1GOH
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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
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1GOG
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1HBH
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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
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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
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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
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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
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2DLA
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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
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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
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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
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7VQP
| Vitamin D receptor complexed with a lithocholic acid derivative | Descriptor: | 3-((R)-4-((3R,5R,8R,9S,10S,13R,14S,17R)-3-(2-hydroxy-2-methylpropyl)-10,13-dimethylhexadecahydro-1H-cyclopenta[a]phenanthren-17-yl)pentanamido)propanoic acid, Mediator of RNA polymerase II transcription subunit 1, Vitamin D3 receptor | Authors: | Kato, K, Numoto, N, Kagechika, H, Tanatani, A, Ito, N. | Deposit date: | 2021-10-20 | Release date: | 2022-03-09 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (1.94 Å) | Cite: | Lithocholic Acid Amides as Potent Vitamin D Receptor Agonists. Biomolecules, 12, 2022
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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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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
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5B1C
| Crystal structure of DEN4 ED3 mutant with L387I | Descriptor: | Envelope protein E, SULFATE ION | Authors: | Kulkarni, M.R, Numoto, N, Ito, N, Kuroda, Y. | Deposit date: | 2015-12-02 | Release date: | 2016-02-24 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.003 Å) | Cite: | Modeling and experimental assessment of a buried Leu-Ile mutation in dengue envelope domain III Biochem.Biophys.Res.Commun., 471, 2016
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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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5B1R
| Crystal structure of mouse CD72a CTLD | Descriptor: | ACETATE ION, B-cell differentiation antigen CD72, GLYCEROL | Authors: | Shinagawa, K, Numoto, N, Tsubata, T, Ito, N. | Deposit date: | 2015-12-15 | Release date: | 2016-10-19 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.2 Å) | Cite: | CD72 negatively regulates B lymphocyte responses to the lupus-related endogenous toll-like receptor 7 ligand Sm/RNP J.Exp.Med., 213, 2016
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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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7VLC
| Oxy-deoxy intermediate of V2 hemoglobin at 78% oxygen saturation | Descriptor: | CALCIUM ION, Extracellular A1 globin, Extracellular A2 globin, ... | Authors: | Numoto, N, Onoda, S, Kawano, Y, Okumura, H, Baba, S, Fukumori, Y, Miki, K, Ito, N. | Deposit date: | 2021-10-02 | Release date: | 2022-05-18 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.2 Å) | Cite: | Structures of oxygen dissociation intermediates of 400 kDa V2 hemoglobin provide coarse snapshots of the protein allostery. Biophys Physicobio., 19, 2022
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7VLD
| Oxy-deoxy intermediate of V2 hemoglobin at 69% oxygen saturation | Descriptor: | CALCIUM ION, Extracellular A1 globin, Extracellular A2 globin, ... | Authors: | Numoto, N, Onoda, S, Kawano, Y, Okumura, H, Baba, S, Fukumori, Y, Miki, K, Ito, N. | Deposit date: | 2021-10-02 | Release date: | 2022-05-18 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.1 Å) | Cite: | Structures of oxygen dissociation intermediates of 400 kDa V2 hemoglobin provide coarse snapshots of the protein allostery. Biophys Physicobio., 19, 2022
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7VLF
| Oxy-deoxy intermediate of V2 hemoglobin at 26% oxygen saturation | Descriptor: | CALCIUM ION, Extracellular A1 globin, Extracellular A2 globin, ... | Authors: | Numoto, N, Onoda, S, Kawano, Y, Okumura, H, Baba, S, Fukumori, Y, Miki, K, Ito, N. | Deposit date: | 2021-10-02 | Release date: | 2022-05-18 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.4 Å) | Cite: | Structures of oxygen dissociation intermediates of 400 kDa V2 hemoglobin provide coarse snapshots of the protein allostery. Biophys Physicobio., 19, 2022
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7VLE
| Oxy-deoxy intermediate of V2 hemoglobin at 55% oxygen saturation | Descriptor: | Extracellular A1 globin, Extracellular A2 globin, Extracellular B1 globin, ... | Authors: | Numoto, N, Onoda, S, Kawano, Y, Okumura, H, Baba, S, Fukumori, Y, Miki, K, Ito, N. | Deposit date: | 2021-10-02 | Release date: | 2022-05-18 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.3 Å) | Cite: | Structures of oxygen dissociation intermediates of 400 kDa V2 hemoglobin provide coarse snapshots of the protein allostery. Biophys Physicobio., 19, 2022
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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
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