7BXQ
 
 | | 2-amino-3-ketobutyrate CoA ligase from Cupriavidus necator L-Threonine binding form | | Descriptor: | 2-amino-3-ketobutyrate coenzyme A ligase, N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-L-allothreonine | | Authors: | Motoyama, T, Nakano, S, Hasebe, F, Miyoshi, N, Ito, S. | | Deposit date: | 2020-04-20 | | Release date: | 2021-04-21 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.49 Å) | | Cite: | Chemoenzymatic synthesis of 3-ethyl-2,5-dimethylpyrazine by L-threonine 3-dehydrogenase and 2-amino-3-ketobutyrate CoA ligase/L-threonine aldolase
Commun Chem, 4, 2021
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7BXP
 | | 2-amino-3-ketobutyrate CoA ligase from Cupriavidus necator | | Descriptor: | 2-amino-3-ketobutyrate coenzyme A ligase | | Authors: | Motoyama, T, Nakano, S, Hasebe, F, Miyoshi, N, Ito, S. | | Deposit date: | 2020-04-20 | | Release date: | 2021-04-21 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Chemoenzymatic synthesis of 3-ethyl-2,5-dimethylpyrazine by L-threonine 3-dehydrogenase and 2-amino-3-ketobutyrate CoA ligase/L-threonine aldolase
Commun Chem, 4, 2021
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7BXR
 | | 2-amino-3-ketobutyrate CoA ligase from Cupriavidus necator 3-Hydroxynorvaline binding form | | Descriptor: | (2S,3R)-2-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]-3-oxidanyl-pentanoic acid, 2-amino-3-ketobutyrate coenzyme A ligase | | Authors: | Motoyama, T, Nakano, S, Hasebe, F, Miyoshi, N, Ito, S. | | Deposit date: | 2020-04-20 | | Release date: | 2021-04-21 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.55 Å) | | Cite: | Chemoenzymatic synthesis of 3-ethyl-2,5-dimethylpyrazine by L-threonine 3-dehydrogenase and 2-amino-3-ketobutyrate CoA ligase/L-threonine aldolase
Commun Chem, 4, 2021
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5ZQU
 | | Crystal structure of tetrameric RXRalpha-LBD complexed with partial agonist CBt-PMN | | Descriptor: | 1-(3,5,5,8,8-pentamethyl-6,7-dihydronaphthalen-2-yl)benzotriazole-5-carboxylic acid, BROMIDE ION, Retinoic acid receptor RXR-alpha | | Authors: | Miyashita, Y, Numoto, N, Arulmozhiraja, S, Nakano, S, Matsuo, N, Shimizu, K, Kakuta, H, Ito, S, Ikura, T, Ito, N, Tokiwa, H. | | Deposit date: | 2018-04-20 | | Release date: | 2019-02-27 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.60038781 Å) | | Cite: | Dual conformation of the ligand induces the partial agonistic activity of retinoid X receptor alpha (RXR alpha ).
FEBS Lett., 593, 2019
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1UD6
 | | Crystal structure of AmyK38 with potassium ion | | Descriptor: | POTASSIUM ION, amylase | | Authors: | Nonaka, T, Fujihashi, M, Kita, A, Hagihara, H, Ozaki, K, Ito, S, Miki, K. | | Deposit date: | 2003-04-28 | | Release date: | 2003-07-22 | | Last modified: | 2024-04-03 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Crystal structure of calcium-free alpha-amylase from Bacillus sp. strain KSM-K38 (AmyK38) and its sodium ion binding sites
J.Biol.Chem., 278, 2003
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5GVC
 | | Human Topoisomerase IIIb topo domain | | Descriptor: | DNA topoisomerase 3-beta-1, MAGNESIUM ION | | Authors: | Goto-Ito, S, Yamagata, A, Sato, Y, Takahashi, T.S, Fukai, S. | | Deposit date: | 2016-09-05 | | Release date: | 2017-06-14 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.436 Å) | | Cite: | Structural basis of the interaction between Topoisomerase III beta and the TDRD3 auxiliary factor
Sci Rep, 7, 2017
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5H1A
 | | Crystal structure of an IclR homolog from Microbacterium sp. strain HM58-2 | | Descriptor: | IclR transcription factor homolog, PHOSPHATE ION | | Authors: | Akiyama, T, Yamada, Y, Takaya, N, Ito, S, Sasaki, Y, Yajima, S. | | Deposit date: | 2016-10-08 | | Release date: | 2017-01-18 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Crystal structure of an IclR homologue from Microbacterium sp. strain HM58-2.
