3WR9
 
 | | Crystal structure of the Anaerobic DesB-Gallate complex | | Descriptor: | 3,4,5-trihydroxybenzoic acid, FE (II) ION, Gallate dioxygenase | | Authors: | Sugimoto, K, Senda, M, Kasai, D, Fukuda, M, Masai, E, Senda, T. | | Deposit date: | 2014-02-21 | | Release date: | 2014-04-30 | | Last modified: | 2024-04-03 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | 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 | | Descriptor: | 3,4,5-trihydroxybenzoic acid, FE (II) ION, Gallate dioxygenase | | Authors: | Sugimoto, K, Senda, M, Kasai, D, Fukuda, M, Masai, E, Senda, T. | | Deposit date: | 2014-02-13 | | Release date: | 2014-04-30 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | 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 | | Descriptor: | FE (II) ION, Gallate dioxygenase | | Authors: | Sugimoto, K, Senda, M, Kasai, D, Fukuda, M, Masai, E, Senda, T. | | Deposit date: | 2014-02-21 | | Release date: | 2014-04-30 | | Last modified: | 2024-04-03 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | 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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3WKU
 | | Crystal structure of the anaerobic DesB-gallate complex | | Descriptor: | 3,4,5-trihydroxybenzoic acid, FE (III) ION, Gallate dioxygenase | | Authors: | Sugimoto, K, Senda, M, Kasai, D, Fukuda, M, Masai, E, Senda, T. | | Deposit date: | 2013-10-31 | | Release date: | 2014-04-30 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (2.7 Å) | | Cite: | 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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3WR8
 | | Crystal structure of DesB from Sphingobium sp. strain SYK-6 | | Descriptor: | FE (II) ION, Gallate dioxygenase | | Authors: | Sugimoto, K, Senda, M, Kasai, D, Fukuda, M, Masai, E, Senda, T. | | Deposit date: | 2014-02-21 | | Release date: | 2014-04-30 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.25 Å) | | Cite: | 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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3A2M
 | | CRYSTAL STRUCTURE OF DBJA (WILD TYPE Type I) | | Descriptor: | CHLORIDE ION, Haloalkane dehalogenase, beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose | | Authors: | Sato, Y, Senda, T. | | Deposit date: | 2009-05-23 | | Release date: | 2010-05-26 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (1.84 Å) | | Cite: | Enantioselectivity of haloalkane dehalogenases and its modulation by surface loop engineering
Angew.Chem.Int.Ed.Engl., 49, 2010
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3WPM
 | | Crystal structure of the anaerobic DesB-gallate complex by co-crystallization | | Descriptor: | 3,4,5-trihydroxybenzoic acid, FE (III) ION, Gallate dioxygenase | | Authors: | Sugimoto, K, Senda, M, Kasai, D, Fukuda, M, Masai, E, Senda, T. | | Deposit date: | 2014-01-14 | | Release date: | 2014-04-30 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | 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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3WR4
 | | Crystal structure of the anaerobic DesB-gallate complex | | Descriptor: | 3,4,5-trihydroxybenzoic acid, FE (III) ION, Gallate dioxygenase | | Authors: | Sugimoto, K, Senda, M, Kasai, D, Fukuda, M, Masai, E, Senda, T. | | Deposit date: | 2014-02-13 | | Release date: | 2014-04-30 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | 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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3A2L
 | | Crystal structure of DBJA (mutant dbja delta) | | Descriptor: | CHLORIDE ION, GLYCEROL, Haloalkane dehalogenase, ... | | Authors: | Sato, Y, Senda, T. | | Deposit date: | 2009-05-23 | | Release date: | 2010-05-26 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (1.78 Å) | | Cite: | Enantioselectivity of haloalkane dehalogenases and its modulation by surface loop engineering
Angew.Chem.Int.Ed.Engl., 49, 2010
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3AFI
 | | Crystal structure of DBJA (HIS-DBJA) | | Descriptor: | CHLORIDE ION, Haloalkane dehalogenase | | Authors: | Sato, Y, Senda, T. | | Deposit date: | 2010-03-02 | | Release date: | 2011-01-19 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (1.75 Å) | | Cite: | Enantioselectivity of haloalkane dehalogenases and its modulation by surface loop engineering
Angew.Chem.Int.Ed.Engl., 49, 2010
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3A2N
 | | Crystal structure of DBJA (Wild Type Type II P21) | | Descriptor: | CHLORIDE ION, Haloalkane dehalogenase | | Authors: | Sato, Y, Senda, T. | | Deposit date: | 2009-05-23 | | Release date: | 2010-05-26 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (1.89 Å) | | Cite: | Enantioselectivity of haloalkane dehalogenases and its modulation by surface loop engineering
