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PDB: 16 件
5EJ8
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BU of 5ej8 by Molmil
EcMenD-ThDP-Mn2+ complex structure soaked with 2-ketoglutarate for 2 min
分子名称: (4S)-4-{3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3lambda~5~-thiazol-2-yl}-4-hydroxybutanoic acid, 1,2-ETHANEDIOL, 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, ...
著者Song, H.G, Dong, C, Chen, Y.Z, Sun, Y.R, Guo, Z.H.
登録日2015-11-01
公開日2016-06-01
最終更新日2024-03-20
実験手法X-RAY DIFFRACTION (1.34 Å)
主引用文献A Thiamine-Dependent Enzyme Utilizes an Active Tetrahedral Intermediate in Vitamin K Biosynthesis
J.Am.Chem.Soc., 138, 2016
5EJ7
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BU of 5ej7 by Molmil
EcMenD-ThDP-Mn2+ complex soaked with 2-ketoglutarate for 21 s
分子名称: (4S)-4-{3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3lambda~5~-thiazol-2-yl}-4-hydroxybutanoic acid, 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase, GLYCEROL, ...
著者Song, H.G, Dong, C, Chen, Y.Z, Sun, Y.R, Guo, Z.H.
登録日2015-11-01
公開日2016-06-01
最終更新日2024-03-20
実験手法X-RAY DIFFRACTION (1.56 Å)
主引用文献A Thiamine-Dependent Enzyme Utilizes an Active Tetrahedral Intermediate in Vitamin K Biosynthesis
J.Am.Chem.Soc., 138, 2016
5EJA
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BU of 5eja by Molmil
EcMenD-ThDP-Mn2+ complex soaked with 2-ketoglutarate for 2 min and soaked with isochorismate for 7 min
分子名称: (4S)-4-{3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3lambda~5~-thiazol-2-yl}-4-hydroxybutanoic acid, 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase, GLYCEROL, ...
著者Song, H.G, Dong, C, Chen, Y.Z, Sun, Y.R, Guo, Z.H.
登録日2015-11-01
公開日2016-06-01
最終更新日2024-03-20
実験手法X-RAY DIFFRACTION (1.6 Å)
主引用文献A Thiamine-Dependent Enzyme Utilizes an Active Tetrahedral Intermediate in Vitamin K Biosynthesis
J.Am.Chem.Soc., 138, 2016
5EJ9
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BU of 5ej9 by Molmil
EcMenD-ThDP-Mn2+ complex soaked with 2-ketoglutarate for 2 min and isochorismate for 13 min
分子名称: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase, FORMIC ACID, GLYCEROL, ...
著者Song, H.G, Dong, C, Chen, Y.Z, Sun, Y.R, Guo, Z.H.
登録日2015-11-01
公開日2016-06-01
最終更新日2023-11-08
実験手法X-RAY DIFFRACTION (1.72 Å)
主引用文献A Thiamine-Dependent Enzyme Utilizes an Active Tetrahedral Intermediate in Vitamin K Biosynthesis
J.Am.Chem.Soc., 138, 2016
5EJM
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BU of 5ejm by Molmil
ThDP-Mn2+ complex of R413A variant of EcMenD soaked with 2-ketoglutarate for 35 min
分子名称: (4~{R})-4-[3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-5-[2-[oxidanyl(phosphonooxy)phosphoryl]oxyethyl]-1,3-thiazol-3-ium-2-yl]-4-oxidanyl-butanoic acid, 1,2-ETHANEDIOL, 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase, ...
著者Song, H.G, Dong, C, Chen, Y.Z, Sun, Y.R, Guo, Z.H.
登録日2015-11-02
公開日2016-11-02
最終更新日2024-03-20
実験手法X-RAY DIFFRACTION (1.72 Å)
主引用文献Two active site arginines are critical determinants of substrate binding and catalysis in MenD, a thiamine-dependent enzyme in menaquinone biosynthesis.
