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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6K4Z
 | | Single-chain Fv antibody of C6 COMPLEXED WITH 2-(4-HYDROXY-3-NITROPHENYL)ACETIC ACID | | Descriptor: | 2-(4-HYDROXY-3-NITROPHENYL)ACETIC ACID, GLYCEROL, SULFATE ION, ... | | Authors: | Nishiguchi, A, Numoto, N, Ito, N, Azuma, T, Oda, M. | | Deposit date: | 2019-05-27 | | Release date: | 2019-09-18 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.65 Å) | | Cite: | Three-dimensional structure of a high affinity anti-(4-hydroxy-3-nitrophenyl)acetyl antibody possessing a glycine residue at position 95 of the heavy chain.
Mol.Immunol., 114, 2019
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6LCB
 | | Crystal structure of human Dishevelled1 PDZ domain with its inhibitor NPL3009 | | Descriptor: | 2-[[3-[(2E)-2-[1,3-bis(oxidanylidene)-1-phenyl-butan-2-ylidene]hydrazinyl]phenyl]sulfonylamino]benzoic acid, SULFATE ION, Segment polarity protein dishevelled homolog DVL-1 | | Authors: | Yasukochi, S, Numoto, N, Tenno, N, Tenno, T, Ito, N, Hiroaki, H. | | Deposit date: | 2019-11-18 | | Release date: | 2020-11-25 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.4 Å) | | Cite: | Crystal structure of human Dishevelled1 PDZ domain with its inhibitor NPL3009
To Be Published
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6LB5
 | | Crystal structure of dimeric RXR-LBD complexed with full agonist NEt-3IB and TIF2 co-activator | | Descriptor: | 6-[ethyl-[3-(2-methylpropoxy)-4-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: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | Crystal structure of dimeric RXR-LBD complexed with full agonist NEt-3IB and TIF2 co-activator
To Be Published
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4X42
 | | Crystal structure of DEN4 ED3 mutant with epitope two residues substituted from DEN3 ED3 | | Descriptor: | Envelope protein E, SULFATE ION | | Authors: | Kulkarni, M.R, Islam, M.M, Numoto, N, Elahi, M.M, Ito, N, Kuroda, Y. | | Deposit date: | 2014-12-02 | | Release date: | 2015-09-09 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.78 Å) | | Cite: | Structural and biophysical analysis of sero-specific immune responses using epitope grafted Dengue ED3 mutants.
Biochim.Biophys.Acta, 1854, 2015
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8GCL
 | | Cryo-EM structure of hAQP2 in DDM | | Descriptor: | Aquaporin-2 | | Authors: | Kamegawa, A, Suzuki, S, Nishikawa, K, Numoto, N, Suzuki, H, Fujiyoshi, Y. | | Deposit date: | 2023-03-02 | | Release date: | 2023-06-21 | | Last modified: | 2024-06-19 | | Method: | ELECTRON MICROSCOPY (2.89 Å) | | Cite: | Structural analysis of the water channel AQP2 by single-particle cryo-EM.
J.Struct.Biol., 215, 2023
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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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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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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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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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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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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: | 2023-11-29 | | 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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8YTN
 | | Single-chain Fv antibody of E11 | | Descriptor: | GLYCEROL, Single-chain Fv antibody of E11 | | Authors: | Yoshida, M, Hanazono, Y, Numoto, N, Ito, N, Oda, M. | | Deposit date: | 2024-03-26 | | Release date: | 2024-07-03 | | Last modified: | 2024-07-10 | | Method: | X-RAY DIFFRACTION (1.72 Å) | | Cite: | Affinity-matured antibody with a disulfide bond in H-CDR3 loop.
Arch.Biochem.Biophys., 758, 2024
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8YTO
 | | Single-chain Fv antibody of E11 complex with NP-glycine | | Descriptor: | 2-[2-(3-nitro-4-oxidanyl-phenyl)ethanoylamino]ethanoic acid, 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, GLYCEROL, ... | | Authors: | Yoshida, M, Hanazono, Y, Numoto, N, Ito, N, Oda, M. | | Deposit date: | 2024-03-26 | | Release date: | 2024-07-03 | | Last modified: | 2024-07-10 | | Method: | X-RAY DIFFRACTION (1.04 Å) | | Cite: | Affinity-matured antibody with a disulfide bond in H-CDR3 loop.
