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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
Descriptor: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase, FORMIC ACID, GLYCEROL, ...
Authors:Song, H.G, Dong, C, Chen, Y.Z, Sun, Y.R, Guo, Z.H.
Deposit date:2015-11-01
Release date:2016-06-01
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (1.72 Å)
Cite: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
Descriptor: (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, ...
Authors:Song, H.G, Dong, C, Chen, Y.Z, Sun, Y.R, Guo, Z.H.
Deposit date:2015-11-01
Release date:2016-06-01
Last modified:2024-03-20
Method:X-RAY DIFFRACTION (1.6 Å)
Cite: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
Descriptor: (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, ...
Authors:Song, H.G, Dong, C, Chen, Y.Z, Sun, Y.R, Guo, Z.H.
Deposit date:2015-11-01
Release date:2016-06-01
Last modified:2024-03-20
Method:X-RAY DIFFRACTION (1.56 Å)
Cite: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
Descriptor: (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, ...
Authors:Song, H.G, Dong, C, Chen, Y.Z, Sun, Y.R, Guo, Z.H.
Deposit date:2015-11-01
Release date:2016-06-01
Last modified:2024-03-20
Method:X-RAY DIFFRACTION (2.3 Å)
Cite:A Thiamine-Dependent Enzyme Utilizes an Active Tetrahedral Intermediate in Vitamin K Biosynthesis
J.Am.Chem.Soc., 138, 2016
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
Descriptor: (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
Authors:Song, H.G, Dong, C, Chen, Y.Z, Sun, Y.R, Guo, Z.H.
Deposit date:2015-11-01
Release date:2016-06-01
Last modified:2024-03-20
Method:X-RAY DIFFRACTION (2.243 Å)
Cite:A Thiamine-Dependent Enzyme Utilizes an Active Tetrahedral Intermediate in Vitamin K Biosynthesis
J.Am.Chem.Soc., 138, 2016
5EJ4
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BU of 5ej4 by Molmil
EcMenD-ThDP-Mn2+ complex soaked with 2-ketoglutarate for 15 min
Descriptor: (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, ...
Authors:Song, H.G, Dong, C, Chen, Y.Z, Sun, Y.R, Guo, Z.H.
Deposit date:2015-11-01
Release date:2016-06-01
Last modified:2024-03-20
Method:X-RAY DIFFRACTION (1.773 Å)
Cite:A Thiamine-Dependent Enzyme Utilizes an Active Tetrahedral Intermediate in Vitamin K Biosynthesis
J.Am.Chem.Soc., 138, 2016
5EJ8
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BU of 5ej8 by Molmil
EcMenD-ThDP-Mn2+ complex structure soaked with 2-ketoglutarate for 2 min
Descriptor: (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, ...
Authors:Song, H.G, Dong, C, Chen, Y.Z, Sun, Y.R, Guo, Z.H.
Deposit date:2015-11-01
Release date:2016-06-01
Last modified:2024-03-20
Method:X-RAY DIFFRACTION (1.34 Å)
Cite:A Thiamine-Dependent Enzyme Utilizes an Active Tetrahedral Intermediate in Vitamin K Biosynthesis
J.Am.Chem.Soc., 138, 2016
4EML
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BU of 4eml by Molmil
Synechocystis sp. PCC 6803 1,4-dihydroxy-2-naphthoyl-coenzyme A synthase (MenB) in complex with bicarbonate
Descriptor: (4S)-2-METHYL-2,4-PENTANEDIOL, BICARBONATE ION, CHLORIDE ION, ...
Authors:Song, H.G.
Deposit date:2012-04-12
Release date:2012-06-20
Last modified:2024-03-20
Method:X-RAY DIFFRACTION (2.043 Å)
Cite:Active site binding and catalytic role of bicarbonate in 1,4-dihydroxy-2-naphthoyl coenzyme A synthases from vitamin K biosynthetic pathways
Biochemistry, 51, 2012
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
Descriptor: (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, ...
Authors:Song, H.G, Dong, C, Chen, Y.Z, Sun, Y.R, Guo, Z.H.
