3B0V
 
 | | tRNA-dihydrouridine synthase from Thermus thermophilus in complex with tRNA | | 分子名称: | FLAVIN MONONUCLEOTIDE, tRNA, tRNA-dihydrouridine synthase | | 著者 | Yu, F, Tanaka, Y, Yamashita, K, Nakamura, A, Yao, M, Tanaka, I. | | 登録日 | 2011-06-14 | | 公開日 | 2011-12-14 | | 最終更新日 | 2017-10-11 | | 実験手法 | X-RAY DIFFRACTION (3.51 Å) | | 主引用文献 | Molecular basis of dihydrouridine formation on tRNA
Proc.Natl.Acad.Sci.USA, 108, 2011
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3B0P
 | | tRNA-dihydrouridine synthase from Thermus thermophilus | | 分子名称: | FLAVIN MONONUCLEOTIDE, tRNA-dihydrouridine synthase | | 著者 | Yu, F, Tanaka, Y, Yamashita, K, Nakamura, A, Yao, M, Tanaka, I. | | 登録日 | 2011-06-12 | | 公開日 | 2011-12-14 | | 最終更新日 | 2024-03-13 | | 実験手法 | X-RAY DIFFRACTION (1.7 Å) | | 主引用文献 | Molecular basis of dihydrouridine formation on tRNA
Proc.Natl.Acad.Sci.USA, 108, 2011
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3AZV
 | | Crystal structure of the receptor binding domain | | 分子名称: | D/C mosaic neurotoxin, SULFATE ION | | 著者 | Nuemket, N, Tanaka, Y, Tsukamoto, K, Tsuji, T, Nakamura, K, Kozaki, S, Yao, M, Tanaka, I. | | 登録日 | 2011-06-02 | | 公開日 | 2011-12-28 | | 最終更新日 | 2017-10-11 | | 実験手法 | X-RAY DIFFRACTION (3.1 Å) | | 主引用文献 | Structural and mutational analyses of the receptor binding domain of botulinum D/C mosaic neurotoxin: insight into the ganglioside binding mechanism
Biochem.Biophys.Res.Commun., 411, 2011
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3AZW
 | | Crystal structure of the receptor binding domain | | 分子名称: | D/C mosaic neurotoxin, SULFATE ION | | 著者 | Nuemket, N, Tanaka, Y, Tsukamoto, K, Tsuji, T, Nakamura, K, Kozaki, S, Yao, M, Tanaka, I. | | 登録日 | 2011-06-02 | | 公開日 | 2011-12-28 | | 最終更新日 | 2024-03-13 | | 実験手法 | X-RAY DIFFRACTION (2.99 Å) | | 主引用文献 | Structural and mutational analyses of the receptor binding domain of botulinum D/C mosaic neurotoxin: insight into the ganglioside binding mechanism
Biochem.Biophys.Res.Commun., 411, 2011
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7F9F
 | | Thrombocorticin | | 分子名称: | MAGNESIUM ION, Thrombocorticin | | 著者 | Kageyama, H, Onodera, K, Sakai, R, Tanaka, Y, Freymann, D.M. | | 登録日 | 2021-07-04 | | 公開日 | 2022-07-06 | | 最終更新日 | 2023-11-29 | | 実験手法 | X-RAY DIFFRACTION (1.411 Å) | | 主引用文献 | A marine sponge-derived lectin reveals hidden pathway for thrombopoietin receptor activation.
Nat Commun, 13, 2022
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7F9J
 | | Thrombocorticin Q25K in complex with Ca2+ | | 分子名称: | CALCIUM ION, Thrombocorticin Q25K mutant | | 著者 | Kageyama, H, Onodera, K, Sakai, R, Tanaka, Y. | | 登録日 | 2021-07-04 | | 公開日 | 2022-07-06 | | 最終更新日 | 2023-11-29 | | 実験手法 | X-RAY DIFFRACTION (1.1 Å) | | 主引用文献 | A marine sponge-derived lectin reveals hidden pathway for thrombopoietin receptor activation.
Nat Commun, 13, 2022
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7F9G
 | | Thrombocorticin in complex with Ca2+ and fucose | | 分子名称: | CALCIUM ION, Thrombocorticin, alpha-L-fucopyranose | | 著者 | Kageyama, H, Onodera, K, Sakai, R, Tanaka, Y. | | 登録日 | 2021-07-04 | | 公開日 | 2022-07-06 | | 最終更新日 | 2023-11-29 | | 実験手法 | X-RAY DIFFRACTION (1.331 Å) | | 主引用文献 | A marine sponge-derived lectin reveals hidden pathway for thrombopoietin receptor activation.
