1VAY
 
 | | Crystal Structure of Uricase from Arthrobacter globiformis with inhibitor 8-azaxanthine | | Descriptor: | 8-AZAXANTHINE, Uric acid oxidase | | Authors: | Hossain, M.T, Suzuki, K, Yamamoto, T, Imamura, S, Sekiguchi, T, Takenaka, A. | | Deposit date: | 2004-02-19 | | Release date: | 2005-06-28 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2.24 Å) | | Cite: | Crystal Structure of Uricase from Arthrobacter Globiformis Complexed with an inhibitor 8-Azaxanthine
To be Published
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1VAX
 | | Crystal Structure of Uricase from Arthrobacter globiformis | | Descriptor: | Uric acid oxidase | | Authors: | Hossain, M.T, Suzuki, K, Yamamoto, T, Imamura, S, Sekiguchi, T, Takenaka, A. | | Deposit date: | 2004-02-19 | | Release date: | 2005-06-28 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (1.99 Å) | | Cite: | Crystal Structure of Uricase from Arthrobacter globiformis
To be Published
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1V5G
 | | Crystal Structure of the Reaction Intermediate between Pyruvate oxidase containing FAD and TPP, and Substrate Pyruvate | | Descriptor: | 2-ACETYL-THIAMINE DIPHOSPHATE, FLAVIN-ADENINE DINUCLEOTIDE, MAGNESIUM ION, ... | | Authors: | Hossain, M.T, Suzuki, K, Yamamoto, T, Imamura, S, Sekiguchi, T, Takenaka, A. | | Deposit date: | 2003-11-22 | | Release date: | 2005-06-28 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.96 Å) | | Cite: | The structures of pyruvate oxidase from Aerococcus viridans with cofactors and with a reaction intermediate reveal the flexibility of the active-site tunnel for catalysis.
Acta Crystallogr.,Sect.F, 63, 2007
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1V5F
 | | Crystal Structure of Pyruvate oxidase complexed with FAD and TPP, from Aerococcus viridans | | Descriptor: | FLAVIN-ADENINE DINUCLEOTIDE, MAGNESIUM ION, Pyruvate oxidase, ... | | Authors: | Hossain, M.T, Suzuki, K, Yamamoto, T, Imamura, S, Sekiguchi, T, Takenaka, A. | | Deposit date: | 2003-11-22 | | Release date: | 2005-06-28 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | The structures of pyruvate oxidase from Aerococcus viridans with cofactors and with a reaction intermediate reveal the flexibility of the active-site tunnel for catalysis.
Acta Crystallogr.,Sect.F, 63, 2007
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1V5E
 | | Crystal Structure of Pyruvate oxidase containing FAD, from Aerococcus viridans | | Descriptor: | FLAVIN-ADENINE DINUCLEOTIDE, Pyruvate oxidase, SULFATE ION | | Authors: | Hossain, M.T, Suzuki, K, Yamamoto, T, Imamura, S, Sekiguchi, T, Takenaka, A. | | Deposit date: | 2003-11-22 | | Release date: | 2005-06-28 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (1.6 Å) | | Cite: | Crystal Structure of Pyruvate oxidase containing FAD, from Aerococcus viridans
To be Published
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2E2G
 | | Crystal structure of archaeal peroxiredoxin, thioredoxin peroxidase from Aeropyrum pernix K1 (pre-oxidation form) | | Descriptor: | Probable peroxiredoxin | | Authors: | Nakamura, T, Yamamoto, T, Abe, M, Matsumura, H, Hagihara, Y, Goto, T, Yamaguchi, T, Inoue, T. | | Deposit date: | 2006-11-13 | | Release date: | 2007-11-20 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | Oxidation of archaeal peroxiredoxin involves a hypervalent sulfur intermediate
Proc.Natl.Acad.Sci.Usa, 105, 2008
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2E2M
 | | Crystal structure of archaeal peroxiredoxin, thioredoxin peroxidase from Aeropyrum pernix K1 (sulfinic acid form) | | Descriptor: | Probable peroxiredoxin | | Authors: | Nakamura, T, Yamamoto, T, Abe, M, Matsumura, H, Hagihara, Y, Goto, T, Yamaguchi, T, Inoue, T. | | Deposit date: | 2006-11-14 | | Release date: | 2007-11-20 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2.6 Å) | | Cite: | Oxidation of archaeal peroxiredoxin involves a hypervalent sulfur intermediate