Acta Crystallogr F Struct Biol Commun, 73, 2017
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5GVD
 | | Human TDRD3 DUF1767-OB domains | | Descriptor: | 1,2-ETHANEDIOL, MAGNESIUM ION, PHOSPHATE ION, ... | | Authors: | Goto-Ito, S, Yamagata, A, Sato, Y, Takahashi, T.S, Fukai, S. | | Deposit date: | 2016-09-05 | | Release date: | 2017-06-14 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.623 Å) | | Cite: | Structural basis of the interaction between Topoisomerase III beta and the TDRD3 auxiliary factor
Sci Rep, 7, 2017
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5GVE
 | | Human TOP3B-TDRD3 complex | | Descriptor: | DNA topoisomerase 3-beta-1, MAGNESIUM ION, Tudor domain-containing protein 3 | | Authors: | Goto-Ito, S, Yamagata, A, Sato, Y, Takahashi, T.S, Fukai, S. | | Deposit date: | 2016-09-05 | | Release date: | 2017-06-14 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (3.606 Å) | | Cite: | Structural basis of the interaction between Topoisomerase III beta and the TDRD3 auxiliary factor
Sci Rep, 7, 2017
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8JHE
 | | Hyper-thermostable ancestral L-amino acid oxidase 2 (HTAncLAAO2) | | Descriptor: | FLAVIN-ADENINE DINUCLEOTIDE, Hyper thermostable ancestral L-amino acid oxidase | | Authors: | Kawamura, Y, Ishida, C, Miyata, R, Miyata, A, Hayashi, S, Fujinami, D, Ito, S, Nakano, S. | | Deposit date: | 2023-05-23 | | Release date: | 2023-10-04 | | Method: | X-RAY DIFFRACTION (2.201 Å) | | Cite: | Structural and functional analysis of hyper-thermostable ancestral L-amino acid oxidase that can convert Trp derivatives to D-forms by chemoenzymatic reaction.
Commun Chem, 6, 2023
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8HYI
 | | Crystal structure of human P-cadherin MEC12 (X dimer) in complex with 2-(2-methyl-5-phenyl-1H-indole-3-yl)ethan-1-amine | | Descriptor: | 2-(2-methyl-5-phenyl-1H-indole-3-yl)ethan-1-amine, CALCIUM ION, Cadherin-3, ... | | Authors: | Senoo, A, Ito, S, Ueno, G, Nagatoishi, S, Tsumoto, K. | | Deposit date: | 2023-01-06 | | Release date: | 2023-08-30 | | Last modified: | 2023-10-11 | | Method: | X-RAY DIFFRACTION (2.85 Å) | | Cite: | Modulation of a conformational ensemble by a small molecule that inhibits key protein-protein interactions involved in cell adhesion.
Protein Sci., 32, 2023
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1EE6
 | | CRYSTAL STRUCTURE OF PECTATE LYASE FROM BACILLUS SP. STRAIN KSM-P15. | | Descriptor: | CALCIUM ION, PECTATE LYASE | | Authors: | Akita, M, Suzuki, A, Kobayashi, T, Ito, S, Yamane, T. | | Deposit date: | 2000-01-31 | | Release date: | 2001-01-31 | | Last modified: | 2011-07-13 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | The first structure of pectate lyase belonging to polysaccharide lyase family 3.