Deposit date:2015-11-02
Release date:2016-11-02
Last modified:2024-03-20
Method:X-RAY DIFFRACTION (1.72 Å)
Cite:Two active site arginines are critical determinants of substrate binding and catalysis in MenD, a thiamine-dependent enzyme in menaquinone biosynthesis.
Biochem. J., 2018
4ELS
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BU of 4els by Molmil
Structure of E. Coli. 1,4-dihydroxy-2- naphthoyl coenzyme A synthases (MENB) in complex with bicarbonate
Descriptor: 1,2-ETHANEDIOL, 1,4-Dihydroxy-2-naphthoyl-CoA synthase, BICARBONATE ION, ...
Authors:Sun, Y.R, Song, H.G, Li, J, Jiang, M, Li, Y, Zhou, J.H, Guo, Z.H.
Deposit date:2012-04-11
Release date:2012-06-06
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (2.303 Å)
Cite:Active site binding and catalytic role of bicarbonate in 1,4-dihydroxy-2-naphthoyl coenzyme A synthases from vitamin K biosynthetic pathways
Biochemistry, 51, 2012
4ELX
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BU of 4elx by Molmil
Structure of apo E.coli. 1,4-dihydroxy-2- naphthoyl CoA synthases with Cl
Descriptor: 1,2-ETHANEDIOL, 1,4-Dihydroxy-2-naphthoyl-CoA synthase, CHLORIDE ION, ...
Authors:Sun, Y.R, Song, H.G, Li, J, Jiang, M, Li, Y, Zhou, J.H, Guo, Z.H.
Deposit date:2012-04-11
Release date:2012-06-06
Last modified:2024-03-20
Method:X-RAY DIFFRACTION (2.191 Å)
Cite:Active site binding and catalytic role of bicarbonate in 1,4-dihydroxy-2-naphthoyl coenzyme A synthases from vitamin K biosynthetic pathways
Biochemistry, 51, 2012
4ELW
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BU of 4elw by Molmil
Structure of E. coli. 1,4-dihydroxy-2- naphthoyl coenzyme A synthases (MENB) in complex with nitrate
Descriptor: 1,4-Dihydroxy-2-naphthoyl-CoA synthase, CHLORIDE ION, GLYCEROL, ...
Authors:Sun, Y.R, Song, H.G, Li, J, Jiang, M, Li, Y, Zhou, J.H, Guo, Z.H.
Deposit date:2012-04-11
Release date:2012-06-06
Last modified:2024-03-20
Method:X-RAY DIFFRACTION (2.551 Å)
Cite:Active site binding and catalytic role of bicarbonate in 1,4-dihydroxy-2-naphthoyl coenzyme A synthases from vitamin K biosynthetic pathways
Biochemistry, 51, 2012
4QII
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BU of 4qii by Molmil
Crystal Structure of type II MenB from Mycobacteria tuberculosis
Descriptor: 1,4-Dihydroxy-2-naphthoyl-CoA synthase, Salicylyl CoA, TRIETHYLENE GLYCOL
Authors:Song, H.G, Tse, Y.S, Sung, H.P, Guo, Z.H.
Deposit date:2014-05-31
Release date:2014-11-19
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (1.64 Å)
Cite:Ligand-dependent active-site closure revealed in the crystal structure of Mycobacterium tuberculosis MenB complexed with product analogues
Acta Crystallogr.,Sect.D, 70, 2014
4QIJ
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BU of 4qij by Molmil
Crystal structure of MenB from Mycobacteria tuberculosis in complex with 1-HNA-CoA
Descriptor: 1,4-Dihydroxy-2-naphthoyl-CoA synthase, 1-hydroxy-2-naphthoyl-CoA
Authors:Song, H.G, Sung, H.P, Tse, Y.S, Guo, Z.H.
Deposit date:2014-05-31
Release date:2014-11-19
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:Ligand-dependent active-site closure revealed in the crystal structure of Mycobacterium tuberculosis MenB complexed with product analogues
Acta Crystallogr.,Sect.D, 70, 2014
4U1T
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BU of 4u1t by Molmil
The crystal structure of holo CalE6, a methionine gamma lyase from Micromonospora echinospora
Descriptor: CalE6, SULFATE ION
Authors:Song, H.G, Guo, Z.H.
