7EM2
 
 | | Crystal structure of the PI5P4Kbeta-XTP complex | | 分子名称: | Phosphatidylinositol 5-phosphate 4-kinase type-2 beta, [(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(oxidanylidene)-3~{H}-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl phosphono hydrogen phosphate, [[(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(oxidanylidene)-3~{H}-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate | | 著者 | Senda, M, Senda, T. | | 登録日 | 2021-04-13 | | 公開日 | 2022-03-30 | | 最終更新日 | 2023-11-29 | | 実験手法 | X-RAY DIFFRACTION (2.6 Å) | | 主引用文献 | The GTP responsiveness of PI5P4K beta evolved from a compromised trade-off between activity and specificity.
Structure, 30, 2022
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7EM5
 | | Crystal structure of the PI5P4Kbeta F205L-XTP complex | | 分子名称: | Phosphatidylinositol 5-phosphate 4-kinase type-2 beta, [(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(oxidanylidene)-3~{H}-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl phosphono hydrogen phosphate, [[(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(oxidanylidene)-3~{H}-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate | | 著者 | Senda, M, Senda, T. | | 登録日 | 2021-04-13 | | 公開日 | 2022-03-30 | | 最終更新日 | 2023-11-29 | | 実験手法 | X-RAY DIFFRACTION (2.8 Å) | | 主引用文献 | The GTP responsiveness of PI5P4K beta evolved from a compromised trade-off between activity and specificity.
Structure, 30, 2022
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7EM1
 | | Crystal structure of the PI5P4Kbeta-ITP complex | | 分子名称: | INOSINE-5'-DIPHOSPHATE, Phosphatidylinositol 5-phosphate 4-kinase type-2 beta, [[(2~{R},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-(6-oxidanylidene-1~{H}-purin-9-yl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate | | 著者 | Senda, M, Senda, T. | | 登録日 | 2021-04-13 | | 公開日 | 2022-03-30 | | 最終更新日 | 2023-11-29 | | 実験手法 | X-RAY DIFFRACTION (2.65 Å) | | 主引用文献 | The GTP responsiveness of PI5P4K beta evolved from a compromised trade-off between activity and specificity.
Structure, 30, 2022
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7EM6
 | | Crystal structure of the PI5P4Kbeta N203D-ITP complex | | 分子名称: | INOSINE-5'-DIPHOSPHATE, Phosphatidylinositol 5-phosphate 4-kinase type-2 beta, [[(2~{R},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-(6-oxidanylidene-1~{H}-purin-9-yl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate | | 著者 | Senda, M, Senda, T. | | 登録日 | 2021-04-13 | | 公開日 | 2022-03-30 | | 最終更新日 | 2023-11-29 | | 実験手法 | X-RAY DIFFRACTION (2.95 Å) | | 主引用文献 | The GTP responsiveness of PI5P4K beta evolved from a compromised trade-off between activity and specificity.
Structure, 30, 2022
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7EM7
 | | Crystal structure of the PI5P4Kbeta N203D-XTP complex | | 分子名称: | Phosphatidylinositol 5-phosphate 4-kinase type-2 beta, [(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(oxidanylidene)-3~{H}-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl phosphono hydrogen phosphate, [[(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(oxidanylidene)-3~{H}-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate | | 著者 | Senda, M, Senda, T. | | 登録日 | 2021-04-13 | | 公開日 | 2022-03-30 | | 最終更新日 | 2023-11-29 | | 実験手法 | X-RAY DIFFRACTION (3.45 Å) | | 主引用文献 | The GTP responsiveness of PI5P4K beta evolved from a compromised trade-off between activity and specificity.
Structure, 30, 2022
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7EM3
 | | Crystal structure of the PI5P4Kbeta-2a-ATP complex | | 分子名称: | Phosphatidylinositol 5-phosphate 4-kinase type-2 beta, [(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(azanyl)purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl phosphono hydrogen phosphate, [[(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(azanyl)purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate | | 著者 | Senda, M, Senda, T. | | 登録日 | 2021-04-13 | | 公開日 | 2022-03-30 | | 最終更新日 | 2023-11-29 | | 実験手法 | X-RAY DIFFRACTION (3.1 Å) | | 主引用文献 | The GTP responsiveness of PI5P4K beta evolved from a compromised trade-off between activity and specificity.
