2CZR
| Crystal structure of TBP-interacting protein (Tk-TIP26) and implications for its inhibition mechanism of the interaction between TBP and TATA-DNA | Descriptor: | GLYCEROL, TBP-interacting protein, ZINC ION | Authors: | Yamamoto, T, Matsuda, T, Inoue, T, Matsumura, H, Morikawa, M, Kanaya, S, Kai, Y. | Deposit date: | 2005-07-15 | Release date: | 2006-02-14 | Last modified: | 2024-03-13 | Method: | X-RAY DIFFRACTION (2.3 Å) | Cite: | Crystal structure of TBP-interacting protein (Tk-TIP26) and implications for its inhibition mechanism of the interaction between TBP and TATA-DNA Protein Sci., 15, 2006
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5FHI
| Crystallographic structure of PsoE without Co | Descriptor: | GLUTATHIONE, Glutathione S-transferase, putative | Authors: | Hara, K, Hashimoto, H, Yamamoto, T, Tsunematsu, Y, Watanabe, K. | Deposit date: | 2015-12-22 | Release date: | 2016-04-20 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (2.41 Å) | Cite: | Oxidative trans to cis Isomerization of Olefins in Polyketide Biosynthesis. Angew. Chem. Int. Ed. Engl., 55, 2016
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5F8B
| Crystallographic Structure of PsoE with Co | Descriptor: | (5~{S},8~{S},9~{R})-2-[(~{E})-hex-1-enyl]-8-methoxy-3-methyl-9-oxidanyl-8-(phenylcarbonyl)-1-oxa-7-azaspiro[4.4]non-2-ene-4,6-dione, COBALT (II) ION, GLUTATHIONE, ... | Authors: | Hara, K, Hashimoto, H, Yamamoto, T, Tsunematsu, Y, Watanabe, K. | Deposit date: | 2015-12-09 | Release date: | 2016-04-20 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (2.54 Å) | Cite: | Oxidative trans to cis Isomerization of Olefins in Polyketide Biosynthesis. Angew. Chem. Int. Ed. Engl., 55, 2016
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4X8Y
| Crystal structure of human PGRMC1 cytochrome b5-like domain | Descriptor: | Membrane-associated progesterone receptor component 1, PROTOPORPHYRIN IX CONTAINING FE | Authors: | Nakane, T, Yamamoto, T, Shimamura, T, Kobayashi, T, Kabe, Y, Suematsu, M. | Deposit date: | 2014-12-11 | Release date: | 2016-03-23 | Last modified: | 2020-02-05 | Method: | X-RAY DIFFRACTION (1.95 Å) | Cite: | Haem-dependent dimerization of PGRMC1/Sigma-2 receptor facilitates cancer proliferation and chemoresistance Nat Commun, 7, 2016
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3NGN
| Crystal structure of the human CNOT6L nuclease domain in complex with AMP | Descriptor: | ADENOSINE MONOPHOSPHATE, CCR4-NOT transcription complex subunit 6-like | Authors: | Wang, H, Morita, M, Yang, W, Bartlam, M, Yamamoto, T, Rao, Z. | Deposit date: | 2010-06-12 | Release date: | 2010-07-28 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (2.4 Å) | Cite: | Crystal structure of the human CNOT6L nuclease domain reveals strict poly(A) substrate specificity. Embo J., 2010
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3NGO
| Crystal structure of the human CNOT6L nuclease domain in complex with poly(A) DNA | Descriptor: | 5'-D(*AP*AP*AP*A)-3', CCR4-NOT transcription complex subunit 6-like, MAGNESIUM ION | Authors: | Wang, H, Morita, M, Yang, W, Bartlam, M, Yamamoto, T, Rao, Z. | Deposit date: | 2010-06-12 | Release date: | 2010-07-28 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (2.2 Å) | Cite: | Crystal structure of the human CNOT6L nuclease domain reveals strict poly(A) substrate specificity. Embo J., 2010
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3NGQ
| Crystal structure of the human CNOT6L nuclease domain | Descriptor: | 3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE, CCR4-NOT transcription complex subunit 6-like, MAGNESIUM ION | Authors: | Wang, H, Morita, M, Yang, W, Bartlam, M, Yamamoto, T, Rao, Z. | Deposit date: | 2010-06-13 | Release date: | 2010-07-28 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (1.8 Å) | Cite: | Crystal structure of the human CNOT6L nuclease domain reveals strict poly(A) substrate specificity. Embo J., 2010
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3DJU
| Crystal structure of human BTG2 | Descriptor: | Protein BTG2 | Authors: | Yang, X, Morita, M, Wang, H, Suzuki, T, Bartlam, M, Yamamoto, T. | Deposit date: | 2008-06-24 | Release date: | 2008-11-11 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (2.26 Å) | Cite: | Crystal structures of human BTG2 and mouse TIS21 involved in suppression of CAF1 deadenylase activity Nucleic Acids Res., 36, 2008
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3DJN
| Crystal structure of mouse TIS21 | Descriptor: | Protein BTG2 | Authors: | Yang, X, Morita, M, Wang, H, Suzuki, T, Bartlam, M, Yamamoto, T. | Deposit date: | 2008-06-24 | Release date: | 2008-11-11 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (2.2 Å) | Cite: | Crystal structures of human BTG2 and mouse TIS21 involved in suppression of CAF1 deadenylase activity Nucleic Acids Res., 36, 2008