Deposit date:2014-07-16
Release date:2015-01-07
Last modified:2023-11-15
Method:X-RAY DIFFRACTION (2 Å)
Cite:Identification and Characterization of a Methionine gamma-Lyase in the Calicheamicin Biosynthetic Cluster of Micromonospora echinospora
Chembiochem, 16, 2015
4U2H
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BU of 4u2h by Molmil
The crystal structure of apo CalE6, a methionine gamma lyase from Micromonospora echinospora
Descriptor: CalE6, SULFATE ION
Authors:Song, H.G, Xu, R.
Deposit date:2014-07-17
Release date:2015-01-07
Last modified:2024-03-20
Method:X-RAY DIFFRACTION (1.85 Å)
Cite:Identification and Characterization of a Methionine gamma-Lyase in the Calicheamicin Biosynthetic Cluster of Micromonospora echinospora
Chembiochem, 16, 2015
4I52
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BU of 4i52 by Molmil
scMenB im complex with 1-hydroxy-2-naphthoyl-CoA
Descriptor: 1-hydroxy-2-naphthoyl-CoA, CHLORIDE ION, Naphthoate synthase
Authors:Song, H.G, Sun, Y.R, Li, J, Li, Y, Jiang, M, Zhou, J.H, Guo, Z.H.
Deposit date:2012-11-28
Release date:2013-05-08
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (2.35 Å)
Cite:Structural basis of the induced-fit mechanism of 1,4-dihydroxy-2-naphthoyl coenzyme a synthase from the crotonase fold superfamily
Plos One, 8, 2013
4I4Z
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BU of 4i4z by Molmil
Synechocystis sp. PCC 6803 1,4-dihydroxy-2-naphthoyl-coenzyme A synthase (MenB) in complex with salicylyl-CoA
Descriptor: BICARBONATE ION, MALONATE ION, Naphthoate synthase, ...
Authors:Song, H.G, Sun, Y.R, Li, J, Li, Y, Jiang, M, Zhou, J.H, Guo, Z.H.
Deposit date:2012-11-28
Release date:2013-05-08
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (2 Å)
Cite:Structural basis of the induced-fit mechanism of 1,4-dihydroxy-2-naphthoyl coenzyme a synthase from the crotonase fold superfamily
Plos One, 8, 2013
8WAG
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BU of 8wag by Molmil
Crystal structure of the C-terminal fragment (residues 716-982) of Arabidopsis thaliana CHUP1
Descriptor: Protein CHUP1, chloroplastic
Authors:Shimada, A, Nakamura, Y, Takano, A, Kohda, D.
Deposit date:2023-09-07
Release date:2024-01-17
Method:X-RAY DIFFRACTION (3.003 Å)
Cite:CHLOROPLAST UNUSUAL POSITIONING 1 is a plant-specific actin polymerization factor regulating chloroplast movement.
Plant Cell, 2023
8WAF
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BU of 8waf by Molmil
Crystal structure of the C-terminal fragment (residues 756-982 with the C864S mutation) of Arabidopsis thaliana CHUP1
Descriptor: Protein CHUP1, chloroplastic
Authors:Shimada, A, Takano, A, Nakamura, Y, Kohda, D.
Deposit date:2023-09-07
Release date:2024-01-17
Method:X-RAY DIFFRACTION (2.8 Å)
Cite:CHLOROPLAST UNUSUAL POSITIONING 1 is a plant-specific actin polymerization factor regulating chloroplast movement.
Plant Cell, 2023
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
Descriptor: (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, ...
Authors:Qin, M.M, Guo, Z.H.
Deposit date:2018-01-03
Release date:2018-11-28
Last modified:2023-11-22
Method:X-RAY DIFFRACTION (2.3 Å)
Cite: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
Descriptor: (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, ...
Authors:Qin, M.M, Guo, Z.H.
Deposit date:2018-01-03
Release date:2018-11-28
Last modified:2023-11-22
Method:X-RAY DIFFRACTION (2.3 Å)
Cite: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
Descriptor: (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, ...
Authors:Qin, M.M, Guo, Z.H.
Deposit date:2018-01-04
Release date:2018-11-28
Last modified:2023-11-22
Method:X-RAY DIFFRACTION (2.35 Å)
Cite: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

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