Acta Crystallogr.,Sect.D, 57, 2001
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1G01
 | | ALKALINE CELLULASE K CATALYTIC DOMAIN | | Descriptor: | ACETIC ACID, CADMIUM ION, ENDOGLUCANASE | | Authors: | Shirai, T, Ishida, H, Noda, J, Yamane, T, Ozaki, K, Hakamada, Y, Ito, S. | | Deposit date: | 2000-10-05 | | Release date: | 2001-08-01 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Crystal structure of alkaline cellulase K: insight into the alkaline adaptation of an industrial enzyme.
J.Mol.Biol., 310, 2001
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1G0C
 | | ALKALINE CELLULASE K CATALYTIC DOMAIN-CELLOBIOSE COMPLEX | | Descriptor: | ACETIC ACID, CADMIUM ION, ENDOGLUCANASE, ... | | Authors: | Shirai, T, Ishida, H, Noda, J, Yamane, T, Ozaki, K, Hakamada, Y, Ito, S. | | Deposit date: | 2000-10-05 | | Release date: | 2001-08-01 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Crystal structure of alkaline cellulase K: insight into the alkaline adaptation of an industrial enzyme.
J.Mol.Biol., 310, 2001
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8J82
 | | GaHNL-12gen (artificial S-hydroxynitrile lyase generated by GAOptimizer) | | Descriptor: | S-hydroxynitrile lyase | | Authors: | Ozawa, H, Unno, I, Sekine, R, Ito, S, Nakano, S. | | Deposit date: | 2023-04-29 | | Release date: | 2024-04-03 | | Method: | X-RAY DIFFRACTION (1.69 Å) | | Cite: | Development of evolutionary algorithm-based protein redesign method
Cell Rep Phys Sci, 5, 2024
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7BS8
 | | Bovine Pancreatic Trypsin with Benzamidine (Cryo) | | Descriptor: | BENZAMIDINE, CALCIUM ION, Cationic trypsin, ... | | Authors: | Maeki, M, Ito, S, Takeda, R, Funakubo, T, Ueno, G, Ishida, A, Tani, H, Yamamoto, M, Tokeshi, M. | | Deposit date: | 2020-03-30 | | Release date: | 2020-08-26 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.37 Å) | | Cite: | Room-temperature crystallography using a microfluidic protein crystal array device and its application to protein-ligand complex structure analysis.
Chem Sci, 11, 2020
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7BS2
 | | Bovine Pancreatic Trypsin with serotonin (Room Temperature) | | Descriptor: | CALCIUM ION, Cationic trypsin, SEROTONIN, ... | | Authors: | Maeki, M, Ito, S, Takeda, R, Funakubo, T, Ueno, G, Ishida, A, Tani, H, Yamamoto, M, Tokeshi, M. | | Deposit date: | 2020-03-30 | | Release date: | 2020-08-26 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Room-temperature crystallography using a microfluidic protein crystal array device and its application to protein-ligand complex structure analysis.
Chem Sci, 11, 2020
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7BRY
 | | Bovine Pancreatic Trypsin with 6-Methoxytryptamine (Room Temperature) | | Descriptor: | 2-(6-methoxy-1H-indol-3-yl)ethanamine, CALCIUM ION, Cationic trypsin, ... | | Authors: | Maeki, M, Ito, S, Takeda, R, Funakubo, T, Ueno, G, Ishida, A, Tani, H, Yamamoto, M, Tokeshi, M. | | Deposit date: | 2020-03-30 | | Release date: | 2020-08-26 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.65 Å) | | Cite: | Room-temperature crystallography using a microfluidic protein crystal array device and its application to protein-ligand complex structure analysis.
Chem Sci, 11, 2020
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7BS5
 | | Bovine Pancreatic Trypsin with 6-Methoxytryptamine (Cryo) | | Descriptor: | 2-(6-methoxy-1H-indol-3-yl)ethanamine, CALCIUM ION, Cationic trypsin, ... | | Authors: | Maeki, M, Ito, S, Takeda, R, Funakubo, T, Ueno, G, Ishida, A, Tani, H, Yamamoto, M, Tokeshi, M. | | Deposit date: | 2020-03-30 | | Release date: | 2020-08-26 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.17 Å) | | Cite: | Room-temperature crystallography using a microfluidic protein crystal array device and its application to protein-ligand complex structure analysis.
