7XZY
 
 | | Cryo-EM structure of the nucleosome containing 193 base-pair DNA with a p53 target sequence | | 分子名称: | DNA (193-MER), Histone H2A type 1-B/E, Histone H2B type 1-J, ... | | 著者 | Nishimura, M, Nozawa, K, Takizawa, Y, Kurumizaka, H. | | 登録日 | 2022-06-03 | | 公開日 | 2022-10-19 | | 最終更新日 | 2024-07-03 | | 実験手法 | ELECTRON MICROSCOPY (3.97 Å) | | 主引用文献 | Structural basis for p53 binding to its nucleosomal target DNA sequence.
Pnas Nexus, 1, 2022
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3A4U
 | | Crystal structure of MCFD2 in complex with carbohydrate recognition domain of ERGIC-53 | | 分子名称: | CALCIUM ION, GLYCEROL, Multiple coagulation factor deficiency protein 2, ... | | 著者 | Nishio, M, Kamiya, Y, Mizushima, T, Wakatsuki, S, Sasakawa, H, Yamamoto, K, Uchiyama, S, Noda, M, McKay, A.R, Fukui, K, Hauri, H.P, Kato, K. | | 登録日 | 2009-07-17 | | 公開日 | 2010-01-05 | | 最終更新日 | 2023-11-01 | | 実験手法 | X-RAY DIFFRACTION (1.84 Å) | | 主引用文献 | Structural basis for the cooperative interplay between the two causative gene products of combined factor V and factor VIII deficiency.
Proc.Natl.Acad.Sci.USA, 107, 2010
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3C3I
 | | Evolution of chlorella virus dUTPase | | 分子名称: | DEOXYURIDINE-5'-DIPHOSPHATE, Deoxyuridine triphosphatase, MAGNESIUM ION | | 著者 | Yamanishi, M, Homma, K, Zhang, Y, Etten, L.V.J, Moriyama, H. | | 登録日 | 2008-01-28 | | 公開日 | 2009-02-10 | | 最終更新日 | 2024-02-21 | | 実験手法 | X-RAY DIFFRACTION (3 Å) | | 主引用文献 | Crystallization and crystal-packing studies of Chlorella virus deoxyuridine triphosphatase.
Acta Crystallogr.,Sect.F, 65, 2009
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1X23
 | | Crystal structure of ubch5c | | 分子名称: | Ubiquitin-conjugating enzyme E2 D3 | | 著者 | Nakanishi, M, Teshima, N, Mizushima, T, Murata, S, Tanaka, K, Yamane, T. | | 登録日 | 2005-04-19 | | 公開日 | 2005-05-03 | | 最終更新日 | 2023-10-25 | | 実験手法 | X-RAY DIFFRACTION (1.85 Å) | | 主引用文献 | Crystal structure of ubch5c
To be Published
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3CA9
 | | Evolution of chlorella virus dUTPase | | 分子名称: | DEOXYURIDINE-5'-DIPHOSPHATE, Deoxyuridine triphosphatase, MAGNESIUM ION | | 著者 | Yamanishi, M, Homma, K, Zhang, Y, Etten, L.V.J, Moriyama, H. | | 登録日 | 2008-02-19 | | 公開日 | 2009-03-03 | | 最終更新日 | 2024-02-21 | | 実験手法 | X-RAY DIFFRACTION (3 Å) | | 主引用文献 | Crystallization and crystal-packing studies of Chlorella virus deoxyuridine triphosphatase.
Acta Crystallogr.,Sect.F, 65, 2009
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3C2T
 | | Evolution of chlorella virus dUTPase | | 分子名称: | DEOXYURIDINE-5'-DIPHOSPHATE, Deoxyuridine triphosphatase, MAGNESIUM ION | | 著者 | Yamanishi, M, Homma, K, Zhang, Y, Etten, L.V.J, Moriyama, H. | | 登録日 | 2008-01-25 | | 公開日 | 2009-02-24 | | 最終更新日 | 2024-02-21 | | 実験手法 | X-RAY DIFFRACTION (3 Å) | | 主引用文献 | Crystallization and crystal-packing studies of Chlorella virus deoxyuridine triphosphatase.
Acta Crystallogr.,Sect.F, 65, 2009
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1Q2H
 | | Phenylalanine Zipper Mediates APS Dimerization | | 分子名称: | adaptor protein with pleckstrin homology and src homology 2 domains | | 著者 | Dhe-Paganon, S, Werner, E.D, Nishi, M, Chi, Y.-I, Shoelson, S.E. | | 登録日 | 2003-07-24 | | 公開日 | 2004-08-03 | | 最終更新日 | 2024-05-22 | | 実験手法 | X-RAY DIFFRACTION (1.7 Å) | | 主引用文献 | A phenylalanine zipper mediates APS dimerization.