Angew.Chem.Int.Ed.Engl., 49, 2010
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5XNY
 | | Crystal structure of CreD | | Descriptor: | CreD | | Authors: | Katsuyama, Y, Sato, Y, Sugai, Y, Higashiyama, Y, Senda, M, Senda, T, Ohnishi, Y. | | Deposit date: | 2017-05-25 | | Release date: | 2018-03-14 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.18 Å) | | Cite: | Crystal structure of the nitrosuccinate lyase CreD in complex with fumarate provides insights into the catalytic mechanism for nitrous acid elimination
FEBS J., 285, 2018
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5XNZ
 | | Crystal structure of CreD complex with fumarate | | Descriptor: | CreD, FUMARIC ACID | | Authors: | Katsuyama, Y, Sato, Y, Sugai, Y, Higashiyama, Y, Senda, M, Senda, T, Ohnishi, Y. | | Deposit date: | 2017-05-25 | | Release date: | 2018-03-14 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Crystal structure of the nitrosuccinate lyase CreD in complex with fumarate provides insights into the catalytic mechanism for nitrous acid elimination
FEBS J., 285, 2018
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7DVE
 | | Crystal structure of FAD-dependent C-glycoside oxidase | | Descriptor: | 6'''-hydroxyparomomycin C oxidase, FLAVIN-ADENINE DINUCLEOTIDE, SULFATE ION | | Authors: | Senda, M, Watanabe, S, Kumano, T, Kobayashi, M, Senda, T. | | Deposit date: | 2021-01-13 | | Release date: | 2021-09-08 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | 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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7E18
 | | Crystal structure of SAR-CoV-2 3CL protease complex with inhibitor YH-53 | | Descriptor: | 1,2-ETHANEDIOL, N-[(2S)-1-[[(2S)-1-(1,3-benzothiazol-2-yl)-1-oxidanylidene-3-[(3S)-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]-4-methoxy-1H-indole-2-carboxamide, Replicase polyprotein 1ab | | Authors: | Senda, M, Konno, S, Hayashi, Y, Senda, T. | | Deposit date: | 2021-02-01 | | Release date: | 2021-06-23 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.65 Å) | | Cite: | 3CL Protease Inhibitors with an Electrophilic Arylketone Moiety as Anti-SARS-CoV-2 Agents.
J.Med.Chem., 65, 2022
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7E19
 | | Crystal structure of SAR-CoV-2 3CL protease complex with inhibitor SH-5 | | Descriptor: | (phenylmethyl) N-[(2S)-1-[[(2S)-1-[[(2S)-1-(1,3-benzothiazol-2-yl)-1-oxidanylidene-3-[(3S)-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]amino]-3-methyl-1-oxidanylidene-butan-2-yl]carbamate, 3C-like proteinase | | Authors: | Senda, M, Konno, S, Hayashi, Y, Senda, T. | | Deposit date: | 2021-02-01 | | Release date: | 2021-06-23 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.15 Å) | | Cite: | 3CL Protease Inhibitors with an Electrophilic Arylketone Moiety as Anti-SARS-CoV-2 Agents.
J.Med.Chem., 65, 2022
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1KW6
 | | Crystal structure of 2,3-dihydroxybiphenyl dioxygenase (BphC) in complex with 2,3-dihydroxybiphenyl at 1.45 A resolution | | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, 2,3-Dihydroxybiphenyl dioxygenase, BIPHENYL-2,3-DIOL, ... | | Authors: | Sato, N, Uragami, Y, Nishizaki, T, Takahashi, Y, Sazaki, G, Sugimoto, K, Nonaka, T, Masai, E, Fukuda, M, Senda, T. | | Deposit date: | 2002-01-28 | | Release date: | 2003-01-28 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (1.45 Å) | | Cite: | Crystal Structures of the Reaction Intermediate and its Homologue of an Extradiol-cleaving Catecholic Dioxygenase
J.Mol.Biol., 321, 2002
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1KW3
 | | Crystal structure of 2,3-dihydroxybiphenyal dioxygenase (BphC) at 1.45 A resolution | | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, 2,3-Dihydroxybiphenyl dioxygenase, FE (II) ION | | Authors: | Sato, N, Uragami, Y, Nishizaki, T, Takahashi, Y, Sazaki, G, Sugimoto, K, Nonaka, T, Masai, E, Fukuda, M, Senda, T. | | Deposit date: | 2002-01-28 | | Release date: | 2003-01-28 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (1.45 Å) | | Cite: | Crystal Structures of the Reaction Intermediate and its Homologue of an Extradiol-cleaving Catecholic Dioxygenase
J.Mol.Biol., 321, 2002
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7E4D
 | | Crystal structure of PlDBR | | Descriptor: | Double Bond Reductase | | Authors: | Sugimoto, K, Senda, M, Senda, T. | | Deposit date: | 2021-02-11 | | Release date: | 2022-02-02 | | Last modified: | 2024-05-29 | | Method: | X-RAY DIFFRACTION (2.6 Å) | | Cite: | Exploration and structure-based engineering of alkenal double bond reductases catalyzing the C alpha C beta double bond reduction of coniferaldehyde.