Chem Sci, 11, 2020
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7BS1
 | | Bovine Pancreatic Trypsin with benzamidine (Room Temperature) | | Descriptor: | BENZAMIDINE, CALCIUM ION, Cationic trypsin | | Authors: | Maeki, M, Ito, S, Takeda, R, Funakubo, T, Ueno, G, Ishida, A, Tani, H, Yamamoto, M, Tokeshi, M. | | Deposit date: | 2020-03-30 | | Release date: | 2020-08-26 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.5 Å) | | Cite: | Room-temperature crystallography using a microfluidic protein crystal array device and its application to protein-ligand complex structure analysis.
Chem Sci, 11, 2020
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7BS9
 | | Bovine Pancreatic Trypsin with serotonin (Cryo) | | Descriptor: | CALCIUM ION, Cationic trypsin, DIMETHYL SULFOXIDE, ... | | Authors: | Maeki, M, Ito, S, Takeda, R, Funakubo, T, Ueno, G, Ishida, A, Tani, H, Yamamoto, M, Tokeshi, M. | | Deposit date: | 2020-03-30 | | Release date: | 2020-08-26 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.05 Å) | | Cite: | Room-temperature crystallography using a microfluidic protein crystal array device and its application to protein-ligand complex structure analysis.
Chem Sci, 11, 2020
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7BRX
 | | Bovine Pancreatic Trypsin with 5-Methoxytryptamine (Room Temperature) | | Descriptor: | 2-(5-methoxy-1H-indol-3-yl)ethanamine, CALCIUM ION, Cationic trypsin | | Authors: | Maeki, M, Ito, S, Takeda, R, Funakubo, T, Ueno, G, Ishida, A, Tani, H, Yamamoto, M, Tokeshi, M. | | Deposit date: | 2020-03-30 | | Release date: | 2020-08-26 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.35 Å) | | Cite: | Room-temperature crystallography using a microfluidic protein crystal array device and its application to protein-ligand complex structure analysis.
Chem Sci, 11, 2020
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7BS4
 | | Bovine Pancreatic Trypsin with 5-Methoxytryptamine (Cryo) | | Descriptor: | 2-(5-methoxy-1H-indol-3-yl)ethanamine, CALCIUM ION, Cationic trypsin, ... | | Authors: | Maeki, M, Ito, S, Takeda, R, Funakubo, T, Ueno, G, Ishida, A, Tani, H, Yamamoto, M, Tokeshi, M. | | Deposit date: | 2020-03-30 | | Release date: | 2020-08-26 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.04 Å) | | Cite: | Room-temperature crystallography using a microfluidic protein crystal array device and its application to protein-ligand complex structure analysis.
Chem Sci, 11, 2020
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7BRV
 | | Bovine Pancreatic Trypsin with 4-Bromobenzamidine (Room Temperature) | | Descriptor: | 4-bromanylbenzenecarboximidamide, CALCIUM ION, Cationic trypsin, ... | | Authors: | Takeda, R, Ito, S, Maeki, M, Funakubo, T, Ueno, G, Ishida, A, Tani, H, Yamamoto, M, Tokeshi, M. | | Deposit date: | 2020-03-30 | | Release date: | 2020-08-26 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.55 Å) | | Cite: | Room-temperature crystallography using a microfluidic protein crystal array device and its application to protein-ligand complex structure analysis.
Chem Sci, 11, 2020
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7BRZ
 | | Bovine Pancreatic Trypsin with 2-Methyltryptamine (Room Temperature) | | Descriptor: | 2-(2-methyl-1H-indol-3-yl)ethanamine, CALCIUM ION, Cationic trypsin, ... | | Authors: | Maeki, M, Ito, S, Takeda, R, Funakubo, T, Ueno, G, Ishida, A, Tani, H, Yamamoto, M, Tokeshi, M. | | Deposit date: | 2020-03-30 | | Release date: | 2020-08-26 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.3 Å) | | Cite: | Room-temperature crystallography using a microfluidic protein crystal array device and its application to protein-ligand complex structure analysis.
Chem Sci, 11, 2020
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