Structure, 30, 2022
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7EM4
 | | Crystal structure of the PI5P4Kbeta F205L-ITP complex | | 分子名称: | INOSINE-5'-DIPHOSPHATE, Phosphatidylinositol 5-phosphate 4-kinase type-2 beta, [[(2~{R},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-(6-oxidanylidene-1~{H}-purin-9-yl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate | | 著者 | Senda, M, Senda, T. | | 登録日 | 2021-04-13 | | 公開日 | 2022-03-30 | | 最終更新日 | 2023-11-29 | | 実験手法 | X-RAY DIFFRACTION (2.8 Å) | | 主引用文献 | The GTP responsiveness of PI5P4K beta evolved from a compromised trade-off between activity and specificity.
Structure, 30, 2022
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7DNN
 | | Crystal structure of the AgCarB2-C2 complex with homoorientin | | 分子名称: | 2-[3,4-bis(oxidanyl)phenyl]-6-[(2S,3R,4R,5S,6R)-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]-5,7-bis(oxidanyl)chromen-4-one, AP_endonuc_2 domain-containing protein, AgCarC2, ... | | 著者 | Senda, M, Kumano, T, Watanabe, S, Kobayashi, M, Senda, T. | | 登録日 | 2020-12-10 | | 公開日 | 2021-10-20 | | 最終更新日 | 2024-05-29 | | 実験手法 | X-RAY DIFFRACTION (2.25 Å) | | 主引用文献 | Structural basis for the metabolism of xenobiotic C-glycosides by intestinal bacteria
Nat Commun, 2021
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7DNM
 | | Crystal structure of the AgCarB2-C2 complex | | 分子名称: | AP_endonuc_2 domain-containing protein, AgCarC2, IODIDE ION, ... | | 著者 | Senda, M, Kumano, T, Watanabe, S, Kobayashi, M, Senda, T. | | 登録日 | 2020-12-10 | | 公開日 | 2021-10-20 | | 最終更新日 | 2024-05-29 | | 実験手法 | X-RAY DIFFRACTION (2.3 Å) | | 主引用文献 | Structural basis for the metabolism of xenobiotic C-glycosides by intestinal bacteria
Nat Commun, 2021
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7DVE
 | | Crystal structure of FAD-dependent C-glycoside oxidase | | 分子名称: | 6'''-hydroxyparomomycin C oxidase, FLAVIN-ADENINE DINUCLEOTIDE, SULFATE ION | | 著者 | Senda, M, Watanabe, S, Kumano, T, Kobayashi, M, Senda, T. | | 登録日 | 2021-01-13 | | 公開日 | 2021-09-08 | | 最終更新日 | 2023-11-29 | | 実験手法 | X-RAY DIFFRACTION (2.4 Å) | | 主引用文献 | FAD-dependent C -glycoside-metabolizing enzymes in microorganisms: Screening, characterization, and crystal structure analysis.
