE T STATE PHOSPHORYLASE B COMPLEX WITH GLUCOSE.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 2.86→8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
拘束条件 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化 | *PLUS Rfactor Rwork: 0.201 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
溶媒の処理 | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
拘束条件 | *PLUS タイプ: x_angle_d / Dev ideal: 3.4 |