Arch.Biochem.Biophys., 758, 2024
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8YTP
 | | Single-chain Fv antibody of E11 complex with NP-glycine under reducing conditions | | Descriptor: | 2-[2-(3-nitro-4-oxidanyl-phenyl)ethanoylamino]ethanoic acid, Single-chain Fv antibody of E11 | | Authors: | Yoshida, M, Hanazono, Y, Numoto, N, Ito, N, Oda, M. | | Deposit date: | 2024-03-26 | | Release date: | 2024-07-03 | | Last modified: | 2024-07-10 | | Method: | X-RAY DIFFRACTION (1.36 Å) | | Cite: | Affinity-matured antibody with a disulfide bond in H-CDR3 loop.
Arch.Biochem.Biophys., 758, 2024
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5GJI
 | | PI3K p85 N-terminal SH2 domain/CD28-derived peptide complex | | Descriptor: | GLYCEROL, Phosphatidylinositol 3-kinase regulatory subunit alpha, SULFATE ION, ... | | Authors: | Inaba, S, Numoto, N, Morii, H, Ogawa, S, Ikura, T, Abe, R, Ito, N, Oda, M. | | Deposit date: | 2016-06-30 | | Release date: | 2016-12-14 | | Last modified: | 2017-05-10 | | Method: | X-RAY DIFFRACTION (0.9 Å) | | Cite: | Crystal Structures and Thermodynamic Analysis Reveal Distinct Mechanisms of CD28 Phosphopeptide Binding to the Src Homology 2 (SH2) Domains of Three Adaptor Proteins
J. Biol. Chem., 292, 2017
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5GJH
 | | Gads SH2 domain/CD28-derived peptide complex | | Descriptor: | GRB2-related adapter protein 2, T-cell-specific surface glycoprotein CD28 | | Authors: | Inaba, S, Numoto, N, Morii, H, Ogawa, S, Ikura, T, Abe, R, Ito, N, Oda, M. | | Deposit date: | 2016-06-30 | | Release date: | 2016-12-14 | | Last modified: | 2023-11-15 | | Method: | X-RAY DIFFRACTION (1.2 Å) | | Cite: | Crystal Structures and Thermodynamic Analysis Reveal Distinct Mechanisms of CD28 Phosphopeptide Binding to the Src Homology 2 (SH2) Domains of Three Adaptor Proteins
J. Biol. Chem., 292, 2017
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6ICH
 | | Grb2 SH2 domain in domain swapped dimer form | | Descriptor: | Growth factor receptor-bound protein 2 | | Authors: | Hosoe, Y, Numoto, N, Inaba, S, Ogawa, S, Morii, H, Abe, R, Ito, N, Oda, M. | | Deposit date: | 2018-09-06 | | Release date: | 2019-07-17 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Structural and functional properties of Grb2 SH2 dimer in CD28 binding.
Biophys Physicobio., 16, 2019
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6ICG
 | | Grb2 SH2 domain in phosphopeptide free form | | Descriptor: | GLYCEROL, Growth factor receptor-bound protein 2, SULFATE ION | | Authors: | Hosoe, Y, Numoto, N, Inaba, S, Ogawa, S, Morii, H, Abe, R, Ito, N, Oda, M. | | Deposit date: | 2018-09-06 | | Release date: | 2019-07-17 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.15 Å) | | Cite: | Structural and functional properties of Grb2 SH2 dimer in CD28 binding.
