1GOH
| |
1GOF
| NOVEL THIOETHER BOND REVEALED BY A 1.7 ANGSTROMS CRYSTAL STRUCTURE OF GALACTOSE OXIDASE | Descriptor: | ACETIC ACID, COPPER (II) ION, GALACTOSE OXIDASE, ... | Authors: | Ito, N, Phillips, S.E.V, Knowles, P.F. | Deposit date: | 1993-09-30 | Release date: | 1994-01-31 | Last modified: | 2023-07-26 | Method: | X-RAY DIFFRACTION (1.7 Å) | Cite: | Novel thioether bond revealed by a 1.7 A crystal structure of galactose oxidase. Nature, 350, 1991
|
|
1GOG
| |
1HBH
| |
1V33
| Crystal structure of DNA primase from Pyrococcus horikoshii | Descriptor: | DNA primase small subunit, PHOSPHATE ION, ZINC ION | Authors: | Ito, N, Nureki, O, Shirouzu, M, Yokoyama, S, Hanaoka, F, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2003-10-25 | Release date: | 2004-03-23 | Last modified: | 2023-12-27 | Method: | X-RAY DIFFRACTION (1.8 Å) | Cite: | Crystal structure of the Pyrococcus horikoshii DNA primase-UTP complex: implications for the mechanism of primer synthesis. Genes Cells, 8, 2003
|
|
1V34
| Crystal structure of Pyrococcus horikoshii DNA primase-UTP complex | Descriptor: | DNA primase small subunit, URIDINE 5'-TRIPHOSPHATE, ZINC ION | Authors: | Ito, N, Nureki, O, Shirouzu, M, Yokoyama, S, Hanaoka, F, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2003-10-25 | Release date: | 2004-03-23 | Last modified: | 2023-12-27 | Method: | X-RAY DIFFRACTION (2.7 Å) | Cite: | Crystal structure of the Pyrococcus horikoshii DNA primase-UTP complex: implications for the mechanism of primer synthesis. Genes Cells, 8, 2003
|
|
2DLA
| |
2Z8H
| Structure of mouse Bach1 BTB domain | Descriptor: | Transcription regulator protein BACH1 | Authors: | Ito, N, Murayama, K. | Deposit date: | 2007-09-05 | Release date: | 2008-09-09 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (2.5 Å) | Cite: | Structure of mouse Bach1 BTB domain To be Published
|
|
5XQW
| Catalytic antibody 7B9 | Descriptor: | Fab fragment of catalytic antibody 7B9, heavy chain, light chain, ... | Authors: | Ito, N, Fujii, I, Tsumuraya, T. | Deposit date: | 2017-06-07 | Release date: | 2018-04-18 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2.2 Å) | Cite: | Structural basis of the broad substrate tolerance of the antibody 7B9-catalyzed hydrolysis of p-nitrobenzyl esters. Bioorg. Med. Chem., 26, 2018
|
|
7D4C
| Structure of L-lysine oxidase precursor | Descriptor: | FLAVIN-ADENINE DINUCLEOTIDE, L-Lysine alpha-oxidase, PHOSPHATE ION | Authors: | Ito, N, Kitagawa, M, Matsumoto, Y, Inagaki, K, Imada, K. | Deposit date: | 2020-09-23 | Release date: | 2021-02-10 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (1.97 Å) | Cite: | Structural basis of enzyme activity regulation by the propeptide of l-lysine alpha-oxidase precursor from Trichoderma viride . J Struct Biol X, 5, 2021
|
|
7E0C
| Structure of L-glutamate oxidase R305E mutant | Descriptor: | FLAVIN-ADENINE DINUCLEOTIDE, L-glutamate oxidase | Authors: | Ito, N, Matsuo, S, Inagaki, K, Imada, K. | Deposit date: | 2021-01-27 | Release date: | 2021-04-07 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.65 Å) | Cite: | A new l-arginine oxidase engineered from l-glutamate oxidase. Protein Sci., 30, 2021
|
|
7E0D
| Structure of L-glutamate oxidase R305E mutant in complex with L-arginine | Descriptor: | ARGININE, FLAVIN-ADENINE DINUCLEOTIDE, L-glutamate oxidase | Authors: | Ito, N, Matsuo, S, Inagaki, K, Imada, K. | Deposit date: | 2021-01-27 | Release date: | 2021-04-07 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.7 Å) | Cite: | A new l-arginine oxidase engineered from l-glutamate oxidase. Protein Sci., 30, 2021
|
|
4WUA
| Crystal structure of human SRPK1 complexed to an inhibitor SRPIN340 | Descriptor: | CITRIC ACID, N-[2-(1-piperidinyl)-5-(trifluoromethyl)phenyl]-4-pyridinecarboxamide, SRSF protein kinase 1, ... | Authors: | Hoshina, M, Ikura, T, Hosoya, T, Hagiwara, M, Ito, N. | Deposit date: | 2014-10-31 | Release date: | 2015-09-16 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Identification of a Dual Inhibitor of SRPK1 and CK2 That Attenuates Pathological Angiogenesis of Macular Degeneration in Mice Mol.Pharmacol., 88, 2015
|
|
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
|
|
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
|
|
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
|
|
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
|
|
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
|
|
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
|
|
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
|
|
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
|
|
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
|
|
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
|
|
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
|
|
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
|
|