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3CU0
| human beta 1,3-glucuronyltransferase I (GlcAT-I) in complex with UDP and GAL-GAL(6-SO4)-XYL(2-PO4)-O-SER | Descriptor: | Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 3, MANGANESE (II) ION, SULFATE ION, ... | Authors: | Tone, Y, Pedersen, L.C, Yamamoto, T, Kitagawa, H, Nishihara-Shimizu, J, Tamura, J, Negishi, M, Sugahara, K. | Deposit date: | 2008-04-15 | Release date: | 2008-05-06 | Last modified: | 2023-08-30 | Method: | X-RAY DIFFRACTION (1.9 Å) | Cite: | 2-o-phosphorylation of xylose and 6-o-sulfation of galactose in the protein linkage region of glycosaminoglycans influence the glucuronyltransferase-I activity involved in the linkage region synthesis. J.Biol.Chem., 283, 2008
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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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8HGM
| Structure of SARS-CoV-2 spike RBD in complex with neutralizing antibody NIV-11 | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, NIV-11 Fab heavy chain, NIV-11 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: | 2022-11-15 | Release date: | 2023-10-25 | 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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8HGL
| SARS-CoV-2 spike in complex with neutralizing antibody NIV-11 | 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-11 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: | 2022-11-15 | Release date: | 2023-10-25 | Last modified: | 2024-05-15 | Method: | ELECTRON MICROSCOPY (2.9 Å) | Cite: | Structural delineation and computational design of SARS-CoV-2-neutralizing antibodies against Omicron subvariants. Nat Commun, 14, 2023
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8HES
| Crystal structure of SARS-CoV-2 RBD and NIV-10 complex | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, NIV-10 Fab H-chain, NIV-10 Fab L-chain, ... | Authors: | Moriyama, S, Anraku, Y, Taminishi, 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: | 2022-11-08 | Release date: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.2 Å) | Cite: | Structural delineation and computational design of SARS-CoV-2-neutralizing antibodies against Omicron subvariants. Nat Commun, 14, 2023
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5H34
| Crystal structure of the C-terminal domain of methionyl-tRNA synthetase (MetRS-C) in Nanoarchaeum equitans | Descriptor: | Methionine-tRNA ligase | Authors: | Suzuki, H, Kaneko, A, Yamamoto, T, Nambo, M, Umehara, T, Yoshida, H, Park, S.Y, Tamura, K. | Deposit date: | 2016-10-20 | Release date: | 2017-06-21 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (1.748 Å) | Cite: | Binding Properties of Split tRNA to the C-terminal Domain of Methionyl-tRNA Synthetase of Nanoarchaeum equitans. J. Mol. Evol., 84, 2017
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9BUV
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8HN3
| Soluble domain of cytochrome c-556 from Chlorobaculum tepidum | Descriptor: | ACETATE ION, Cytochrome c-556, GLYCEROL, ... | Authors: | Kishimoto, H, Azai, C, Yamamoto, T, Mutoh, R, Nakaniwa, T, Tanaka, H, Kurisu, G, Oh-oka, H. | Deposit date: | 2022-12-07 | Release date: | 2023-07-05 | Method: | X-RAY DIFFRACTION (1.65 Å) | Cite: | Soluble domains of cytochrome c-556 and Rieske iron-sulfur protein from Chlorobaculum tepidum: Crystal structures and interaction analysis. Curr Res Struct Biol, 5, 2023
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2NVL
| Crystal structure of archaeal peroxiredoxin, thioredoxin peroxidase from Aeropyrum pernix K1 (sulfonic acid form) | Descriptor: | Probable peroxiredoxin | Authors: | Nakamura, T, Yamamoto, T, Abe, M, Matsumura, H, Hagihara, Y, Goto, T, Yamaguchi, T, Inoue, T. | Deposit date: | 2006-11-13 | Release date: | 2007-11-20 | Last modified: | 2023-11-15 | Method: | X-RAY DIFFRACTION (2.36 Å) | Cite: | Oxidation of archaeal peroxiredoxin involves a hypervalent sulfur intermediate Proc.Natl.Acad.Sci.Usa, 105, 2008
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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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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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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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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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