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PDB: 117 件

1UC5
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Structure of diol dehydratase complexed with (R)-1,2-propanediol
分子名称: AMMONIUM ION, CYANOCOBALAMIN, POTASSIUM ION, ...
著者Shibata, N, Nakanishi, Y, Fukuoka, M, Yamanishi, M, Yasuoka, N, Toraya, T.
登録日2003-04-08
公開日2003-07-22
最終更新日2023-10-25
実験手法X-RAY DIFFRACTION (2.3 Å)
主引用文献Structural rationalization for the lack of stereospecificity in coenzyme B12-dependent diol dehydratase
J.Biol.Chem., 278, 2003
1EEX
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CRYSTAL STRUCTURE OF THE DIOL DEHYDRATASE-ADENINYLPENTYLCOBALAMIN COMPLEX FROM KLEBSIELLA OXYTOCA
分子名称: CO-(ADENIN-9-YL-PENTYL)-COBALAMIN, POTASSIUM ION, PROPANEDIOL DEHYDRATASE, ...
著者Shibata, N, Masuda, J, Toraya, T, Morimoto, Y, Yasuoka, N.
登録日2000-02-04
公開日2001-02-07
最終更新日2024-03-13
実験手法X-RAY DIFFRACTION (1.7 Å)
主引用文献How a protein generates a catalytic radical from coenzyme B(12): X-ray structure of a diol-dehydratase-adeninylpentylcobalamin complex.
Structure Fold.Des., 8, 2000
1DIO
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DIOL DEHYDRATASE-CYANOCOBALAMIN COMPLEX FROM KLEBSIELLA OXYTOCA
分子名称: COBALAMIN, POTASSIUM ION, PROTEIN (DIOL DEHYDRATASE), ...
著者Shibata, N, Masuda, J, Tobimatsu, T, Toraya, T, Suto, K, Morimoto, Y, Yasuoka, N.
登録日1999-01-27
公開日2000-01-30
最終更新日2023-12-27
実験手法X-RAY DIFFRACTION (2.2 Å)
主引用文献A new mode of B12 binding and the direct participation of a potassium ion in enzyme catalysis: X-ray structure of diol dehydratase.
Structure Fold.Des., 7, 1999
1A7V
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BU of 1a7v by Molmil
CYTOCHROME C' FROM RHODOPSEUDOMONAS PALUSTRIS
分子名称: CYTOCHROME C', PROTOPORPHYRIN IX CONTAINING FE
著者Shibata, N, Iba, S, Misaki, S, Meyer, T.E, Bartsch, R.G, Cusanovich, M.A, Higuchi, Y, Yasuoka, N.
登録日1998-03-18
公開日1998-06-17
最終更新日2023-08-02
実験手法X-RAY DIFFRACTION (2.3 Å)
主引用文献Basis for monomer stabilization in Rhodopseudomonas palustris cytochrome c' derived from the crystal structure.
J.Mol.Biol., 284, 1998
2D0P
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BU of 2d0p by Molmil
Structure of diol dehydratase-reactivating factor in nucleotide free form
分子名称: CALCIUM ION, SULFATE ION, diol dehydratase-reactivating factor large subunit, ...
著者Shibata, N, Mori, K, Hieda, N, Higuchi, Y, Yamanishi, M, Toraya, T.
登録日2005-08-05
公開日2006-02-28
最終更新日2024-03-13
実験手法X-RAY DIFFRACTION (3 Å)
主引用文献Release of a damaged cofactor from a coenzyme B12-dependent enzyme: X-ray structures of diol dehydratase-reactivating factor
Structure, 13, 2005
2D0O
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Structure of diol dehydratase-reactivating factor complexed with ADP and Mg2+
分子名称: ADENOSINE-5'-DIPHOSPHATE, MAGNESIUM ION, SULFATE ION, ...
著者Shibata, N, Mori, K, Hieda, N, Higuchi, Y, Yamanishi, M, Toraya, T.
