5ZRQ
 
 | | Crystal structure of PET-degrading cutinase Cut190 S176A/S226P/R228S mutant in Zn(2+)-bound state | | 分子名称: | Alpha/beta hydrolase family protein, CALCIUM ION, GLYCEROL, ... | | 著者 | Numoto, N, Kamiya, N, Bekker, G.J, Yamagami, Y, Inaba, S, Ishii, K, Uchiyama, S, Kawai, F, Ito, N, Oda, M. | | 登録日 | 2018-04-25 | | 公開日 | 2018-09-12 | | 最終更新日 | 2024-10-16 | | 実験手法 | X-RAY DIFFRACTION (1.12 Å) | | 主引用文献 | Structural Dynamics of the PET-Degrading Cutinase-like Enzyme from Saccharomonospora viridis AHK190 in Substrate-Bound States Elucidates the Ca2+-Driven Catalytic Cycle.
Biochemistry, 57, 2018
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5GJI
 | | PI3K p85 N-terminal SH2 domain/CD28-derived peptide complex | | 分子名称: | GLYCEROL, Phosphatidylinositol 3-kinase regulatory subunit alpha, SULFATE ION, ... | | 著者 | Inaba, S, Numoto, N, Morii, H, Ogawa, S, Ikura, T, Abe, R, Ito, N, Oda, M. | | 登録日 | 2016-06-30 | | 公開日 | 2016-12-14 | | 最終更新日 | 2017-05-10 | | 実験手法 | X-RAY DIFFRACTION (0.9 Å) | | 主引用文献 | 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 | | 分子名称: | GRB2-related adapter protein 2, T-cell-specific surface glycoprotein CD28 | | 著者 | Inaba, S, Numoto, N, Morii, H, Ogawa, S, Ikura, T, Abe, R, Ito, N, Oda, M. | | 登録日 | 2016-06-30 | | 公開日 | 2016-12-14 | | 最終更新日 | 2023-11-15 | | 実験手法 | X-RAY DIFFRACTION (1.2 Å) | | 主引用文献 | 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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6ICG
 | | Grb2 SH2 domain in phosphopeptide free form | | 分子名称: | GLYCEROL, Growth factor receptor-bound protein 2, SULFATE ION | | 著者 | Hosoe, Y, Numoto, N, Inaba, S, Ogawa, S, Morii, H, Abe, R, Ito, N, Oda, M. | | 登録日 | 2018-09-06 | | 公開日 | 2019-07-17 | | 最終更新日 | 2023-11-22 | | 実験手法 | X-RAY DIFFRACTION (1.15 Å) | | 主引用文献 | Structural and functional properties of Grb2 SH2 dimer in CD28 binding.
Biophys Physicobio., 16, 2019
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6K4Z
 | | Single-chain Fv antibody of C6 COMPLEXED WITH 2-(4-HYDROXY-3-NITROPHENYL)ACETIC ACID | | 分子名称: | 2-(4-HYDROXY-3-NITROPHENYL)ACETIC ACID, GLYCEROL, SULFATE ION, ... | | 著者 | Nishiguchi, A, Numoto, N, Ito, N, Azuma, T, Oda, M. | | 登録日 | 2019-05-27 | | 公開日 | 2019-09-18 | | 最終更新日 | 2023-11-22 | | 実験手法 | X-RAY DIFFRACTION (1.65 Å) | | 主引用文献 | 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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5AUL
 | | PI3K p85 C-terminal SH2 domain/CD28-derived peptide complex | | 分子名称: | GLYCEROL, Phosphatidylinositol 3-kinase regulatory subunit alpha, T-cell-specific surface glycoprotein CD28 | | 著者 | Inaba, S, Numoto, N, Morii, H, Ikura, T, Oda, M, Ito, N. | | 登録日 | 2015-04-28 | | 公開日 | 2016-05-25 | | 最終更新日 | 2023-11-15 | | 実験手法 | X-RAY DIFFRACTION (1.1 Å) | | 主引用文献 | 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 | | 分子名称: | Growth factor receptor-bound protein 2 | | 著者 | Hosoe, Y, Numoto, N, Inaba, S, Ogawa, S, Morii, H, Abe, R, Ito, N, Oda, M. | | 登録日 | 2018-09-06 | | 公開日 | 2019-07-17 | | 最終更新日 | 2023-11-22 | | 実験手法 | X-RAY DIFFRACTION (2 Å) | | 主引用文献 | Structural and functional properties of Grb2 SH2 dimer in CD28 binding.
