7XLF
 
 | | Crystal structure of CH3-THF complex of methylenetetrahydrofolate reductase from Sphingobium sp. SYK-6 | | Descriptor: | 5,10-methylenetetrahydrofolate reductase, 5-METHYL-5,6,7,8-TETRAHYDROFOLIC ACID, DI(HYDROXYETHYL)ETHER, ... | | Authors: | Yu, H.Y, Senda, M, Senda, T. | | Deposit date: | 2022-04-21 | | Release date: | 2023-04-26 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.85 Å) | | Cite: | Crystal structural of methylenetetrahydrofolate reductase from Sphingobium sp. SYK-6
To Be Published
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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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6K4H
 | | Crystal structure of the PI5P4Kbeta-AMPPNP complex | | Descriptor: | PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER, Phosphatidylinositol 5-phosphate 4-kinase type-2 beta | | Authors: | Takeuchi, K, Senda, M, Senda, T. | | Deposit date: | 2019-05-23 | | Release date: | 2020-05-27 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.55 Å) | | Cite: | The GTP responsiveness of PI5P4K beta evolved from a compromised trade-off between activity and specificity.
Structure, 2022
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6K4G
 | | Crystal structure of the PI5P4Kbeta-GMPPNP complex | | Descriptor: | PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER, Phosphatidylinositol 5-phosphate 4-kinase type-2 beta | | Authors: | Takeuchi, K, Senda, M, Senda, T. | | Deposit date: | 2019-05-23 | | Release date: | 2020-05-27 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.7 Å) | | Cite: | The GTP responsiveness of PI5P4K beta evolved from a compromised trade-off between activity and specificity.
Structure, 2022
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1KR6
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1KS7
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1KKK
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1KL6
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1KTO
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1KEI
 | | Thermolysin (substrate-free) | | Descriptor: | CALCIUM ION, LYSINE, Thermolysin, ... | | Authors: | Senda, M, Senda, T, Kidokoro, S. | | Deposit date: | 2001-11-16 | | Release date: | 2002-11-16 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (1.6 Å) | | Cite: | Crystal structure analyses of thermolysin in complex with its inhibitors
To be Published
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1KJO
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1KRO
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1KJP
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5X1N
 | | Vanillate/3-O-methylgallate O-demethylase, LigM, protocatechuate-tetrahydrofolate complex form | | Descriptor: | (6S)-5,6,7,8-TETRAHYDROFOLATE, 1,2-ETHANEDIOL, 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, ... | | Authors: | Harada, A, Senda, T. | | Deposit date: | 2017-01-26 | | Release date: | 2017-05-17 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | The crystal structure of a new O-demethylase from Sphingobium sp. strain SYK-6
FEBS J., 284, 2017
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6KNF
 | | CryoEM map and model of Nitrite Reductase at pH 6.2 | | Descriptor: | COPPER (II) ION, Copper-containing nitrite reductase | | Authors: | Adachi, N, Yamaguchi, T, Moriya, T, Kawasaki, M, Koiwai, K, Shinoda, A, Yamada, Y, Yumoto, F, Kohzuma, T, Senda, T. | | Deposit date: | 2019-08-05 | | Release date: | 2020-08-12 | | Last modified: | 2024-05-29 | | Method: | ELECTRON MICROSCOPY (2.99 Å) | | Cite: | 2.85 and 2.99 angstrom resolution structures of 110 kDa nitrite reductase determined by 200 kV cryogenic electron microscopy.
J.Struct.Biol., 213, 2021
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5X1I
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5X1M
 | | Vanillate/3-O-methylgallate O-demethylase, LigM, protocatechuate-tetrahydrofolate complex form | | Descriptor: | (6S)-5,6,7,8-TETRAHYDROFOLATE, 1,2-ETHANEDIOL, 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, ... | | Authors: | Harada, A, Senda, T. | | Deposit date: | 2017-01-26 | | Release date: | 2017-05-17 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | The crystal structure of a new O-demethylase from Sphingobium sp. strain SYK-6
FEBS J., 284, 2017
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6KNG
 | | CryoEM map and model of Nitrite Reductase at pH 8.1 | | Descriptor: | COPPER (II) ION, Copper-containing nitrite reductase | | Authors: | Adachi, N, Yamaguchi, T, Moriya, T, Kawasaki, M, Koiwai, K, Shinoda, A, Yamada, Y, Yumoto, F, Kohzuma, T, Senda, T. | | Deposit date: | 2019-08-05 | | Release date: | 2020-08-12 | | Last modified: | 2024-05-29 | | Method: | ELECTRON MICROSCOPY (2.85 Å) | | Cite: | 2.85 and 2.99 angstrom resolution structures of 110 kDa nitrite reductase determined by 200 kV cryogenic electron microscopy.
