6LB6
| Crystal structure of dimeric RXR-LBD complexed with partial agonist NEt-4IB and TIF2 co-activator | Descriptor: | 6-[ethyl-[4-(2-methylpropoxy)-3-propan-2-yl-phenyl]amino]pyridine-3-carboxylic acid, Nuclear receptor coactivator 2, Retinoic acid receptor RXR-alpha | Authors: | Imai, D, Numoto, N, Nakano, S, Kakuta, H, Ito, N. | Deposit date: | 2019-11-13 | Release date: | 2020-11-18 | Last modified: | 2024-10-02 | Method: | X-RAY DIFFRACTION (2.4 Å) | Cite: | Structural basis for the full and partial agonist activities of retinoid X receptor alpha ligands with an iso-butoxy and an isopropyl group Biochem.Biophys.Res.Commun., 734, 2024
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7F1I
| Designed enzyme RA61 M48K/I72D mutant: form II | Descriptor: | Engineered Retroaldolase | Authors: | Fujioka, T, Oka, M, Numoto, N, Ito, N, Oda, M, Tanaka, F. | Deposit date: | 2021-06-09 | Release date: | 2021-11-24 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (1.4 Å) | Cite: | Varying the Directionality of Protein Catalysts for Aldol and Retro-Aldol Reactions. Chembiochem, 23, 2022
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7F1H
| Designed enzyme RA61 M48K/I72D mutant: form I | Descriptor: | Engineered Retroaldolase, FORMIC ACID, GLYCEROL | Authors: | Fujioka, T, Oka, M, Numoto, N, Ito, N, Oda, M, Tanaka, F. | Deposit date: | 2021-06-09 | Release date: | 2021-11-24 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (1.14 Å) | Cite: | Varying the Directionality of Protein Catalysts for Aldol and Retro-Aldol Reactions. Chembiochem, 23, 2022
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7F1K
| Designed enzyme RA61 M48K/I72D mutant: form IV | Descriptor: | Engineered Retroaldolase | Authors: | Fujioka, T, Oka, M, Numoto, N, Ito, N, Oda, M, Tanaka, F. | Deposit date: | 2021-06-09 | Release date: | 2021-11-24 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (1.05 Å) | Cite: | Varying the Directionality of Protein Catalysts for Aldol and Retro-Aldol Reactions. Chembiochem, 23, 2022
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7F1J
| Designed enzyme RA61 M48K/I72D mutant: form III | Descriptor: | Engineered Retroaldolase | Authors: | Fujioka, T, Oka, M, Numoto, N, Ito, N, Oda, M, Tanaka, F. | Deposit date: | 2021-06-09 | Release date: | 2021-11-24 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (1.6 Å) | Cite: | Varying the Directionality of Protein Catalysts for Aldol and Retro-Aldol Reactions. Chembiochem, 23, 2022
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7F1L
| Designed enzyme RA61 M48K/I72D mutant: form V | Descriptor: | CHLORIDE ION, Engineered Retroaldolase, IMIDAZOLE | Authors: | Fujioka, T, Oka, M, Numoto, N, Ito, N, Oda, M, Tanaka, F. | Deposit date: | 2021-06-09 | Release date: | 2021-11-24 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (1.7 Å) | Cite: | Varying the Directionality of Protein Catalysts for Aldol and Retro-Aldol Reactions. Chembiochem, 23, 2022
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2E0I
| Crystal structure of archaeal photolyase from Sulfolobus tokodaii with two FAD molecules: Implication of a novel light-harvesting cofactor | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, 432aa long hypothetical deoxyribodipyrimidine photolyase, FLAVIN-ADENINE DINUCLEOTIDE | Authors: | Fujihashi, M, Numoto, N, Kobayashi, Y, Mizushima, A, Tsujimura, M, Nakamura, A, Kawarabayashi, Y, Miki, K. | Deposit date: | 2006-10-10 | Release date: | 2006-11-28 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (2.8 Å) | Cite: | Crystal Structure of Archaeal Photolyase from Sulfolobus tokodaii with Two FAD Molecules: Implication of a Novel Light-harvesting Cofactor J.Mol.Biol., 365, 2007