Nat.Struct.Mol.Biol., 11, 2004
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1UC4
 | | Structure of diol dehydratase complexed with (S)-1,2-propanediol | | 分子名称: | AMMONIUM ION, CYANOCOBALAMIN, POTASSIUM ION, ... | | 著者 | Shibata, N, Nakanishi, Y, Fukuoka, M, Yamanishi, M, Yasuoka, N, Toraya, T. | | 登録日 | 2003-04-08 | | 公開日 | 2003-07-22 | | 最終更新日 | 2023-10-25 | | 実験手法 | X-RAY DIFFRACTION (1.8 Å) | | 主引用文献 | Structural rationalization for the lack of stereospecificity in coenzyme B12-dependent diol dehydratase
J.BIOL.CHEM., 278, 2003
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8IP9
 | | Wheat 40S ribosome in complex with a tRNAi | | 分子名称: | 18S ribosomal RNA, 40S ribosomal protein S23, 40S ribosomal protein eS1, ... | | 著者 | Yokoyama, T, Tanaka, M, Saito, H, Nishimoto, M, Tsuda, K, Sotta, N, Shigematsu, H, Shirouzu, M, Iwasaki, S, Ito, T, Fujiwara, T. | | 登録日 | 2023-03-14 | | 公開日 | 2024-02-21 | | 最終更新日 | 2024-05-15 | | 実験手法 | ELECTRON MICROSCOPY (3 Å) | | 主引用文献 | Boric acid intercepts 80S ribosome migration from AUG-stop by stabilizing eRF1.
Nat.Chem.Biol., 20, 2024
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8IPA
 | | Wheat 80S ribosome stalled on AUG-Stop boron dependently with cycloheximide | | 分子名称: | 18S ribosomal RNA, 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione, 40S ribosomal protein eL8, ... | | 著者 | Yokoyama, T, Tanaka, M, Saito, H, Nishimoto, M, Tsuda, K, Sotta, N, Shigematsu, H, Shirouzu, M, Iwasaki, S, Ito, T, Fujiwara, T. | | 登録日 | 2023-03-14 | | 公開日 | 2024-02-21 | | 最終更新日 | 2024-05-15 | | 実験手法 | ELECTRON MICROSCOPY (3.4 Å) | | 主引用文献 | Boric acid intercepts 80S ribosome migration from AUG-stop by stabilizing eRF1.
Nat.Chem.Biol., 20, 2024
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8IPB
 | | Wheat 80S ribosome pausing on AUG-Stop with cycloheximide | | 分子名称: | 18S ribosomal RNA, 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione, 40S ribosomal protein eL8, ... | | 著者 | Yokoyama, T, Tanaka, M, Saito, H, Nishimoto, M, Tsuda, K, Sotta, N, Shigematsu, H, Shirouzu, M, Iwasaki, S, Ito, T, Fujiwara, T. | | 登録日 | 2023-03-14 | | 公開日 | 2024-02-21 | | 最終更新日 | 2024-05-15 | | 実験手法 | ELECTRON MICROSCOPY (3.4 Å) | | 主引用文献 | Boric acid intercepts 80S ribosome migration from AUG-stop by stabilizing eRF1.
Nat.Chem.Biol., 20, 2024
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7YV1
 | | Human K-Ras G12D (GDP-bound) in complex with cyclic peptide inhibitor LUNA18 and KA30L Fab | | 分子名称: | GUANOSINE-5'-DIPHOSPHATE, Isoform 2B of GTPase KRas, KA30L Fab H-chain, ... | | 著者 | Irie, M, Fukami, T.A, Matsuo, A, Saka, K, Nishimura, M, Saito, H, Torizawa, T, Tanada, M, Ohta, A. | | 登録日 | 2022-08-18 | | 公開日 | 2023-07-26 | | 最終更新日 | 2023-11-22 | | 実験手法 | X-RAY DIFFRACTION (1.454 Å) | | 主引用文献 | Validation of a New Methodology to Create Oral Drugs beyond the Rule of 5 for Intracellular Tough Targets.