Biochem. J., 2018
5EJ4
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BU of 5ej4 by Molmil
EcMenD-ThDP-Mn2+ complex soaked with 2-ketoglutarate for 15 min
分子名称: (4S)-4-{3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3lambda~5~-thiazol-2-yl}-4-hydroxybutanoic acid, 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase, FORMIC ACID, ...
著者Song, H.G, Dong, C, Chen, Y.Z, Sun, Y.R, Guo, Z.H.
登録日2015-11-01
公開日2016-06-01
最終更新日2024-03-20
実験手法X-RAY DIFFRACTION (1.773 Å)
主引用文献A Thiamine-Dependent Enzyme Utilizes an Active Tetrahedral Intermediate in Vitamin K Biosynthesis
J.Am.Chem.Soc., 138, 2016
3HWW
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BU of 3hww by Molmil
Crystal structure of menaquinone synthesis protein MenD from E. coli in complex with oxoglutarate
分子名称: 2-OXOGLUTARIC ACID, 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase, CHLORIDE ION, ...
著者Priyadarshi, A, Hwang, K.Y.
登録日2009-06-19
公開日2009-11-03
最終更新日2023-11-01
実験手法X-RAY DIFFRACTION (1.95 Å)
主引用文献Structural and functional analysis of Vitamin K2 synthesis protein MenD.
Biochem.Biophys.Res.Commun., 388, 2009
5EJ6
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BU of 5ej6 by Molmil
EcMenD-ThDP-Mn2+ complex soaked with 2-ketoglutarate for 2min then soaked with isochorismate for 2 min
分子名称: (4S)-4-{3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3lambda~5~-thiazol-2-yl}-4-hydroxybutanoic acid, 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase, MANGANESE (II) ION
著者Song, H.G, Dong, C, Chen, Y.Z, Sun, Y.R, Guo, Z.H.
登録日2015-11-01
公開日2016-06-01
最終更新日2024-03-20
実験手法X-RAY DIFFRACTION (2.243 Å)
主引用文献A Thiamine-Dependent Enzyme Utilizes an Active Tetrahedral Intermediate in Vitamin K Biosynthesis
J.Am.Chem.Soc., 138, 2016
5EJ5
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BU of 5ej5 by Molmil
EcMenD-ThDP-Mn2+ complex soaked with 2-ketoglutarate for 1.5 h
分子名称: (4S)-4-{3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3lambda~5~-thiazol-2-yl}-4-hydroxybutanoic acid, 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase, GLYCEROL, ...
著者Song, H.G, Dong, C, Chen, Y.Z, Sun, Y.R, Guo, Z.H.
登録日2015-11-01
公開日2016-06-01
最終更新日2024-03-20
実験手法X-RAY DIFFRACTION (2.3 Å)
主引用文献A Thiamine-Dependent Enzyme Utilizes an Active Tetrahedral Intermediate in Vitamin K Biosynthesis
J.Am.Chem.Soc., 138, 2016
5Z2R
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BU of 5z2r by Molmil
ThDP-Mn2+ complex of R395K variant of EcMenD soaked with 2-ketoglutarate for 5 min
分子名称: (4S)-4-{3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3lambda~5~-thiazol-2-yl}-4-hydroxybutanoic acid, 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase, FORMIC ACID, ...
著者Qin, M.M, Guo, Z.H.
登録日2018-01-03
公開日2018-11-28
最終更新日2023-11-22
実験手法X-RAY DIFFRACTION (2.3 Å)
主引用文献Two active site arginines are critical determinants of substrate binding and catalysis in MenD: a thiamine-dependent enzyme in menaquinone biosynthesis.
Biochem. J., 475, 2018
5Z2P
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BU of 5z2p by Molmil
ThDP-Mn2+ complex of R413K variant of EcMenD soaked with 2-ketoglutarate for 5 min
分子名称: (4S)-4-{3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3lambda~5~-thiazol-2-yl}-4-hydroxybutanoic acid, 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase, FORMIC ACID, ...
著者Qin, M.M, Guo, Z.H.