Proc.Natl.Acad.Sci.Usa, 105, 2008
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1I5P
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2EB2
 | | Crystal structure of mutated EGFR kinase domain (G719S) | | Descriptor: | Epidermal growth factor receptor | | Authors: | Yoshikawa, S, Kukimoto-Niino, M, Chen, L, Liu, Z.J, Wang, B.C, Shirouzu, M, Senba, K, Yamamoto, T, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2007-02-06 | | Release date: | 2008-02-12 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Structural basis for the altered drug sensitivities of non-small cell lung cancer-associated mutants of human epidermal growth factor receptor
Oncogene, 2012
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2EB3
 | | Crystal structure of mutated EGFR kinase domain (L858R) in complex with AMPPNP | | Descriptor: | Epidermal growth factor receptor, PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER | | Authors: | Yoshikawa, S, Kukimoto-Niino, M, Shirouzu, M, Senba, K, Yamamoto, T, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2007-02-06 | | Release date: | 2008-02-12 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2.84 Å) | | Cite: | Structural basis for the altered drug sensitivities of non-small cell lung cancer-associated mutants of human epidermal growth factor receptor
Oncogene, 2012
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7YH7
 | | SARS-CoV-2 spike in complex with neutralizing antibody NIV-8 (state 2) | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, NIV-8 Fab heavy chain, ... | | Authors: | Moriyama, S, Anraku, Y, Muranishi, S, Adachi, Y, Kuroda, D, Higuchi, Y, Kotaki, R, Tonouchi, K, Yumoto, K, Suzuki, T, Kita, S, Someya, T, Fukuhara, H, Kuroda, Y, Yamamoto, T, Onodera, T, Fukushi, S, Maeda, K, Nakamura-Uchiyama, F, Hashiguchi, T, Hoshino, A, Maenaka, K, Takahashi, Y. | | Deposit date: | 2022-07-13 | | Release date: | 2023-07-19 | | Last modified: | 2024-05-15 | | Method: | ELECTRON MICROSCOPY (3.3 Å) | | Cite: | Structural delineation and computational design of SARS-CoV-2-neutralizing antibodies against Omicron subvariants.
Nat Commun, 14, 2023
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7YH6
 | | Structure of SARS-CoV-2 spike RBD in complex with neutralizing antibody NIV-8 | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, NIV-8 Fab heavy chain, NIV-8 Fab light chain, ... | | Authors: | Moriyama, S, Anraku, Y, Muranishi, S, Adachi, Y, Kuroda, D, Higuchi, Y, Kotaki, R, Tonouchi, K, Yumoto, K, Suzuki, T, Kita, S, Someya, T, Fukuhara, H, Kuroda, Y, Yamamoto, T, Onodera, T, Fukushi, S, Maeda, K, Nakamura-Uchiyama, F, Hashiguchi, T, Hoshino, A, Maenaka, K, Takahashi, Y. | | Deposit date: | 2022-07-12 | | Release date: | 2023-07-19 | | Last modified: | 2024-05-15 | | Method: | ELECTRON MICROSCOPY (3.4 Å) | | Cite: | Structural delineation and computational design of SARS-CoV-2-neutralizing antibodies against Omicron subvariants.
Nat Commun, 14, 2023
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6JT4
 | | Crystal Structure of BACE1 in complex with N-{3-[(4S,6S)-2-amino-4-methyl-6-(trifluoromethyl)-5,6-dihydro-4H-1,3-thiazin-4-yl]-4-fluorophenyl}-5-(fluoromethoxy)pyrazine-2-carboxamide | | Descriptor: | Beta-secretase 1, GLYCEROL, IODIDE ION, ... | | Authors: | Anan, K, Iso, Y, Oguma, T, Nakahara, K, Suzuki, S, Yamamoto, T, Matsuoka, E, Ito, H, Sakaguchi, G, Ando, S, Morimoto, K, Kanegawa, N, Kido, Y, Kawachi, T, Fukushima, T, Teisman, A, Urmaliya, V, Dhuyvetter, D, Borghys, H, Austin, N, Bergh, A.V.D, Verboven, P, Bischoff, F, Gijsen, H.J.M, Yamano, Y, Kusakabe, K.I. | | Deposit date: | 2019-04-08 | | Release date: | 2020-01-15 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Trifluoromethyl Dihydrothiazine-Based beta-Secretase (BACE1) Inhibitors with Robust Central beta-Amyloid Reduction and Minimal Covalent Binding Burden.