登録日2005-08-05
公開日2006-02-28
最終更新日2024-03-13
実験手法X-RAY DIFFRACTION (2 Å)
主引用文献Release of a damaged cofactor from a coenzyme B12-dependent enzyme: X-ray structures of diol dehydratase-reactivating factor
Structure, 13, 2005
6IQX
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High resolution structure of bilirubin oxidase from Myrothecium verrucaria - M467Q mutant, aerobically prepared
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, ACETATE ION, Bilirubin oxidase, ...
著者Shibata, N, Akter, M, Higuchi, Y.
登録日2018-11-09
公開日2018-11-21
最終更新日2023-11-22
実験手法X-RAY DIFFRACTION (1.432 Å)
主引用文献Redox Potential-Dependent Formation of an Unusual His-Trp Bond in Bilirubin Oxidase.
Chemistry, 24, 2018
6IQY
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High resolution structure of bilirubin oxidase from Myrothecium verrucaria - M467Q mutant, anaerobically prepared
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, ACETATE ION, Bilirubin oxidase, ...
著者Shibata, N, Akter, M, Higuchi, Y.
登録日2018-11-09
公開日2018-11-21
最終更新日2023-11-22
実験手法X-RAY DIFFRACTION (1.6 Å)
主引用文献Redox Potential-Dependent Formation of an Unusual His-Trp Bond in Bilirubin Oxidase.
Chemistry, 24, 2018
6IQZ
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High resolution structure of bilirubin oxidase from Myrothecium verrucaria - wild type
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Bilirubin oxidase, COPPER (II) ION, ...
著者Shibata, N, Akter, M, Higuchi, Y.
登録日2018-11-09
公開日2018-11-21
最終更新日2023-11-22
実験手法X-RAY DIFFRACTION (1.46 Å)
主引用文献Redox Potential-Dependent Formation of an Unusual His-Trp Bond in Bilirubin Oxidase.
Chemistry, 24, 2018
7XRM
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Ethanolamine ammonia-lyase complexed with AdoMeCbl
分子名称: (2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-ethyl-oxolane-3,4-diol, AMMONIUM ION, COBALAMIN, ...
著者Shibata, N, Toraya, T.
登録日2022-05-10
公開日2023-03-29
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (2.13 Å)
主引用文献Structural Insights into the Very Low Activity of the Homocoenzyme B 12 Adenosylmethylcobalamin in Coenzyme B 12 -Dependent Diol Dehydratase and Ethanolamine Ammonia-Lyase.
Chemistry, 28, 2022
7XRN
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Ethanolamine ammonia-lyase complexed with AdoMeCbl in the presence of substrate
分子名称: (2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-ethyl-oxolane-3,4-diol, AMMONIUM ION, COBALAMIN, ...
著者Shibata, N, Toraya, T.
登録日2022-05-10
公開日2023-03-29
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (2.07 Å)
主引用文献Structural Insights into the Very Low Activity of the Homocoenzyme B 12 Adenosylmethylcobalamin in Coenzyme B 12 -Dependent Diol Dehydratase and Ethanolamine Ammonia-Lyase.
Chemistry, 28, 2022
7XRK
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Diol dehydratase complexed with AdoMeCbl
分子名称: (2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-ethyl-oxolane-3,4-diol, CALCIUM ION, COBALAMIN, ...
著者Shibata, N, Toraya, T.
登録日2022-05-10
公開日2023-03-29
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (2.3 Å)
主引用文献Structural Insights into the Very Low Activity of the Homocoenzyme B 12 Adenosylmethylcobalamin in Coenzyme B 12 -Dependent Diol Dehydratase and Ethanolamine Ammonia-Lyase.
Chemistry, 28, 2022
7XRL
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BU of 7xrl by Molmil
Diol dehydratase complexed with AdoMeCbl and 1,2-propanediol
分子名称: (2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-ethyl-oxolane-3,4-diol, AMMONIUM ION, CALCIUM ION, ...
