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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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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5ZNO
| Crystal structure of PET-degrading cutinase Cut190 S176A/S226P/R228S/ mutant in Ca(2+)-bound state | Descriptor: | Alpha/beta hydrolase family protein, CALCIUM ION, GLYCEROL | Authors: | Numoto, N, Inaba, S, Yamagami, Y, Kamiya, N, Bekker, G.J, Ishii, K, Uchiyama, S, Kawai, F, Ito, N, Oda, M. | Deposit date: | 2018-04-10 | Release date: | 2018-09-12 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (1.60264349 Å) | Cite: | 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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5ZRS
| Crystal structure of PET-degrading cutinase Cut190 S176A/S226P/R228S mutant in monoethyl adipate bound state | Descriptor: | 6-ethoxy-6-oxohexanoic acid, Alpha/beta hydrolase family protein, CALCIUM ION, ... | Authors: | Numoto, N, Kamiya, N, Bekker, G.J, Yamagami, Y, Inaba, S, Ishii, K, Uchiyama, S, Kawai, F, Ito, N, Oda, M. | Deposit date: | 2018-04-25 | Release date: | 2018-09-12 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (1.4 Å) | Cite: | 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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5ZRR
| Crystal structure of PET-degrading cutinase Cut190 S176A/S226P/R228S mutant in monoethyl succinate bound state | Descriptor: | 4-ethoxy-4-oxobutanoic acid, Alpha/beta hydrolase family protein, GLYCEROL, ... | Authors: | Numoto, N, Kamiya, N, Bekker, G.J, Yamagami, Y, Inaba, S, Ishii, K, Uchiyama, S, Kawai, F, Ito, N, Oda, M. | Deposit date: | 2018-04-25 | Release date: | 2018-09-12 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (1.34 Å) | Cite: | 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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5ZRQ
| Crystal structure of PET-degrading cutinase Cut190 S176A/S226P/R228S mutant in Zn(2+)-bound state | Descriptor: | Alpha/beta hydrolase family protein, CALCIUM ION, GLYCEROL, ... | Authors: | Numoto, N, Kamiya, N, Bekker, G.J, Yamagami, Y, Inaba, S, Ishii, K, Uchiyama, S, Kawai, F, Ito, N, Oda, M. | Deposit date: | 2018-04-25 | Release date: | 2018-09-12 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (1.12 Å) | Cite: | 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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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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6IF6
| Structure of the periplasmic domain of SflA | Descriptor: | GLYCEROL, PHOSPHATE ION, Protein SflA | Authors: | Nishikawa, S, Sakuma, M, Kojima, S, Homma, M, Imada, K. | Deposit date: | 2018-09-18 | Release date: | 2019-05-01 | Last modified: | 2024-03-27 | Method: | X-RAY DIFFRACTION (1.9 Å) | Cite: | Structure of the periplasmic domain of SflA involved in spatial regulation of the flagellar biogenesis of Vibrio reveals a TPR/SLR-like fold. J.Biochem., 166, 2019
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3VT4
| Crystal structures of rat VDR-LBD with R270L mutation | Descriptor: | (1R,2Z,3R,5E,7E)-17-{(1S)-1-[(2-ethyl-2-hydroxybutyl)sulfanyl]ethyl}-2-(2-hydroxyethylidene)-9,10-secoestra-5,7,16-triene-1,3-diol, COACTIVATOR PEPTIDE DRIP, Vitamin D3 receptor | Authors: | Nakabayashi, M, Shimizu, M, Ikura, T, Ito, N. | Deposit date: | 2012-05-19 | Release date: | 2013-05-22 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.9 Å) | Cite: | Crystal structures of hereditary vitamin D-resistant rickets-associated vitamin D receptor mutants R270L and W282R bound to 1,25-dihydroxyvitamin D3 and synthetic ligands. J.Med.Chem., 56, 2013
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3VT7
| Crystal structures of rat VDR-LBD with W282R mutation | Descriptor: | 5-{2-[1-(5-HYDROXY-1,5-DIMETHYL-HEXYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-4-METHYLENE-CYCLOHEXANE-1,3-DIOL, COACTIVATOR PEPTIDE DRIP, Vitamin D3 receptor | Authors: | Nakabayashi, M, Shimizu, M, Ikura, T, Ito, N. | Deposit date: | 2012-05-19 | Release date: | 2013-05-22 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.65 Å) | Cite: | Crystal structures of hereditary vitamin D-resistant rickets-associated vitamin D receptor mutants R270L and W282R bound to 1,25-dihydroxyvitamin D3 and synthetic ligands. J.Med.Chem., 56, 2013