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8IF4
| Structure of human alpha-2/delta-1 without mirogabalin | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Voltage-dependent calcium channel subunit alpha-2/delta-1 | Authors: | Kozai, D, Numoto, N, Fujiyoshi, Y. | Deposit date: | 2023-02-17 | Release date: | 2023-04-05 | Last modified: | 2024-10-16 | Method: | ELECTRON MICROSCOPY (3.23 Å) | Cite: | Recognition Mechanism of a Novel Gabapentinoid Drug, Mirogabalin, for Recombinant Human alpha 2 delta 1, a Voltage-Gated Calcium Channel Subunit. J.Mol.Biol., 435, 2023
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8IF3
| Structure of human alpha-2/delta-1 with mirogabalin | Descriptor: | 2-[(1R,5S,6S)-6-(aminomethyl)-3-ethyl-6-bicyclo[3.2.0]hept-3-enyl]acetic acid, 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ... | Authors: | Kozai, D, Numoto, N, Fujiyoshi, Y. | Deposit date: | 2023-02-17 | Release date: | 2023-04-05 | Last modified: | 2023-04-12 | Method: | ELECTRON MICROSCOPY (3.2 Å) | Cite: | Recognition Mechanism of a Novel Gabapentinoid Drug, Mirogabalin, for Recombinant Human alpha 2 delta 1, a Voltage-Gated Calcium Channel Subunit. J.Mol.Biol., 435, 2023
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8JT7
| Structure of arginine oxidase from Pseudomonas sp. TRU 7192 | Descriptor: | Amine oxidoreductase, FLAVIN-ADENINE DINUCLEOTIDE | Authors: | Yamaguchi, H, Numoto, N, Suzuki, H, Nishikawa, K, Kamegawa, A, Takahashi, K, Sugiki, M, Fujiyoshi, Y. | Deposit date: | 2023-06-21 | Release date: | 2024-06-26 | Method: | ELECTRON MICROSCOPY (2.34 Å) | Cite: | Structural basis of arginine oxidase from Pseudomonas sp. TRU 7192 To Be Published
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7CTR
| Closed form of PET-degrading cutinase Cut190 with thermostability-improving mutations of S226P/R228S/Q138A/D250C-E296C/Q123H/N202H | Descriptor: | 1,4-DIETHYLENE DIOXIDE, Alpha/beta hydrolase family protein | Authors: | Emori, M, Numoto, N, Senga, A, Bekker, G.J, Kamiya, N, Ito, N, Kawai, F, Oda, M. | Deposit date: | 2020-08-20 | Release date: | 2021-02-03 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (1.2 Å) | Cite: | Structural basis of mutants of PET-degrading enzyme from Saccharomonospora viridis AHK190 with high activity and thermal stability. Proteins, 89, 2021
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7CTS
| Open form of PET-degrading cutinase Cut190 with thermostability-improving mutations of S226P/R228S/Q138A/D250C-E296C/Q123H/N202H and S176A inactivation | Descriptor: | 1,4-DIETHYLENE DIOXIDE, Alpha/beta hydrolase family protein, BICINE, ... | Authors: | Emori, M, Numoto, N, Senga, A, Bekker, G.J, Kamiya, N, Ito, N, Kawai, F, Oda, M. | Deposit date: | 2020-08-20 | Release date: | 2021-02-03 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (1.1 Å) | Cite: | Structural basis of mutants of PET-degrading enzyme from Saccharomonospora viridis AHK190 with high activity and thermal stability. Proteins, 89, 2021
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7C7V