Nat Commun, 13, 2022
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7F91
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7FBL
 | | Thrombocorticin in complex with Ca2+ and mannose | | 分子名称: | CALCIUM ION, Thrombocorticin, alpha-D-mannopyranose | | 著者 | Kageyama, H, Onodera, K, Sakai, R, Tanaka, Y. | | 登録日 | 2021-07-11 | | 公開日 | 2022-07-13 | | 最終更新日 | 2023-11-29 | | 実験手法 | X-RAY DIFFRACTION (1.419 Å) | | 主引用文献 | A marine sponge-derived lectin reveals hidden pathway for thrombopoietin receptor activation.
Nat Commun, 13, 2022
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5B5O
 | | Crystal structure of the catalytic domain of MMP-13 complexed with N-phenyl-4-((4H-1,2,4-triazol-3-ylsulfanyl)methyl)-1,3-thiazol-2-amine | | 分子名称: | 1,2-ETHANEDIOL, CALCIUM ION, Collagenase 3, ... | | 著者 | Oki, H, Tanaka, Y. | | 登録日 | 2016-05-13 | | 公開日 | 2017-01-18 | | 最終更新日 | 2023-11-08 | | 実験手法 | X-RAY DIFFRACTION (1.2 Å) | | 主引用文献 | Discovery of Novel, Highly Potent, and Selective Matrix Metalloproteinase (MMP)-13 Inhibitors with a 1,2,4-Triazol-3-yl Moiety as a Zinc Binding Group Using a Structure-Based Design Approach
J. Med. Chem., 60, 2017
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3VV6
 | | Crystal Structure of beta secetase in complex with 2-amino-3-methyl-6-((1S, 2R)-2-phenylcyclopropyl)pyrimidin-4(3H)-one | | 分子名称: | 2-amino-3-methyl-6-[(1S,2R)-2-phenylcyclopropyl]pyrimidin-4(3H)-one, Beta-secretase 1, GLYCEROL, ... | | 著者 | Yonezawa, S, Yamamoto, T, Yamakawa, H, Muto, C, Hosono, M, Hattori, K, Higashino, K, Sakagami, M, Togame, H, Tanaka, Y, Nakano, T, Takemoto, H, Arisawa, M, Shuto, S. | | 登録日 | 2012-07-17 | | 公開日 | 2012-10-24 | | 最終更新日 | 2017-11-22 | | 実験手法 | X-RAY DIFFRACTION (2.05 Å) | | 主引用文献 | Conformational restriction approach to beta-secretase (BACE1) inhibitors: effect of a cyclopropane ring to induce an alternative binding mode
J.Med.Chem., 55, 2012
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3VV8
 | | Crystal structure of beta secetase in complex with 2-amino-3-methyl-6-((1S,2R)-2-(3'-methylbiphenyl-4-yl)cyclopropyl)pyrimidin-4(3H)-one | | 分子名称: | 2-amino-3-methyl-6-[(1S,2R)-2-(3'-methylbiphenyl-4-yl)cyclopropyl]pyrimidin-4(3H)-one, Beta-secretase 1, GLYCEROL | | 著者 | Yonezawa, S, Yamamoto, T, Yamakawa, H, Muto, C, Hosono, M, Hattori, K, Higashino, K, Sakagami, M, Togame, H, Tanaka, Y, Nakano, T, Takemoto, H, Arisawa, M, Shuto, S. | | 登録日 | 2012-07-17 | | 公開日 | 2012-10-24 | | 最終更新日 | 2013-09-04 | | 実験手法 | X-RAY DIFFRACTION (2.5 Å) | | 主引用文献 | Conformational restriction approach to beta-secretase (BACE1) inhibitors: effect of a cyclopropane ring to induce an alternative binding mode.