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3VT5
| Crystal structures of rat VDR-LBD with R270L mutation | Descriptor: | (1R,2E,3R,5Z,7E)-17-{(1S)-1-[(2-ethyl-2-hydroxybutyl)sulfanyl]ethyl}-2-(2-hydroxyethylidene)-9,10-secoestra-5,7,16-triene-1,3-diol, COACTIVATOR PEPTIDE DRIP, Vitamin D3 receptor | Authors: | Nakabayashi, M, Shimizu, M, Ikura, T, Ito, N. | Deposit date: | 2012-05-19 | Release date: | 2013-05-22 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.11 Å) | Cite: | Crystal structures of hereditary vitamin D-resistant rickets-associated vitamin D receptor mutants R270L and W282R bound to 1,25-dihydroxyvitamin D3 and synthetic ligands. J.Med.Chem., 56, 2013
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3VT6
| Crystal structure of rat VDR-LBD with 2-Substituted-16-ene-22-thia-1alpha,25-dihydroxy-26,27-dimethyl-19-norvitamin D3 | Descriptor: | (1R,2Z,3R,5E,7E)-17-{(1S)-1-[(2-ethyl-2-hydroxybutyl)sulfanyl]ethyl}-2-(2-hydroxyethylidene)-9,10-secoestra-5,7,16-triene-1,3-diol, COACTIVATOR PEPTIDE DRIP, Vitamin D3 receptor | Authors: | Nakabayashi, M, Shimizu, M, Ikura, T, Ito, N. | Deposit date: | 2012-05-19 | Release date: | 2013-05-22 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.3 Å) | Cite: | Crystal structures of hereditary vitamin D-resistant rickets-associated vitamin D receptor mutants R270L and W282R bound to 1,25-dihydroxyvitamin D3 and synthetic ligands. J.Med.Chem., 56, 2013
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3VT3
| Crystal structures of rat VDR-LBD with R270L mutation | Descriptor: | 1,2-ETHANEDIOL, 5-{2-[1-(5-HYDROXY-1,5-DIMETHYL-HEXYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-4-METHYLENE-CYCLOHEXANE-1,3-DIOL, COACTIVATOR PEPTIDE DRIP, ... | Authors: | Nakabayashi, M, Shimizu, M, Ikura, T, Ito, N. | Deposit date: | 2012-05-19 | Release date: | 2013-05-22 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.7 Å) | Cite: | Crystal structures of hereditary vitamin D-resistant rickets-associated vitamin D receptor mutants R270L and W282R bound to 1,25-dihydroxyvitamin D3 and synthetic ligands. J.Med.Chem., 56, 2013
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3VT9
| Crystal structures of rat VDR-LBD with W282R mutation | Descriptor: | (1R,2Z,3R,5E,7E,9beta,17beta)-2-(2-hydroxyethylidene)-17-[(2R)-6-hydroxy-6-methylheptan-2-yl]-9-(prop-2-en-1-yl)-9,10-secoestra-5,7-diene-1,3-diol, COACTIVATOR PEPTIDE DRIP, Vitamin D3 receptor | Authors: | Nakabayashi, M, Shimizu, M, Ikura, T, Ito, N. | Deposit date: | 2012-05-19 | Release date: | 2013-05-22 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.35 Å) | Cite: | Crystal structures of hereditary vitamin D-resistant rickets-associated vitamin D receptor mutants R270L and W282R bound to 1,25-dihydroxyvitamin D3 and synthetic ligands. J.Med.Chem., 56, 2013
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3VT8
| Crystal structures of rat VDR-LBD with W282R mutation | Descriptor: | (1R,3R,7E,9beta,17beta)-9-butyl-17-[(2R)-6-hydroxy-6-methylheptan-2-yl]-9,10-secoestra-5,7-diene-1,3-diol, COACTIVATOR PEPTIDE DRIP, Vitamin D3 receptor | Authors: | Nakabayashi, M, Shimizu, M, Ikura, T, Ito, N. | Deposit date: | 2012-05-19 | Release date: | 2013-05-22 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.1 Å) | Cite: | Crystal structures of hereditary vitamin D-resistant rickets-associated vitamin D receptor mutants R270L and W282R bound to 1,25-dihydroxyvitamin D3 and synthetic ligands. J.Med.Chem., 56, 2013
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3ATG
| endo-1,3-beta-glucanase from Cellulosimicrobium cellulans | Descriptor: | CALCIUM ION, GLUCANASE, GLYCEROL, ... | Authors: | Tanabe, Y, Pang, Z, Oda, M, Mikami, B. | Deposit date: | 2011-01-04 | Release date: | 2012-01-18 | Last modified: | 2024-03-13 | Method: | X-RAY DIFFRACTION (1.66 Å) | Cite: | 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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