Biophys Physicobio., 16, 2019
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5XZH
 | | Vitamin D receptor with a synthetic ligand ADRO2 | | Descriptor: | (1R,3S,5Z)-5-[(2E)-2-[(1R,3aS,7aR)-1-[(2R,6R)-6-(1-adamantyl)-6-oxidanyl-hex-4-yn-2-yl]-7a-methyl-2,3,3a,5,6,7-hexahydro-1H-inden-4-ylidene]ethylidene]-4-methylidene-cyclohexane-1,3-diol, Mediator of RNA polymerase II transcription subunit 1, Vitamin D3 receptor | | Authors: | Otero, R, Numoto, N, Ikura, T, Yamada, S, Mourino, A, Makishima, M, Ito, N. | | Deposit date: | 2017-07-12 | | Release date: | 2018-07-25 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | 25 S-Adamantyl-23-yne-26,27-dinor-1 alpha ,25-dihydroxyvitamin D3: Synthesis, Tissue Selective Biological Activities, and X-ray Crystal Structural Analysis of Its Vitamin D Receptor Complex.
J. Med. Chem., 61, 2018
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5XZF
 | | Vitamin D receptor with a synthetic ligand ADRO1 | | Descriptor: | (1R,3S,5Z)-5-[(2E)-2-[(1R,3aS,7aR)-1-[(2R,6S)-6-(1-adamantyl)-6-oxidanyl-hex-4-yn-2-yl]-7a-methyl-2,3,3a,5,6,7-hexahydro-1H-inden-4-ylidene]ethylidene]-4-methylidene-cyclohexane-1,3-diol, FORMIC ACID, Mediator of RNA polymerase II transcription subunit 1, ... | | Authors: | Otero, R, Numoto, N, Ikura, T, Yamada, S, Mourino, A, Makishima, M, Ito, N. | | Deposit date: | 2017-07-12 | | Release date: | 2018-07-25 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | 25 S-Adamantyl-23-yne-26,27-dinor-1 alpha ,25-dihydroxyvitamin D3: Synthesis, Tissue Selective Biological Activities, and X-ray Crystal Structural Analysis of Its Vitamin D Receptor Complex.
J. Med. Chem., 61, 2018
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8IBL
 | | MES bound form of PET-degrading cutinase Cut190 with thermostability-improving mutations of S226P/R228S/Q138A/D250C-E296C/Q123H/N202H and S176A inactivation | | Descriptor: | 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, Alpha/beta hydrolase family protein, CALCIUM ION, ... | | Authors: | Emori, M, Numoto, N, Kamiya, N, Oda, M. | | Deposit date: | 2023-02-10 | | Release date: | 2023-03-15 | | Method: | X-RAY DIFFRACTION (2.6 Å) | | Cite: | Improvement of thermostability and activity of PET-degrading enzyme Cut190 towards a detailed understanding and application of the enzymatic reaction mechanism.
Biorxiv, 2023
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8IBM
 | | Sulfate bound form of PET-degrading cutinase Cut190 with thermostability-improving mutations of S226P/R228S/Q138A/D250C-E296C/Q123H/N202H and S176A inactivation | | Descriptor: | Alpha/beta hydrolase family protein, CALCIUM ION, SULFATE ION | | Authors: | Emori, M, Numoto, N, Kamiya, N, Oda, M. | | Deposit date: | 2023-02-10 | | Release date: | 2023-03-15 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Improvement of thermostability and activity of PET-degrading enzyme Cut190 towards a detailed understanding and application of the enzymatic reaction mechanism.
Biorxiv, 2023
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5AUL
 | | PI3K p85 C-terminal SH2 domain/CD28-derived peptide complex | | Descriptor: | GLYCEROL, Phosphatidylinositol 3-kinase regulatory subunit alpha, T-cell-specific surface glycoprotein CD28 | | Authors: | Inaba, S, Numoto, N, Morii, H, Ikura, T, Oda, M, Ito, N. | | Deposit date: | 2015-04-28 | | Release date: | 2016-05-25 | | Last modified: | 2023-11-15 | | Method: | X-RAY DIFFRACTION (1.1 Å) | | Cite: | Crystal Structures and Thermodynamic Analysis Reveal Distinct Mechanisms of CD28 Phosphopeptide Binding to the Src Homology 2 (SH2) Domains of Three Adaptor Proteins
J. Biol. Chem., 292, 2017
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