登録日2018-01-03
公開日2018-11-28
最終更新日2023-11-22
実験手法X-RAY DIFFRACTION (2.3 Å)
主引用文献Two active site arginines are critical determinants of substrate binding and catalysis in MenD: a thiamine-dependent enzyme in menaquinone biosynthesis.
Biochem. J., 475, 2018
5Z2U
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BU of 5z2u by Molmil
ThDP-Mn2+ complex of R395A variant of EcMenD soaked with 2-ketoglutarate for 5 min
分子名称: (4S)-4-{3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3lambda~5~-thiazol-2-yl}-4-hydroxybutanoic acid, 1,2-ETHANEDIOL, 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase, ...
著者Qin, M.M, Guo, Z.H.
登録日2018-01-04
公開日2018-11-28
最終更新日2023-11-22
実験手法X-RAY DIFFRACTION (2.35 Å)
主引用文献Two active site arginines are critical determinants of substrate binding and catalysis in MenD: a thiamine-dependent enzyme in menaquinone biosynthesis.
Biochem. J., 475, 2018
2JLC
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BU of 2jlc by Molmil
Crystal structure of E.coli MenD, 2-succinyl-5-enolpyruvyl-6-hydroxy- 3-cyclohexadiene-1-carboxylate synthase - native protein
分子名称: 2-SUCCINYL-5-ENOLPYRUVYL-6-HYDROXY-3-CYCLOHEXENE -1-CARBOXYLATE SYNTHASE, MANGANESE (II) ION, THIAMINE DIPHOSPHATE
著者Dawson, A, Fyfe, P.K, Hunter, W.N.
登録日2008-09-08
公開日2008-10-21
最終更新日2023-12-13
実験手法X-RAY DIFFRACTION (2.5 Å)
主引用文献Specificity and Reactivity in Menaquinone Biosynthesis: The Structure of Escherichia Coli Mend (2-Succinyl-5-Enolpyruvyl-6-Hydroxy-3-Cyclohexadiene-1-Carboxylate Synthase).
J.Mol.Biol., 384, 2008
3HWX
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BU of 3hwx by Molmil
Crystal structure of menaquinone synthesis protein MenD from E. coli in complex with ThDP
分子名称: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase, GLYCEROL, MAGNESIUM ION, ...
著者Priyadarshi, A, Hwang, K.Y.
登録日2009-06-19
公開日2009-11-03
最終更新日2023-11-01
実験手法X-RAY DIFFRACTION (2.6 Å)
主引用文献Structural and functional analysis of Vitamin K2 synthesis protein MenD.
Biochem.Biophys.Res.Commun., 388, 2009
3FLM
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BU of 3flm by Molmil
Crystal structure of menD from E.coli
分子名称: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
著者Priyadarshi, A, Hwang, K.Y.
登録日2008-12-19
公開日2009-03-24
最終更新日2023-11-01
実験手法X-RAY DIFFRACTION (2.7 Å)
主引用文献Structural insights of the MenD from Escherichia coli reveal ThDP affinity.
Biochem.Biophys.Res.Commun., 380, 2009
2JLA
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BU of 2jla by Molmil
Crystal structure of E.coli MenD, 2-succinyl-5-enolpyruvyl-6-hydroxy- 3-cyclohexadiene-1-carboxylate synthase - SeMet protein
分子名称: 2-SUCCINYL-5-ENOLPYRUVYL-6-HYDROXY-3-CYCLOHEXENE -1-CARBOXYLATE SYNTHASE, CHLORIDE ION, MANGANESE (II) ION, ...
著者Dawson, A, Fyfe, P.K, Hunter, W.N.
登録日2008-09-05
公開日2008-10-21
最終更新日2011-07-13
実験手法X-RAY DIFFRACTION (2.81 Å)
主引用文献Specificity and Reactivity in Menaquinone Biosynthesis: The Structure of Escherichia Coli Mend (2-Succinyl-5-Enolpyruvyl-6-Hydroxy-3-Cyclohexadiene-1-Carboxylate Synthase).
J.Mol.Biol., 384, 2008

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