著者Shibata, N, Toraya, T.
登録日2022-05-10
公開日2023-03-29
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (1.75 Å)
主引用文献Structural Insights into the Very Low Activity of the Homocoenzyme B 12 Adenosylmethylcobalamin in Coenzyme B 12 -Dependent Diol Dehydratase and Ethanolamine Ammonia-Lyase.
Chemistry, 28, 2022
1IWB
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BU of 1iwb by Molmil
Crystal structure of diol dehydratase
分子名称: COBALAMIN, DIOL DEHYDRATASE alpha chain, DIOL DEHYDRATASE beta chain, ...
著者Shibata, N, Masuda, J, Morimoto, Y, Yasuoka, N, Toraya, T.
登録日2002-05-01
公開日2003-05-01
最終更新日2024-05-29
実験手法X-RAY DIFFRACTION (1.85 Å)
主引用文献Substrate-induced conformational change of a coenzyme B12-dependent enzyme: crystal structure of the substrate-free form of diol dehydratase
Biochemistry, 41, 2002
1IUZ
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BU of 1iuz by Molmil
PLASTOCYANIN
分子名称: COPPER (II) ION, PLASTOCYANIN, SULFATE ION
著者Shibata, N.
登録日1996-10-06
公開日1997-08-20
最終更新日2024-02-07
実験手法X-RAY DIFFRACTION (1.6 Å)
主引用文献Novel insight into the copper-ligand geometry in the crystal structure of Ulva pertusa plastocyanin at 1.6-A resolution. Structural basis for regulation of the copper site by residue 88.
J.Biol.Chem., 274, 1999
2E84
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BU of 2e84 by Molmil
Crystal structure of High-Molecular Weight Cytochrome c from Desulfovibrio vulgaris (Miyazaki F) in the presence of zinc ion
分子名称: High-molecular-weight cytochrome c, PROTOPORPHYRIN IX CONTAINING FE, SODIUM ION, ...
著者Shibata, N, Suto, K, Sato, M, Morimoto, Y, Kitamura, M, Higuchi, Y.
登録日2007-01-17
公開日2008-01-15
最終更新日2024-03-13
実験手法X-RAY DIFFRACTION (2.7 Å)
主引用文献Structure of High-Molecular Weight Cytochrome c from Desulfovibrio vulgaris (Miyazaki F)
To be Published
2E83
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BU of 2e83 by Molmil
T31V mutant of FMN-binding protein from Desulfovibrio vulgaris (Miyazaki F)
分子名称: FLAVIN MONONUCLEOTIDE, FMN-binding protein
著者Shibata, N, Higuchi, Y.
登録日2007-01-17
公開日2008-01-15
最終更新日2023-10-25
実験手法X-RAY DIFFRACTION (1.52 Å)
主引用文献Structure of T31V mutant of FMN-binding protein from Desulfovibrio vulgaris Miyazaki F
To be Published
2E8I
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BU of 2e8i by Molmil
Structure of 6-aminohexanoate-dimer hydrolase, D1 mutant
分子名称: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, 6-aminohexanoate-dimer hydrolase, GLYCEROL, ...
著者Shibata, N, Higuchi, Y, Negoro, S.
登録日2007-01-20
公開日2008-01-15
最終更新日2023-10-25
実験手法X-RAY DIFFRACTION (1.45 Å)
主引用文献Molecular design of a nylon-6 byproduct-degrading enzyme from a carboxylesterase with a beta-lactamase fold.
Febs J., 276, 2009
2D5G
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BU of 2d5g by Molmil
Structure of ubiquitin fold protein R767E mutant
分子名称: Axin-1, MERCURY (II) ION
著者Shibata, N, Higuchi, Y.