Proc.Natl.Acad.Sci.USA, 118, 2021
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7D98
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3ANV
 | | Crystal structure of D-serine dehydratase from chicken kidney (2,3-DAP complex) | | 分子名称: | 3-amino-D-alanine, CHLORIDE ION, D-serine dehydratase, ... | | 著者 | Tanaka, H, Senda, M, Venugopalan, N, Yamamoto, A, Senda, T, Ishida, T, Horiike, K. | | 登録日 | 2010-09-09 | | 公開日 | 2011-06-15 | | 最終更新日 | 2024-03-13 | | 実験手法 | X-RAY DIFFRACTION (2.09 Å) | | 主引用文献 | Crystal structure of a zinc-dependent D-serine dehydratase from chicken kidney
J.Biol.Chem., 286, 2011
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3ANU
 | | Crystal structure of D-serine dehydratase from chicken kidney | | 分子名称: | CHLORIDE ION, D-serine dehydratase, PYRIDOXAL-5'-PHOSPHATE, ... | | 著者 | Tanaka, H, Senda, M, Venugopalan, N, Yamamoto, A, Senda, T, Ishida, T, Horiike, K. | | 登録日 | 2010-09-09 | | 公開日 | 2011-06-15 | | 最終更新日 | 2013-08-07 | | 実験手法 | X-RAY DIFFRACTION (1.9 Å) | | 主引用文献 | Crystal structure of a zinc-dependent D-serine dehydratase from chicken kidney
J.Biol.Chem., 286, 2011
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3AWN
 | | Crystal structure of D-serine dehydratase from chicken kidney (EDTA treated) | | 分子名称: | D-serine dehydratase, PYRIDOXAL-5'-PHOSPHATE | | 著者 | Tanaka, H, Senda, M, Venugopalan, N, Yamamoto, A, Senda, T, Ishida, T, Horiike, K. | | 登録日 | 2011-03-25 | | 公開日 | 2011-06-15 | | 最終更新日 | 2023-11-01 | | 実験手法 | X-RAY DIFFRACTION (2.8 Å) | | 主引用文献 | Crystal structure of a zinc-dependent D-serine dehydratase from chicken kidney.
J.Biol.Chem., 286, 2011
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3AWO
 | | Crystal structure of D-serine dehydratase in complex with D-serine from chicken kidney (EDTA-treated) | | 分子名称: | D-SERINE, D-serine dehydratase, PYRIDOXAL-5'-PHOSPHATE | | 著者 | Tanaka, H, Senda, M, Venugopalan, N, Yamamoto, A, Senda, T, Ishida, T, Horiike, K. | | 登録日 | 2011-03-25 | | 公開日 | 2011-06-15 | | 最終更新日 | 2024-03-13 | | 実験手法 | X-RAY DIFFRACTION (2.65 Å) | | 主引用文献 | Crystal structure of a zinc-dependent D-serine dehydratase from chicken kidney.
J.Biol.Chem., 286, 2011
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3WRB
 | | Crystal structure of the anaerobic H124F DESb-Gallate complex | | 分子名称: | 3,4,5-trihydroxybenzoic acid, FE (II) ION, Gallate dioxygenase | | 著者 | Sugimoto, K, Senda, M, Kasai, D, Fukuda, M, Masai, E, Senda, T. | | 登録日 | 2014-02-21 | | 公開日 | 2014-04-30 | | 最終更新日 | 2024-04-03 | | 実験手法 | X-RAY DIFFRACTION (2.1 Å) | | 主引用文献 | Molecular Mechanism of Strict Substrate Specificity of an Extradiol Dioxygenase, DesB, Derived from Sphingobium sp. SYK-6
Plos One, 9, 2014
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3WRC
 | | Crystal structure of the anaerobic DesB-Protocatechuate (PCA) complex | | 分子名称: | 3,4-DIHYDROXYBENZOIC ACID, FE (II) ION, Gallate dioxygenase | | 著者 | Sugimoto, K, Senda, M, Kasai, D, Fukuda, M, Masai, E, Senda, T. | | 登録日 | 2014-02-21 | | 公開日 | 2014-04-30 | | 最終更新日 | 2024-04-03 | | 実験手法 | X-RAY DIFFRACTION (2.4 Å) | | 主引用文献 | Molecular Mechanism of Strict Substrate Specificity of an Extradiol Dioxygenase, DesB, Derived from Sphingobium sp. SYK-6
Plos One, 9, 2014
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3WR9