J.Med.Chem., 55, 2012
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3VV7
 | | Crystal Structure of beta secetase in complex with 2-amino-6-((1S,2R)-2-(3'-methoxybiphenyl-3-yl)cyclopropyl)-3-methylpyrimidin-4(3H)-one | | 分子名称: | 2-amino-6-[(1S,2R)-2-(3'-methoxybiphenyl-3-yl)cyclopropyl]-3-methylpyrimidin-4(3H)-one, Beta-secretase 1, GLYCEROL, ... | | 著者 | Yonezawa, S, Yamamoto, T, Yamakawa, H, Muto, C, Hosono, M, Hattori, K, Higashino, K, Sakagami, M, Togame, H, Tanaka, Y, Nakano, T, Takemoto, H, Arisawa, M, Shuto, S. | | 登録日 | 2012-07-17 | | 公開日 | 2012-10-24 | | 最終更新日 | 2013-09-04 | | 実験手法 | X-RAY DIFFRACTION (2.1 Å) | | 主引用文献 | Conformational restriction approach to beta-secretase (BACE1) inhibitors: effect of a cyclopropane ring to induce an alternative binding mode.
J.Med.Chem., 55, 2012
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2CUO
 | | Collagen model peptide (PRO-PRO-GLY)9 | | 分子名称: | COLLAGEN MODEL PEPTIDE (PRO-PRO-GLY)9 | | 著者 | Hongo, C, Noguchi, K, Okuyama, K, Tanaka, Y, Nishino, N. | | 登録日 | 2005-05-27 | | 公開日 | 2005-06-14 | | 最終更新日 | 2023-10-25 | | 実験手法 | X-RAY DIFFRACTION (1.33 Å) | | 主引用文献 | Repetitive interactions observed in the crystal structure of a collagen-model peptide, [(Pro-Pro-Gly)9]3
J.Biochem.(Tokyo), 138, 2005
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7EQE
 | | Crystal Structure of a transcription factor | | 分子名称: | TetR/AcrR family transcriptional regulator | | 著者 | Uehara, S, Tsugita, A, Matsui, T, Yokoyama, T, Ostash, I, Ostash, B, Tanaka, Y. | | 登録日 | 2021-05-01 | | 公開日 | 2022-04-27 | | 最終更新日 | 2022-10-19 | | 実験手法 | X-RAY DIFFRACTION (2.399 Å) | | 主引用文献 | The carbohydrate tail of landomycin A is responsible for its interaction with the repressor protein LanK.
Febs J., 289, 2022
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2F08
 | | Crystal structure of a major house dust mite allergen, Derf 2 | | 分子名称: | O-ACETALDEHYDYL-HEXAETHYLENE GLYCOL, mite allergen Der f II | | 著者 | Mikami, B, Tanaka, Y, Minato, N, Suzuki, M, Korematsu, S. | | 登録日 | 2005-11-12 | | 公開日 | 2005-11-29 | | 最終更新日 | 2011-07-13 | | 実験手法 | X-RAY DIFFRACTION (2.2 Å) | | 主引用文献 | Crystal structure and some properties of a major house dust mite allergen, Derf 2
Biochem.Biophys.Res.Commun., 339, 2006
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7WAX
 | | MurJ inward occluded form | | 分子名称: | (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, (4S)-2-METHYL-2,4-PENTANEDIOL, lipid II flippase MurJ | | 著者 | Tsukazaki, T, Kohga, H, Tanaka, Y, Yoshikaie, K, Taniguchi, K, Fujimoto, K. | | 登録日 | 2021-12-15 | | 公開日 | 2022-06-01 | | 最終更新日 | 2024-05-29 | | 実験手法 | X-RAY DIFFRACTION (2.35 Å) | | 主引用文献 | Crystal structure of the lipid flippase MurJ in a "squeezed" form distinct from its inward- and outward-facing forms.
Structure, 30, 2022
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7WAW
 | | MurJ inward closed form | | 分子名称: | (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, lipid II flippase MurJ | | 著者 | Tsukazaki, T, Kohga, H, Tanaka, Y, Yoshikaie, K, Taniguchi, K, Fujimoto, K. | | 登録日 | 2021-12-15 | | 公開日 | 2022-06-01 | | 最終更新日 | 2024-05-29 | | 実験手法 | X-RAY DIFFRACTION (2.8 Å) | | 主引用文献 | Crystal structure of the lipid flippase MurJ in a "squeezed" form distinct from its inward- and outward-facing forms.
Structure, 30, 2022
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7WAG
 | | Crystal structure of MurJ squeezed form | | 分子名称: | (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, DI(HYDROXYETHYL)ETHER, Lipid II flippase MurJ | | 著者 | Tsukazaki, T, Kohga, H, Tanaka, Y, Yoshikaie, K, Taniguchi, K, Fujimoto, K. | | 登録日 | 2021-12-14 | | 公開日 | 2022-06-01 | | 最終更新日 | 2023-11-29 | | 実験手法 | X-RAY DIFFRACTION (2.55 Å) | | 主引用文献 | Crystal structure of the lipid flippase MurJ in a "squeezed" form distinct from its inward- and outward-facing forms.