Chemmedchem, 14, 2019
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2D5R
 | | Crystal Structure of a Tob-hCaf1 Complex | | Descriptor: | CCR4-NOT transcription complex subunit 7, Tob1 protein | | Authors: | Horiuchi, M, Suzuki, N.N, Muroya, N, Takahasi, K, Nishida, M, Yoshida, Y, Ikematsu, N, Nakamura, T, Kawamura-Tsuzuku, J, Yamamoto, T, Inagaki, F. | | Deposit date: | 2005-11-04 | | Release date: | 2006-12-12 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Structural basis for the antiproliferative activity of the Tob-hCaf1 complex.
J.Biol.Chem., 284, 2009
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2DJI
 | | Crystal Structure of Pyruvate Oxidase from Aerococcus viridans containing FAD | | Descriptor: | FLAVIN-ADENINE DINUCLEOTIDE, Pyruvate oxidase, SULFATE ION | | Authors: | Juan, E.C.M, Hossain, M.T, Suzuki, K, Yamamoto, T, Imamura, S, Sekiguchi, T, Takenaka, A. | | Deposit date: | 2006-04-03 | | Release date: | 2007-05-29 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (1.6 Å) | | Cite: | The structures of pyruvate oxidase from Aerococcus viridans with cofactors and with a reaction intermediate reveal the flexibility of the active-site tunnel for catalysis.
Acta Crystallogr.,Sect.F, 63, 2007
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5YGX
 | | Structure of BACE1 in complex with N-(3-((4R,5R,6S)-2-amino-6-(1,1-difluoroethyl)-5-fluoro-4-methyl-5,6-dihydro-4H-1,3-oxazin-4-yl)-4-fluorophenyl)-5-(fluoromethoxy)pyrazine-2-carboxamide | | Descriptor: | Beta-secretase 1, DIMETHYL SULFOXIDE, GLYCEROL, ... | | Authors: | Nakahara, K, Fuchino, K, Komano, K, Asada, N, Tadano, G, Hasegawa, T, Yamamoto, T, Sako, Y, Ogawa, M, Unemura, C, Hosono, M, Sakaguchi, G, Ando, S, Ohnishi, S, Kido, Y, Fukushima, T, Dhuyvetter, D, Borghys, H, Gijsen, H, Yamano, Y, Iso, Y, Kusakabe, K. | | Deposit date: | 2017-09-27 | | Release date: | 2018-08-08 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Discovery of Potent and Centrally Active 6-Substituted 5-Fluoro-1,3-dihydro-oxazine beta-Secretase (BACE1) Inhibitors via Active Conformation Stabilization
J. Med. Chem., 61, 2018
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2DV6
 | | Crystal structure of nitrite reductase from Hyphomicrobium denitrificans | | Descriptor: | COPPER (II) ION, Nitrite reductase, POTASSIUM ION | | Authors: | Nojiri, M, Xie, Y, Yamamoto, T, Inoue, T, Suzuki, S, Kai, Y. | | Deposit date: | 2006-07-28 | | Release date: | 2007-02-20 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Structure and function of a hexameric copper-containing nitrite reductase.
Proc.Natl.Acad.Sci.USA, 104, 2007
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5CI9
 | | Crystal structure of human Tob in complex with inhibitor fragment 6 | | Descriptor: | 1-(propan-2-yl)-1H-benzimidazole-5-carboxylic acid, Protein Tob1, SODIUM ION | | Authors: | Bai, Y, Tashiro, S, Nagatoishi, S, Suzuki, T, Tsumoto, K, Bartlam, M, Yamamoto, T. | | Deposit date: | 2015-07-11 | | Release date: | 2015-11-18 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Structural basis for inhibition of the Tob-CNOT7 interaction by a fragment screening approach
Protein Cell, 6, 2015
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5CI8
 | | Crystal structure of human Tob in complex with inhibitor fragment 1 | | Descriptor: | Protein Tob1, pyrrolo[1,2-a]quinoxalin-4(5H)-one | | Authors: | Bai, Y, Tashiro, S, Nagatoishi, S, Suzuki, T, Tsumoto, K, Bartlam, M, Yamamoto, T. | | Deposit date: | 2015-07-11 | | Release date: | 2015-11-18 | | Last modified: | 2015-12-09 | | Method: | X-RAY DIFFRACTION (2.328 Å) | | Cite: | Structural basis for inhibition of the Tob-CNOT7 interaction by a fragment screening approach
Protein Cell, 6, 2015
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2ZCT