 | | Crystal structure of the Anaerobic DesB-Gallate complex | | 分子名称: | 3,4,5-trihydroxybenzoic acid, FE (II) ION, Gallate dioxygenase | | 著者 | Sugimoto, K, Senda, M, Kasai, D, Fukuda, M, Masai, E, Senda, T. | | 登録日 | 2014-02-21 | | 公開日 | 2014-04-30 | | 最終更新日 | 2024-04-03 | | 実験手法 | X-RAY DIFFRACTION (2.4 Å) | | 主引用文献 | Molecular Mechanism of Strict Substrate Specificity of an Extradiol Dioxygenase, DesB, Derived from Sphingobium sp. SYK-6
Plos One, 9, 2014
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3WRA
 | | Crystal structure of the desB-Gallate complex exposed to Aerobic Atomosphere | | 分子名称: | FE (II) ION, Gallate dioxygenase | | 著者 | Sugimoto, K, Senda, M, Kasai, D, Fukuda, M, Masai, E, Senda, T. | | 登録日 | 2014-02-21 | | 公開日 | 2014-04-30 | | 最終更新日 | 2024-04-03 | | 実験手法 | X-RAY DIFFRACTION (2.1 Å) | | 主引用文献 | Molecular Mechanism of Strict Substrate Specificity of an Extradiol Dioxygenase, DesB, Derived from Sphingobium sp. SYK-6
Plos One, 9, 2014
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3WR3
 | | Crystal structure of the anaerobic DesB-gallate complex | | 分子名称: | 3,4,5-trihydroxybenzoic acid, FE (II) ION, Gallate dioxygenase | | 著者 | Sugimoto, K, Senda, M, Kasai, D, Fukuda, M, Masai, E, Senda, T. | | 登録日 | 2014-02-13 | | 公開日 | 2014-04-30 | | 最終更新日 | 2023-11-08 | | 実験手法 | X-RAY DIFFRACTION (2.5 Å) | | 主引用文献 | Molecular Mechanism of Strict Substrate Specificity of an Extradiol Dioxygenase, DesB, Derived from Sphingobium sp. SYK-6
Plos One, 9, 2014
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2E50
 | | Crystal structure of SET/TAF-1beta/INHAT | | 分子名称: | Protein SET, alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose | | 著者 | Muto, S, Senda, M, Senda, T, Horikoshi, M. | | 登録日 | 2006-12-18 | | 公開日 | 2007-02-20 | | 最終更新日 | 2024-05-29 | | 実験手法 | X-RAY DIFFRACTION (2.3 Å) | | 主引用文献 | Relationship between the structure of SET/TAF-Ibeta/INHAT and its histone chaperone activity
Proc.Natl.Acad.Sci.Usa, 104, 2007
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7D6R
 | | Crystal structure of the Stx2a complexed with MMA betaAla peptide | | 分子名称: | 3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE, MMA betaAla peptide, Shiga toxin 2 B subunit, ... | | 著者 | Takahashi, M, Tamada, M, Hibino, M, Senda, M, Okuda, A, Miyazawa, A, Senda, T, Nishikawa, K. | | 登録日 | 2020-10-01 | | 公開日 | 2021-04-14 | | 最終更新日 | 2024-10-09 | | 実験手法 | X-RAY DIFFRACTION (1.6 Å) | | 主引用文献 | Identification of a peptide motif that potently inhibits two functionally distinct subunits of Shiga toxin.
Commun Biol, 4, 2021
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7D6Q
 | | Crystal structure of the Stx2a | | 分子名称: | 3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE, Shiga toxin 2 B subunit, rRNA N-glycosylase | | 著者 | Takahashi, M, Tamada, M, Hibino, M, Senda, M, Okuda, A, Miyazawa, A, Senda, T, Nishikawa, K. | | 登録日 | 2020-10-01 | | 公開日 | 2021-04-14 | | 最終更新日 | 2024-11-06 | | 実験手法 | X-RAY DIFFRACTION (1.8 Å) | | 主引用文献 | Identification of a peptide motif that potently inhibits two functionally distinct subunits of Shiga toxin.
Commun Biol, 4, 2021
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8JW3
 | | The crystal structure of the viral terpene synthase from Orpheovirus IHUMI-LCC2 | | 分子名称: | SULFATE ION, Terpenoid synthase | | 著者 | Jung, Y, Mitsuhashi, T, Senda, M, Sato, S, Senda, T, Fujita, M. | | 登録日 | 2023-06-28 | | 公開日 | 2023-12-20 | | 実験手法 | X-RAY DIFFRACTION (1.45 Å) | | 主引用文献 | Function and Structure of a Terpene Synthase Encoded in a Giant Virus Genome.
J.Am.Chem.Soc., 145, 2023
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2GR3
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