Biophys Physicobio., 16, 2019
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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 | | 分子名称: | 1,4-DIETHYLENE DIOXIDE, Alpha/beta hydrolase family protein, BICINE, ... | | 著者 | Emori, M, Numoto, N, Senga, A, Bekker, G.J, Kamiya, N, Ito, N, Kawai, F, Oda, M. | | 登録日 | 2020-08-20 | | 公開日 | 2021-02-03 | | 最終更新日 | 2023-11-29 | | 実験手法 | X-RAY DIFFRACTION (1.1 Å) | | 主引用文献 | 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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7CTR
 | | Closed form of PET-degrading cutinase Cut190 with thermostability-improving mutations of S226P/R228S/Q138A/D250C-E296C/Q123H/N202H | | 分子名称: | 1,4-DIETHYLENE DIOXIDE, Alpha/beta hydrolase family protein | | 著者 | Emori, M, Numoto, N, Senga, A, Bekker, G.J, Kamiya, N, Ito, N, Kawai, F, Oda, M. | | 登録日 | 2020-08-20 | | 公開日 | 2021-02-03 | | 最終更新日 | 2023-11-29 | | 実験手法 | X-RAY DIFFRACTION (1.2 Å) | | 主引用文献 | 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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7F1I
 | | Designed enzyme RA61 M48K/I72D mutant: form II | | 分子名称: | Engineered Retroaldolase | | 著者 | Fujioka, T, Oka, M, Numoto, N, Ito, N, Oda, M, Tanaka, F. | | 登録日 | 2021-06-09 | | 公開日 | 2021-11-24 | | 最終更新日 | 2023-11-29 | | 実験手法 | X-RAY DIFFRACTION (1.4 Å) | | 主引用文献 | 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 | | 分子名称: | Engineered Retroaldolase, FORMIC ACID, GLYCEROL | | 著者 | Fujioka, T, Oka, M, Numoto, N, Ito, N, Oda, M, Tanaka, F. | | 登録日 | 2021-06-09 | | 公開日 | 2021-11-24 | | 最終更新日 | 2023-11-29 | | 実験手法 | X-RAY DIFFRACTION (1.14 Å) | | 主引用文献 | 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 | | 分子名称: | Engineered Retroaldolase | | 著者 | Fujioka, T, Oka, M, Numoto, N, Ito, N, Oda, M, Tanaka, F. | | 登録日 | 2021-06-09 | | 公開日 | 2021-11-24 | | 最終更新日 | 2023-11-29 | | 実験手法 | X-RAY DIFFRACTION (1.6 Å) | | 主引用文献 | 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 | | 分子名称: | Engineered Retroaldolase | | 著者 | Fujioka, T, Oka, M, Numoto, N, Ito, N, Oda, M, Tanaka, F. | | 登録日 | 2021-06-09 | | 公開日 | 2021-11-24 | | 最終更新日 | 2023-11-29 | | 実験手法 | X-RAY DIFFRACTION (1.05 Å) | | 主引用文献 | 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 | | 分子名称: | CHLORIDE ION, Engineered Retroaldolase, IMIDAZOLE | | 著者 | Fujioka, T, Oka, M, Numoto, N, Ito, N, Oda, M, Tanaka, F. | | 登録日 | 2021-06-09 | | 公開日 | 2021-11-24 | | 最終更新日 | 2023-11-29 | | 実験手法 | X-RAY DIFFRACTION (1.7 Å) | | 主引用文献 | Varying the Directionality of Protein Catalysts for Aldol and Retro-Aldol Reactions.