 | | Oxidation of archaeal peroxiredoxin involves a hypervalent sulfur intermediate | | Descriptor: | Probable peroxiredoxin | | Authors: | Nakamura, T, Hagihara, Y, Abe, M, Inoue, T, Yamamoto, T, Matsumura, H. | | Deposit date: | 2007-11-12 | | Release date: | 2008-05-27 | | Last modified: | 2021-11-10 | | Method: | X-RAY DIFFRACTION (1.7 Å) | | Cite: | Oxidation of archaeal peroxiredoxin involves a hypervalent sulfur intermediate
Proc.Natl.Acad.Sci.Usa, 105, 2008
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3WIR
 | | Crystal structure of kojibiose phosphorylase complexed with glucose | | Descriptor: | GLYCEROL, Kojibiose phosphorylase, PHOSPHATE ION, ... | | Authors: | Okada, S, Yamamoto, T, Watanabe, H, Nishimoto, T, Chaen, H, Fukuda, S, Wakagi, T, Fushinobu, S. | | Deposit date: | 2013-09-24 | | Release date: | 2014-02-05 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.05 Å) | | Cite: | Structural and mutational analysis of substrate recognition in kojibiose phosphorylase
Febs J., 281, 2014
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3WIQ
 | | Crystal structure of kojibiose phosphorylase complexed with kojibiose | | Descriptor: | Kojibiose phosphorylase, SULFATE ION, alpha-D-glucopyranose-(1-2)-beta-D-glucopyranose | | Authors: | Okada, S, Yamamoto, T, Watanabe, H, Nishimoto, T, Chaen, H, Fukuda, S, Wakagi, T, Fushinobu, S. | | Deposit date: | 2013-09-24 | | Release date: | 2014-02-05 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.8 Å) | | Cite: | Structural and mutational analysis of substrate recognition in kojibiose phosphorylase
Febs J., 281, 2014
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6JG0
 | | Crystal structure of the N-terminal domain single mutant (S92E) of the human mitochondrial calcium uniporter fused with T4 lysozyme | | Descriptor: | Endolysin,Calcium uniporter protein, SULFATE ION | | Authors: | Lee, Y, Park, J, Min, C.K, Kang, J.Y, Kim, T.G, Yamamoto, T, Kim, D.H, Eom, S.H. | | Deposit date: | 2019-02-13 | | Release date: | 2020-02-19 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Crystal structure of calcium channel domain
To Be Published
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6JT3
 | | Crystal Structure of BACE1 in complex with N-{3-[(4R,5R,6R)-2-amino-5-fluoro-4,6-dimethyl-5,6-dihydro-4H-1,3-thiazin-4-yl]-4-fluorophenyl}-5-(fluoromethoxy)pyrazine-2-carboxamide | | Descriptor: | Beta-secretase 1, DIMETHYL SULFOXIDE, GLYCEROL, ... | | Authors: | Tadano, G, Komano, K, Yoshida, S, Suzuki, S, Nakahara, K, Fuchino, K, Fujimoto, K, Matsuoka, E, Yamamoto, T, Asada, N, Ito, H, Sakaguchi, G, Kanegawa, N, Kido, Y, Ando, S, Fukushima, T, Teisman, A, Urmaliya, V, Dhuyvetter, D, Borghys, H, Bergh, A.V.D, Austin, N, Gijsen, H.J.M, Yamano, Y, Iso, Y, Kusakabe, K.I. | | Deposit date: | 2019-04-08 | | Release date: | 2019-10-30 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | Discovery of an Extremely Potent Thiazine-Based beta-Secretase Inhibitor with Reduced Cardiovascular and Liver Toxicity at a Low Projected Human Dose.
J.Med.Chem., 62, 2019
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5YGY
 | | Crystal Structure of BACE1 in complex with (S)-N-(3-(2-amino-6-(fluoromethyl)-4 -methyl-4H-1,3-oxazin-4-yl)-4-fluorophenyl)-5-cyanopicolinamide | | Descriptor: | Beta-secretase 1, GLYCEROL, IODIDE ION, ... | | Authors: | Fuchino, K, Mitsuoka, Y, Masui, M, Kurose, N, Yoshida, S, Komano, K, Yamamoto, T, Ogawa, M, Unemura, C, Hosono, M, Ito, H, Sakaguchi, G, Ando, S, Ohnishi, S, Kido, Y, Fukushima, T, Miyajima, H, Hiroyama, S, Koyabu, K, Dhuyvetter, D, Borghys, H, Gijsen, H, Yamano, Y, Iso, Y, Kusakabe, K. | | Deposit date: | 2017-09-27 | | Release date: | 2018-05-23 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Rational Design of Novel 1,3-Oxazine Based beta-Secretase (BACE1) Inhibitors: Incorporation of a Double Bond To Reduce P-gp Efflux Leading to Robust A beta Reduction in the Brain
J. Med. Chem., 61, 2018
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