J.Struct.Biol., 213, 2021
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6KFQ
 | | Crystal structure of thermophilic rhodopsin from Rubrobacter xylanophilus | | Descriptor: | RETINAL, Rhodopsin, SULFATE ION, ... | | Authors: | Suzuki, K, Akiyama, T, Hayashi, T, Yasuda, S, Kanehara, K, Kojima, K, Tanabe, M, Kato, R, Senda, T, Sudo, Y, Kinoshita, M, Murata, T. | | Deposit date: | 2019-07-08 | | Release date: | 2020-04-08 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.84 Å) | | Cite: | How Does a Microbial Rhodopsin RxR Realize Its Exceptionally High Thermostability with the Proton-Pumping Function Being Retained?
J.Phys.Chem.B, 124, 2020
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5X1J
 | | Vanillate/3-O-methylgallate O-demethylase, LigM, vanillate complex form | | Descriptor: | 1,2-ETHANEDIOL, 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, 4-HYDROXY-3-METHOXYBENZOATE, ... | | Authors: | Harada, A, Senda, T. | | Deposit date: | 2017-01-26 | | Release date: | 2017-05-17 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | The crystal structure of a new O-demethylase from Sphingobium sp. strain SYK-6
FEBS J., 284, 2017
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5X1K
 | | Vanillate/3-O-methylgallate O-demethylase, LigM, 3-O-methylgallate complex form | | Descriptor: | 1,2-ETHANEDIOL, 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, 3-methoxy-4,5-bis(oxidanyl)benzoic acid, ... | | Authors: | Harada, A, Senda, T. | | Deposit date: | 2017-01-26 | | Release date: | 2017-05-17 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.15 Å) | | Cite: | The crystal structure of a new O-demethylase from Sphingobium sp. strain SYK-6
FEBS J., 284, 2017
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7EXZ
 | | DgpB-DgpC complex apo 2.5 angstrom | | Descriptor: | 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, AP_endonuc_2 domain-containing protein, DgpB, ... | | Authors: | Mori, T, Senda, M, Senda, T, Abe, I. | | Deposit date: | 2021-05-29 | | Release date: | 2021-11-03 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | C-Glycoside metabolism in the gut and in nature: Identification, characterization, structural analyses and distribution of C-C bond-cleaving enzymes.
Nat Commun, 12, 2021
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7EXB
 | | DfgA-DfgB complex apo 2.4 angstrom | | Descriptor: | DfgB, MANGANESE (II) ION, SULFATE ION, ... | | Authors: | Mori, T, Senda, M, Senda, T, Abe, I. | | Deposit date: | 2021-05-26 | | Release date: | 2021-11-03 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | C-Glycoside metabolism in the gut and in nature: Identification, characterization, structural analyses and distribution of C-C bond-cleaving enzymes.
Nat Commun, 12, 2021
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7EBV
 | | Crystal structure of Aedes aegypti Noppera-bo, glutathione S-transferase epsilon 8, in luteolin- and glutathione-bound form | | Descriptor: | 2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-4H-chromen-4-one, CALCIUM ION, GLUTATHIONE, ... | | Authors: | Inaba, K, Koiwai, K, Senda, M, Senda, T, Niwa, R. | | Deposit date: | 2021-03-11 | | Release date: | 2022-01-26 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.5 Å) | | Cite: | Molecular action of larvicidal flavonoids on ecdysteroidogenic glutathione S-transferase Noppera-bo in Aedes aegypti.
Bmc Biol., 20, 2022
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