| Vitamin D3 receptor/lithochoric acid derivative complex | Descriptor: | (4R)-4-[(3R,5R,8R,9S,10S,13R,14S,17R)-10,13-dimethyl-3-(2-methyl-2-oxidanyl-propyl)-2,3,4,5,6,7,8,9,11,12,14,15,16,17-tetradecahydro-1H-cyclopenta[a]phenanthren-17-yl]pentanoic acid, FORMIC ACID, Mediator of RNA polymerase II transcription subunit 1, ... | Authors: | Masuno, H, Numoto, N, Kagechika, H, Ito, N. | Deposit date: | 2020-05-26 | Release date: | 2021-01-20 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Lithocholic Acid Derivatives as Potent Vitamin D Receptor Agonists. J.Med.Chem., 64, 2021
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7C7W
| Vitamin D3 receptor/lithochoric acid derivative complex | Descriptor: | (4R)-4-[(3S,5R,8R,9S,10S,13R,14S,17R)-10,13-dimethyl-3-(2-methyl-2-oxidanyl-propyl)-2,3,4,5,6,7,8,9,11,12,14,15,16,17-tetradecahydro-1H-cyclopenta[a]phenanthren-17-yl]pentanoic acid, FORMIC ACID, Mediator of RNA polymerase II transcription subunit 1, ... | Authors: | Masuno, H, Numoto, N, Kagechika, H, Ito, N. | Deposit date: | 2020-05-26 | Release date: | 2021-01-20 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (1.9 Å) | Cite: | Lithocholic Acid Derivatives as Potent Vitamin D Receptor Agonists. J.Med.Chem., 64, 2021
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7CIO
| Molecular interactions of cytoplasmic region of CTLA-4 with SH2 domains of PI3-kinase | Descriptor: | Cytotoxic T-lymphocyte protein 4, Phosphatidylinositol 3-kinase regulatory subunit alpha | Authors: | Iiyama, M, Numoto, N, Ogawa, S, Kuroda, M, Morii, H, Abe, R, Ito, N, Oda, M. | Deposit date: | 2020-07-08 | Release date: | 2020-12-09 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (1.1 Å) | Cite: | Molecular interactions of the CTLA-4 cytoplasmic region with the phosphoinositide 3-kinase SH2 domains. Mol.Immunol., 131, 2021
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7CEF
| Crystal structure of PET-degrading cutinase Cut190 /S226P/R228S/ mutant with the C-terminal three residues deletion | Descriptor: | Alpha/beta hydrolase family protein, CALCIUM ION, ZINC ION | Authors: | Senga, A, Numoto, N, Ito, N, Kawai, F, Oda, M. | Deposit date: | 2020-06-23 | Release date: | 2020-08-26 | Last modified: | 2024-10-16 | Method: | X-RAY DIFFRACTION (1.6 Å) | Cite: | Multiple structural states of Ca2+-regulated PET hydrolase, Cut190, and its correlation with activity and stability. J.Biochem., 169, 2021
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7CEH
| Crystal structure of PET-degrading cutinase Cut190 S176A/S226P/R228S/ mutant with the C-terminal three residues deletion in ligand ejecting form | Descriptor: | Alpha/beta hydrolase family protein, CALCIUM ION | Authors: | Senga, A, Numoto, N, Ito, N, Kawai, F, Oda, M. | Deposit date: | 2020-06-23 | Release date: | 2020-08-26 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (1.09 Å) | Cite: | Multiple structural states of Ca2+-regulated PET hydrolase, Cut190, and its correlation with activity and stability. J.Biochem., 169, 2021
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3W3A
| Crystal structure of V1-ATPase at 3.9 angstrom resolution | Descriptor: | ADENOSINE-5'-DIPHOSPHATE, V-type ATP synthase alpha chain, V-type ATP synthase beta chain, ... | Authors: | Nagamatsu, Y, Takeda, K, Kuranaga, T, Numoto, N, Miki, K. | Deposit date: | 2012-12-14 | Release date: | 2013-05-15 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (3.9 Å) | Cite: | Origin of Asymmetry at the Intersubunit Interfaces of V1-ATPase from Thermusthermophilus J.Mol.Biol., 425, 2013
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8T8A
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