Chembiochem, 23, 2022
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7CEF
 | | Crystal structure of PET-degrading cutinase Cut190 /S226P/R228S/ mutant with the C-terminal three residues deletion | | 分子名称: | Alpha/beta hydrolase family protein, CALCIUM ION, ZINC ION | | 著者 | Senga, A, Numoto, N, Ito, N, Kawai, F, Oda, M. | | 登録日 | 2020-06-23 | | 公開日 | 2020-08-26 | | 最終更新日 | 2024-10-16 | | 実験手法 | X-RAY DIFFRACTION (1.6 Å) | | 主引用文献 | 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 | | 分子名称: | Alpha/beta hydrolase family protein, CALCIUM ION | | 著者 | Senga, A, Numoto, N, Ito, N, Kawai, F, Oda, M. | | 登録日 | 2020-06-23 | | 公開日 | 2020-08-26 | | 最終更新日 | 2024-10-30 | | 実験手法 | X-RAY DIFFRACTION (1.09 Å) | | 主引用文献 | Multiple structural states of Ca2+-regulated PET hydrolase, Cut190, and its correlation with activity and stability.
J.Biochem., 169, 2021
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3WA4
 | | Grb2 SH2 domain/CD28-derived peptide complex | | 分子名称: | ACETIC ACID, CADMIUM ION, Growth factor receptor-bound protein 2, ... | | 著者 | Higo, K, Oda, M, Ito, N. | | 登録日 | 2013-04-23 | | 公開日 | 2014-02-26 | | 最終更新日 | 2024-10-16 | | 実験手法 | X-RAY DIFFRACTION (1.35 Å) | | 主引用文献 | High Resolution Crystal Structure of the Grb2 SH2 Domain with a Phosphopeptide Derived from CD28
Plos One, 8, 2013
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3ATG
 | | endo-1,3-beta-glucanase from Cellulosimicrobium cellulans | | 分子名称: | CALCIUM ION, GLUCANASE, GLYCEROL, ... | | 著者 | Tanabe, Y, Pang, Z, Oda, M, Mikami, B. | | 登録日 | 2011-01-04 | | 公開日 | 2012-01-18 | | 最終更新日 | 2024-03-13 | | 実験手法 | X-RAY DIFFRACTION (1.66 Å) | | 主引用文献 | Structural and thermodynamic characterization of endo-1,3-beta-glucanase: Insights into the substrate recognition mechanism.
Biochim. Biophys. Acta, 1866, 2018
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2DDT
 | | Crystal structure of sphingomyelinase from Bacillus cereus with magnesium ion | | 分子名称: | 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, MAGNESIUM ION, SULFATE ION, ... | | 著者 | Ago, H, Oda, M, Tsuge, H, Katunuma, N, Miyano, M, Sakurai, J, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | 登録日 | 2006-02-02 | | 公開日 | 2006-05-02 | | 最終更新日 | 2024-03-13 | | 実験手法 | X-RAY DIFFRACTION (1.8 Å) | | 主引用文献 | Structural basis of the sphingomyelin phosphodiesterase activity in neutral sphingomyelinase from Bacillus cereus.
J.Biol.Chem., 281, 2006
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2DDS
 | | Crystal structure of sphingomyelinase from Bacillus cereus with cobalt ion | | 分子名称: | COBALT (II) ION, Sphingomyelin phosphodiesterase | | 著者 | Ago, H, Oda, M, Takahashi, M, Tsuge, H, Ochi, S, Katunuma, N, Miyano, M, Sakurai, J, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | 登録日 | 2006-02-02 | | 公開日 | 2006-05-02 | | 最終更新日 | 2011-07-13 | | 実験手法 | X-RAY DIFFRACTION (1.8 Å) | | 主引用文献 | Structural Basis of the Sphingomyelin Phosphodiesterase Activity in Neutral Sphingomyelinase from Bacillus cereus.