登録日2005-11-01
公開日2006-11-01
最終更新日2024-05-29
実験手法X-RAY DIFFRACTION (3.2 Å)
主引用文献Structure of ubiquitin fold protein R767E mutant
to be published
3ABQ
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BU of 3abq by Molmil
Crystal structure of ethanolamine ammonia-lyase from Escherichia coli complexed with CN-Cbl and 2-amino-1-propanol
分子名称: (2S)-2-aminopropan-1-ol, COBALAMIN, Ethanolamine ammonia-lyase heavy chain, ...
著者Shibata, N.
登録日2009-12-21
公開日2010-06-02
最終更新日2023-11-15
実験手法X-RAY DIFFRACTION (2.05 Å)
主引用文献Crystal structures of ethanolamine ammonia-lyase complexed with coenzyme B12 analogs and substrates.
J.Biol.Chem., 285, 2010
3ABR
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BU of 3abr by Molmil
Crystal structure of ethanolamine ammonia-lyase from Escherichia coli complexed with CN-Cbl (substrate-free form)
分子名称: COBALAMIN, Ethanolamine ammonia-lyase heavy chain, Ethanolamine ammonia-lyase light chain, ...
著者Shibata, N.
登録日2009-12-21
公開日2010-06-02
最終更新日2023-11-01
実験手法X-RAY DIFFRACTION (2.1 Å)
主引用文献Crystal structures of ethanolamine ammonia-lyase complexed with coenzyme B12 analogs and substrates.
J.Biol.Chem., 285, 2010
3ABO
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BU of 3abo by Molmil
Crystal structure of ethanolamine ammonia-lyase from Escherichia coli complexed with CN-Cbl and ethanolamine
分子名称: COBALAMIN, ETHANOLAMINE, Ethanolamine ammonia-lyase heavy chain, ...
著者Shibata, N.
登録日2009-12-21
公開日2010-06-02
最終更新日2023-11-15
実験手法X-RAY DIFFRACTION (2.1 Å)
主引用文献Crystal structures of ethanolamine ammonia-lyase complexed with coenzyme B12 analogs and substrates.
J.Biol.Chem., 285, 2010
3ABS
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BU of 3abs by Molmil
Crystal structure of ethanolamine ammonia-lyase from Escherichia coli complexed with adeninylpentylcobalamin and ethanolamine
分子名称: CO-(ADENIN-9-YL-PENTYL)-COBALAMIN, ETHANOLAMINE, Ethanolamine ammonia-lyase heavy chain, ...
著者Shibata, N.
登録日2009-12-21
公開日2010-06-02
最終更新日2023-11-15
実験手法X-RAY DIFFRACTION (2.25 Å)
主引用文献Crystal structures of ethanolamine ammonia-lyase complexed with coenzyme B12 analogs and substrates.
J.Biol.Chem., 285, 2010
1UC4
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BU of 1uc4 by Molmil
Structure of diol dehydratase complexed with (S)-1,2-propanediol
分子名称: AMMONIUM ION, CYANOCOBALAMIN, POTASSIUM ION, ...
著者Shibata, N, Nakanishi, Y, Fukuoka, M, Yamanishi, M, Yasuoka, N, Toraya, T.
登録日2003-04-08
公開日2003-07-22
最終更新日2023-10-25
実験手法X-RAY DIFFRACTION (1.8 Å)
主引用文献Structural rationalization for the lack of stereospecificity in coenzyme B12-dependent diol dehydratase
J.BIOL.CHEM., 278, 2003
5YRV
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Diol dehydratase, AdoCbl/1,2-propanediol, anaerobically-prepared crystal
分子名称: 5'-DEOXYADENOSINE, CALCIUM ION, CHLORIDE ION, ...
著者Shibata, N.
登録日2017-11-10
公開日2018-09-19
最終更新日2023-11-22
実験手法X-RAY DIFFRACTION (1.55 Å)
主引用文献Direct Participation of a Peripheral Side Chain of a Corrin Ring in Coenzyme B12Catalysis.
Angew. Chem. Int. Ed. Engl., 57, 2018

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