J.Am.Chem.Soc., 145, 2023
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5X3D
 | | Crystal structure of HEP-CMP-bound form of cytidylyltransferase (CyTase) domain of Fom1 from Streptomyces wedmorensis | | 分子名称: | Phosphoenolpyruvate phosphomutase, [[(2R,3S,4R,5R)-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-(2-hydroxyethyl)phosphinic acid | | 著者 | Tomita, T, Cho, S.H, Kuzuyama, T, Nishiyama, M. | | 登録日 | 2017-02-04 | | 公開日 | 2017-09-13 | | 最終更新日 | 2024-03-27 | | 実験手法 | X-RAY DIFFRACTION (1.93 Å) | | 主引用文献 | Fosfomycin Biosynthesis via Transient Cytidylylation of 2-Hydroxyethylphosphonate by the Bifunctional Fom1 Enzyme
ACS Chem. Biol., 12, 2017
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7YLZ
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5B6Q
 | | Crystal structure of monomeric cytochrome c5 from Shewanella violacea | | 分子名称: | HEME C, IMIDAZOLE, Soluble cytochrome cA | | 著者 | Masanari, M, Fujii, S, Kawahara, K, Oki, H, Tsujino, H, Maruno, T, Kobayashi, Y, Ohkubo, T, Nishiyama, M, Harada, Y, Wakai, S, Sambongi, Y. | | 登録日 | 2016-06-01 | | 公開日 | 2016-10-19 | | 最終更新日 | 2019-10-02 | | 実験手法 | X-RAY DIFFRACTION (1.78 Å) | | 主引用文献 | Comparative study on stabilization mechanism of monomeric cytochrome c5 from deep-sea piezophilic Shewanella violacea
Biosci.Biotechnol.Biochem., 2016
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2DEP
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5XOY
 | | Crystal structure of LysK from Thermus thermophilus in complex with Lysine | | 分子名称: | LYSINE, SULFATE ION, [LysW]-lysine hydrolase | | 著者 | Tomita, T, Fujita, S, Hasebe, F, Cho, S.-H, Yoshida, A, Kuzuyama, T, Nishiyama, M. | | 登録日 | 2017-05-31 | | 公開日 | 2017-09-13 | | 最終更新日 | 2023-11-22 | | 実験手法 | X-RAY DIFFRACTION (2.39 Å) | | 主引用文献 | Crystal structure of LysK, an enzyme catalyzing the last step of lysine biosynthesis in Thermus thermophilus, in complex with lysine: Insight into the mechanism for recognition of the amino-group carrier protein, LysW
Biochem. Biophys. Res. Commun., 491, 2017
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2DT9
 | | Crystal structure of the regulatory subunit of aspartate kinase from Thermus flavus | | 分子名称: | ACETATE ION, Aspartokinase, THREONINE | | 著者 | Yoshida, A, Tomita, T, Fushinobu, S, Kuzuyama, T, Nishiyama, M. | | 登録日 | 2006-07-11 | | 公開日 | 2007-07-17 | | 最終更新日 | 2024-03-13 | | 実験手法 | X-RAY DIFFRACTION (2.15 Å) | | 主引用文献 | Crystal structures of the regulatory subunit of Thr-sensitive aspartate kinase from Thermus thermophilus
Febs J., 276, 2009
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4WH2
 | | N-acetylhexosamine 1-kinase in complex with ADP | | 分子名称: | ACETIC ACID, ADENOSINE-5'-DIPHOSPHATE, GLYCEROL, ... | | 著者 | Sato, M, Arakawa, T, Nam, Y.W, Nishimoto, M, Kitaoka, M, Fushinobu, S. | | 登録日 | 2014-09-19 | | 公開日 | 2015-02-18 | | 最終更新日 | 2024-03-20 | | 実験手法 | X-RAY DIFFRACTION (1.847 Å) | | 主引用文献 | Open-close structural change upon ligand binding and two magnesium ions required for the catalysis of N-acetylhexosamine 1-kinase
Biochim.Biophys.Acta, 1854, 2015
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4WH1
 | | N-Acetylhexosamine 1-kinase (ligand free) | | 分子名称: | ACETIC ACID, GLYCEROL, N-acetylhexosamine 1-kinase | | 著者 | Sato, M, Arakawa, T, Nam, Y.W, Nishimoto, M, Kitaoka, M, Fushinobu, S. | | 登録日 | 2014-09-19 | | 公開日 | 2015-02-11 | | 最終更新日 | 2024-03-20 | | 実験手法 | X-RAY DIFFRACTION (2.05 Å) | | 主引用文献 | Open-close structural change upon ligand binding and two magnesium ions required for the catalysis of N-acetylhexosamine 1-kinase