J.Biol.Chem., 281, 2006
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2DDR
 | | Crystal structure of sphingomyelinase from Bacillus cereus with calcium ion | | 分子名称: | CALCIUM ION, Sphingomyelin phosphodiesterase | | 著者 | Ago, H, Oda, M, Takahashi, M, Tsuge, H, Ochi, S, Katunuma, N, Miyano, M, Sakurai, J, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | 登録日 | 2006-02-02 | | 公開日 | 2006-05-02 | | 最終更新日 | 2011-07-13 | | 実験手法 | X-RAY DIFFRACTION (1.4 Å) | | 主引用文献 | Structural Basis of the Sphingomyelin Phosphodiesterase Activity in Neutral Sphingomyelinase from Bacillus cereus.
J.Biol.Chem., 281, 2006
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2AHJ
 | | NITRILE HYDRATASE COMPLEXED WITH NITRIC OXIDE | | 分子名称: | 1,4-DIETHYLENE DIOXIDE, FE (III) ION, NITRIC OXIDE, ... | | 著者 | Nagashima, S, Nakasako, M, Dohmae, N, Tsujimura, M, Takio, K, Odaka, M, Yohda, M, Kamiya, N, Endo, I. | | 登録日 | 1997-12-24 | | 公開日 | 1999-01-27 | | 最終更新日 | 2022-12-21 | | 実験手法 | X-RAY DIFFRACTION (1.7 Å) | | 主引用文献 | Novel non-heme iron center of nitrile hydratase with a claw setting of oxygen atoms.
Nat.Struct.Biol., 5, 1998
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3ZTS
 | | Hexagonal form P6122 of the Aquifex aeolicus nucleoside diphosphate kinase (FINAL STAGE OF RADIATION DAMAGE) | | 分子名称: | NUCLEOSIDE DIPHOSPHATE KINASE | | 著者 | Boissier, F, Georgescauld, F, Moynie, L, Dupuy, J.-W, Sarger, C, Podar, M, Lascu, I, Giraud, M.-F, Dautant, A. | | 登録日 | 2011-07-12 | | 公開日 | 2012-03-14 | | 最終更新日 | 2024-10-16 | | 実験手法 | X-RAY DIFFRACTION (2.3 Å) | | 主引用文献 | An Inter-Subunit Disulphide Bridge Stabilizes the Tetrameric Nucleoside Diphosphate Kinase of Aquifex Aeolicus
Proteins, 80, 2012
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3ZTR
 | | Hexagonal form P6122 of the Aquifex aeolicus nucleoside diphosphate kinase (FIRST STAGE OF RADIATION DAMAGE) | | 分子名称: | NUCLEOSIDE DIPHOSPHATE KINASE | | 著者 | Boissier, F, Georgescauld, F, Moynie, L, Dupuy, J.-W, Sarger, C, Podar, M, Lascu, I, Giraud, M.-F, Dautant, A. | | 登録日 | 2011-07-12 | | 公開日 | 2012-03-14 | | 最終更新日 | 2024-10-16 | | 実験手法 | X-RAY DIFFRACTION (2.3 Å) | | 主引用文献 | An Inter-Subunit Disulphide Bridge Stabilizes the Tetrameric Nucleoside Diphosphate Kinase of Aquifex Aeolicus
Proteins, 80, 2012
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3ZTP
 | | Orthorhombic crystal form P21212 of the Aquifex aeolicus nucleoside diphosphate kinase | | 分子名称: | GLYCEROL, NUCLEOSIDE DIPHOSPHATE KINASE, SULFATE ION | | 著者 | Boissier, F, Georgescauld, F, Moynie, L, Dupuy, J.-W, Sarger, C, Podar, M, Lascu, I, Giraud, M.-F, Dautant, A. | | 登録日 | 2011-07-12 | | 公開日 | 2012-03-14 | | 最終更新日 | 2024-10-16 | | 実験手法 | X-RAY DIFFRACTION (1.37 Å) | | 主引用文献 | An Intersubunit Disulfide Bridge Stabilizes the Tetrameric Nucleoside Diphosphate Kinase of Aquifex Aeolicus.
Proteins, 80, 2012
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