N Biotechnol, 68, 2022
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1KWC
 | | The His145Ala mutant of 2,3-dihydroxybiphenyl dioxygenase in complex with 2,3-dihydroxybiphenyl | | Descriptor: | 2,3-dihydroxybiphenyl dioxygenase, BIPHENYL-2,3-DIOL | | Authors: | Sato, N, Uragami, Y, Nishizaki, T, Takahashi, Y, Sazaki, G, Sugimoto, K, Nonaka, T, Masai, E, Fukuda, M, Senda, T. | | Deposit date: | 2002-01-29 | | Release date: | 2003-01-29 | | Last modified: | 2024-05-29 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Crystal Structures of the Reaction Intermediate and its Homologue of an Extradiol-cleaving Catecholic Dioxygenase
J.Mol.Biol., 321, 2002
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1KW9
 | | Crystal structure of 2,3-dihydroxybiphenyl dioxygenase (BphC) in complex with 2,3-dihydroxybiphenyl at 2.0A resolution | | Descriptor: | 2,3-Dihydroxybiphenyl dioxygenase, BIPHENYL-2,3-DIOL, FE (II) ION | | Authors: | Sato, N, Uragami, Y, Nishizaki, T, Takahashi, Y, Sazaki, G, Sugimoto, K, Nonaka, T, Masai, E, Fukuda, M, Senda, T. | | Deposit date: | 2002-01-29 | | Release date: | 2003-01-29 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (1.95 Å) | | Cite: | Crystal Structures of the Reaction Intermediate and its Homologue of an Extradiol-cleaving Catecholic Dioxygenase
J.Mol.Biol., 321, 2002
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1KWB
 | | Crystal structure of the His145Ala mutant of 2,3-dihydroxybipheny dioxygenase (BphC) | | Descriptor: | 2,3-Dihydroxybiphenyl dioxygenase | | Authors: | Sato, N, Uragami, Y, Nishizaki, T, Takahashi, Y, Sazaki, G, Sugimoto, K, Nonaka, T, Masai, E, Fukuda, M, Senda, T. | | Deposit date: | 2002-01-29 | | Release date: | 2003-01-29 | | Last modified: | 2024-05-29 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Crystal Structures of the Reaction Intermediate and its Homologue of an Extradiol-cleaving Catecholic Dioxygenase
J.Mol.Biol., 321, 2002
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1KW8
 | | Crystal structure of BphC-2,3-dihydroxybiphenyl-NO complex | | Descriptor: | 2,3-Dihydroxybiphenyl dioxygenase, BIPHENYL-2,3-DIOL, FE (II) ION, ... | | Authors: | Sato, N, Uragami, Y, Nishizaki, T, Takahashi, Y, Sazaki, G, Sugimoto, K, Nonaka, T, Masai, E, Fukuda, M, Senda, T. | | Deposit date: | 2002-01-29 | | Release date: | 2003-01-29 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Crystal Structures of the Reaction Intermediate and its Homologue of an Extradiol-cleaving Catecholic Dioxygenase
J.Mol.Biol., 321, 2002
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7EM6
 | | Crystal structure of the PI5P4Kbeta N203D-ITP complex | | Descriptor: | 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 | | Authors: | Senda, M, Senda, T. | | Deposit date: | 2021-04-13 | | Release date: | 2022-03-30 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.95 Å) | | Cite: | The GTP responsiveness of PI5P4K beta evolved from a compromised trade-off between activity and specificity.
Structure, 30, 2022
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7EM2
 | | Crystal structure of the PI5P4Kbeta-XTP complex | | Descriptor: | 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 | | Authors: | Senda, M, Senda, T. | | Deposit date: | 2021-04-13 | | Release date: | 2022-03-30 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.6 Å) | | Cite: | The GTP responsiveness of PI5P4K beta evolved from a compromised trade-off between activity and specificity.
Structure, 30, 2022
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