Biochim.Biophys.Acta, 1854, 2015
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4WH3
 | | N-acetylhexosamine 1-kinase in complex with ATP | | 分子名称: | ACETIC ACID, ADENOSINE-5'-TRIPHOSPHATE, GLYCEROL, ... | | 著者 | Sato, M, Arakawa, T, Nam, Y.W, Nishimoto, M, Kitaoka, M, Fushinobu, S. | | 登録日 | 2014-09-19 | | 公開日 | 2015-02-18 | | 最終更新日 | 2020-02-05 | | 実験手法 | X-RAY DIFFRACTION (1.8 Å) | | 主引用文献 | Open-close structural change upon ligand binding and two magnesium ions required for the catalysis of N-acetylhexosamine 1-kinase
Biochim.Biophys.Acta, 1854, 2015
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8J3T
 | | Complex structure of human cytomegalovirus protease and a non-covalent small-molecule ligand | | 分子名称: | (4R)-1-[1-[(S)-[1-cyclopentyl-3-(2-methylphenyl)pyrazol-4-yl]-(4-methylphenyl)methyl]-2-oxidanylidene-pyridin-3-yl]-3-methyl-2-oxidanylidene-N-(3-oxidanylidene-2-azabicyclo[2.2.2]octan-4-yl)imidazolidine-4-carboxamide, Assemblin | | 著者 | Yoshida, S, Sako, Y, Nikaido, E, Ueda, T, Kozono, I, Ichihashi, Y, Nakahashi, A, Onishi, M, Yamatsu, Y, Kato, T, Nishikawa, J, Tachibana, Y. | | 登録日 | 2023-04-18 | | 公開日 | 2023-11-08 | | 最終更新日 | 2023-11-29 | | 実験手法 | X-RAY DIFFRACTION (2.9 Å) | | 主引用文献 | Peptide-to-Small Molecule: Discovery of Non-Covalent, Active-Site Inhibitors of beta-Herpesvirus Proteases.
Acs Med.Chem.Lett., 14, 2023
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5WVO
 | | Crystal structure of DNMT1 RFTS domain in complex with K18/K23 mono-ubiquitylated histone H3 | | 分子名称: | DNA (cytosine-5)-methyltransferase 1, Histone H3.1, Ubiquitin, ... | | 著者 | Ishiyama, S, Nishiyama, A, Nakanishi, M, Arita, K. | | 登録日 | 2016-12-28 | | 公開日 | 2017-11-15 | | 最終更新日 | 2023-11-22 | | 実験手法 | X-RAY DIFFRACTION (1.997 Å) | | 主引用文献 | Structure of the Dnmt1 Reader Module Complexed with a Unique Two-Mono-Ubiquitin Mark on Histone H3 Reveals the Basis for DNA Methylation Maintenance
Mol. Cell, 68, 2017
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8J3S
 | | Complex structure of human cytomegalovirus protease and a macrocyclic peptide ligand | | 分子名称: | Assemblin, PHE-ILE-THR-GLY-HIS-TYR-TRP-VAL-ARG-PHE-LEU-PRO-CYS-GLY | | 著者 | Yoshida, S, Sako, Y, Nikaido, E, Ueda, T, Kozono, I, Ichihashi, Y, Nakahashi, A, Onishi, M, Yamatsu, Y, Kato, T, Nishikawa, J, Tachibana, Y. | | 登録日 | 2023-04-18 | | 公開日 | 2023-11-08 | | 最終更新日 | 2023-11-29 | | 実験手法 | X-RAY DIFFRACTION (3.09 Å) | | 主引用文献 | Peptide-to-Small Molecule: Discovery of Non-Covalent, Active-Site Inhibitors of beta-Herpesvirus Proteases.
Acs Med.Chem.Lett., 14, 2023
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2DTJ
 | | Crystal structure of regulatory subunit of aspartate kinase from Corynebacterium glutamicum | | 分子名称: | Aspartokinase, CITRIC ACID, THREONINE | | 著者 | Yoshida, A, Tomita, T, Fushinobu, S, Kuzuyama, T, Nishiyama, M. | | 登録日 | 2006-07-12 | | 公開日 | 2007-05-01 | | 最終更新日 | 2023-11-08 | | 実験手法 | X-RAY DIFFRACTION (1.58 Å) | | 主引用文献 | Structural Insight into Concerted Inhibition of alpha(2)beta(2)-Type Aspartate Kinase from Corynebacterium glutamicum
J.Mol.Biol., 368, 2007
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