Structure, 30, 2022
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2YVZ
 | | Crystal structure of magnesium transporter MgtE cytosolic domain, Mg2+-free form | | 分子名称: | Mg2+ transporter MgtE | | 著者 | Hattori, M, Tanaka, Y, Fukai, S, Ishitani, R, Nureki, O. | | 登録日 | 2007-04-18 | | 公開日 | 2007-09-04 | | 最終更新日 | 2011-07-13 | | 実験手法 | X-RAY DIFFRACTION (3.9 Å) | | 主引用文献 | Crystal structure of the MgtE Mg(2+) transporter
Nature, 448, 2007
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2YVY
 | | Crystal structure of magnesium transporter MgtE cytosolic domain, Mg2+ bound form | | 分子名称: | MAGNESIUM ION, Mg2+ transporter MgtE | | 著者 | Hattori, M, Tanaka, Y, Fukai, S, Ishitani, R, Nureki, O. | | 登録日 | 2007-04-18 | | 公開日 | 2007-09-04 | | 最終更新日 | 2024-03-13 | | 実験手法 | X-RAY DIFFRACTION (2.3 Å) | | 主引用文献 | Crystal structure of the MgtE Mg(2+) transporter
Nature, 448, 2007
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3VOF
 | | Cellobiohydrolase mutant, CcCel6C D102A, in the closed form | | 分子名称: | Cellobiohydrolase, beta-D-glucopyranose | | 著者 | Tamura, M, Miyazaki, T, Tanaka, Y, Yoshida, M, Nishikawa, A, Tonozuka, T. | | 登録日 | 2012-01-23 | | 公開日 | 2012-03-21 | | 最終更新日 | 2023-11-08 | | 実験手法 | X-RAY DIFFRACTION (1.6 Å) | | 主引用文献 | Comparison of the structural changes in two cellobiohydrolases, CcCel6A and CcCel6C, from Coprinopsis cinerea - a tweezer-like motion in the structure of CcCel6C
Febs J., 279, 2012
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2Z92
 | | Crystal structure of the Fab fragment of anti-ciguatoxin antibody 10C9 in complex with CTX3C_ABCDE | | 分子名称: | (4Z)-2,8:7,12:11,15:14,18:17,22-PENTAANHYDRO-4,5,6,9,10,13,19,20,21-NONADEOXY-D-ARABINO-D-ALLO-D-ALLO-DOCOSA-4,9,20-TRIENITOL, Anti-ciguatoxin antibody 10C9 Fab heavy chain, Anti-ciguatoxin antibody 10C9 Fab light chain, ... | | 著者 | Ui, M, Tanaka, Y, Tsumoto, K. | | 登録日 | 2007-09-14 | | 公開日 | 2008-05-06 | | 最終更新日 | 2023-11-01 | | 実験手法 | X-RAY DIFFRACTION (2.3 Å) | | 主引用文献 | How Protein Recognizes Ladder-like Polycyclic Ethers: INTERACTIONS BETWEEN CIGUATOXIN (CTX3C) FRAGMENTS AND ITS SPECIFIC ANTIBODY 10C9
J.Biol.Chem., 283, 2008
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2Z93
 | | Crystal structure of Fab fragment of anti-ciguatoxin antibody 10C9 in complex with CTX3C-ABCD | | 分子名称: | 1,6:5,9:8,12:11,16-TETRAANHYDRO-2,3,4,10,13,14-HEXADEOXY-D-GLYCERO-D-ALLO-D-GULO-HEPTADECA-2,13-DIENITOL, Anti-ciguatoxin antibody 10C9 Fab heavy chain, Anti-ciguatoxin antibody 10C9 Fab light chain | | 著者 | Ui, M, Tanaka, Y, Tsumoto, K. | | 登録日 | 2007-09-14 | | 公開日 | 2008-05-06 | | 最終更新日 | 2023-11-01 | | 実験手法 | X-RAY DIFFRACTION (2.4 Å) | | 主引用文献 | How Protein Recognizes Ladder-like Polycyclic Ethers: INTERACTIONS BETWEEN CIGUATOXIN (CTX3C) FRAGMENTS AND ITS SPECIFIC ANTIBODY 10C9
J.Biol.Chem., 283, 2008
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2Z91
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