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PDB: 167 件
8JLD
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Cryo-EM structure of the 145 bp human nucleosome containing acetylated H3 tail
分子名称: DNA (145-MER), Histone H2A type 1-B/E, Histone H2B type 1-J, ...
著者Oishi, T, Hatazawa, S, Kujirai, T, Kato, J, Kobayashi, Y, Ogasawara, M, Akatsu, M, Takizawa, Y, Kurumizaka, H.
登録日2023-06-02
公開日2023-10-04
最終更新日2023-11-15
実験手法ELECTRON MICROSCOPY (2.48 Å)
主引用文献Contributions of histone tail clipping and acetylation in nucleosome transcription by RNA polymerase II.
Nucleic Acids Res., 51, 2023
8JLA
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Cryo-EM structure of the human nucleosome lacking N-terminal region of H2A, H2B, H3, and H4
分子名称: DNA (193-MER), Histone H2A type 1-B/E, Histone H2B type 1-J, ...
著者Oishi, T, Hatazawa, S, Kujirai, T, Kato, J, Kobayashi, Y, Ogasawara, M, Akatsu, M, Takizawa, Y, Kurumizaka, H.
登録日2023-06-02
公開日2023-10-04
最終更新日2023-11-08
実験手法ELECTRON MICROSCOPY (3.44 Å)
主引用文献Contributions of histone tail clipping and acetylation in nucleosome transcription by RNA polymerase II.
Nucleic Acids Res., 51, 2023
6A3K
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BU of 6a3k by Molmil
Crystal structure of cytochrome c' from Shewanella benthica DB6705
分子名称: Cytochrome c, HEME C, PENTAETHYLENE GLYCOL
著者Suka, A, Oki, H, Kato, Y, Kawahara, K, Ohkubo, T, Maruno, T, Kobayashi, Y, Fujii, S, Wakai, S, Sambongi, Y.
登録日2018-06-15
公開日2019-06-12
最終更新日2019-10-02
実験手法X-RAY DIFFRACTION (1.71 Å)
主引用文献Stability of cytochromes c' from psychrophilic and piezophilic Shewanella species: implications for complex multiple adaptation to low temperature and high hydrostatic pressure.
Extremophiles, 23, 2019
6LUG
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BU of 6lug by Molmil
Crystal structure of N(omega)-hydroxy-L-arginine hydrolase
分子名称: MANGANESE (II) ION, N(omega)-hydroxy-L-arginine amidinohydrolase
著者Oda, K, Matoba, Y.
登録日2020-01-28
公開日2020-06-17
最終更新日2024-03-27
実験手法X-RAY DIFFRACTION (1.9 Å)
主引用文献Crystal structure of an Nomega-hydroxy-L-arginine hydrolase found in the D-cycloserine biosynthetic pathway.
Acta Crystallogr D Struct Biol, 76, 2020
5B6Q
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BU of 5b6q by Molmil
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
5B3I
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BU of 5b3i by Molmil
Homo-dimeric structure of cytochrome c' from Thermophilic Hydrogenophilus thermoluteolus
分子名称: Cytochrome c prime, HEME C
著者Fujii, S, Oki, H, Kawahara, K, Yamane, D, Yamanaka, M, Maruno, T, Kobayashi, Y, Masanari, M, Wakai, S, Nishihara, H, Ohkubo, T, Sambongi, Y.
登録日2016-02-29
公開日2017-03-01
最終更新日2023-11-08
実験手法X-RAY DIFFRACTION (1.89 Å)
主引用文献Structural and functional insights into thermally stable cytochrome c' from a thermophile
Protein Sci., 26, 2017
5AX6
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BU of 5ax6 by Molmil
The crystal structure of CofB, the minor pilin subunit of CFA/III from human enterotoxigenic Escherichia coli.
分子名称: ACETATE ION, CofB
著者Kawahara, K, Oki, K, Fukaksua, F, Maruno, T, Kobayashi, Y, Daisuke, M, Taniguchi, T, Honda, T, Iida, T, Nakamura, S, Ohkubo, T.
登録日2015-07-16
公開日2016-03-09
最終更新日2020-02-26
実験手法X-RAY DIFFRACTION (1.88 Å)
主引用文献Homo-trimeric Structure of the Type IVb Minor Pilin CofB Suggests Mechanism of CFA/III Pilus Assembly in Human Enterotoxigenic Escherichia coli
J.Mol.Biol., 428, 2016
8IUS
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BU of 8ius by Molmil
Crystal structure of Manganese-free N(omega)-hydroxy-L-arginine hydrolase with reduced Cys86
分子名称: MAGNESIUM ION, MANGANESE (II) ION, N(omega)-hydroxy-L-arginine amidinohydrolase
著者Oda, K, Matoba, Y.
登録日2023-03-25
公開日2024-03-27
実験手法X-RAY DIFFRACTION (2.14 Å)
主引用文献Copper inactivates DcsB by oxidation of the Cys86 to cysteine sulfinic aicd
To Be Published
8IUU
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BU of 8iuu by Molmil
Crystal structure of Manganese-rebound N(omega)-hydroxy-L-arginine hydrolase with oxidized Cys86
分子名称: MAGNESIUM ION, MANGANESE (II) ION, N(omega)-hydroxy-L-arginine amidinohydrolase
著者Oda, K, Matoba, Y.
登録日2023-03-25
公開日2024-03-27
実験手法X-RAY DIFFRACTION (1.26 Å)
主引用文献Copper inactivates DcsB by oxidation of the Cys86 to cysteine sulfinic aicd
To Be Published
8IUV
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BU of 8iuv by Molmil
Crystal structure of Manganese-free N(omega)-hydroxy-L-arginine hydrolase with oxidized Cys86
分子名称: MAGNESIUM ION, MANGANESE (II) ION, N(omega)-hydroxy-L-arginine amidinohydrolase
著者Oda, K, Matoba, Y.
登録日2023-03-25
公開日2024-03-27
実験手法X-RAY DIFFRACTION (1.75 Å)
主引用文献Copper inactivates DcsB by oxidation of the Cys86 to cysteine sulfinic aicd
To Be Published
8IUW
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BU of 8iuw by Molmil
Crystal structure of Copper-bound N(omega)-hydroxy-L-arginine hydrolase with oxidized Cys86
分子名称: COPPER (I) ION, COPPER (II) ION, MAGNESIUM ION, ...
著者Oda, K, Matoba, Y.
登録日2023-03-25
公開日2024-03-27
実験手法X-RAY DIFFRACTION (1.5 Å)
主引用文献Copper inactivates DcsB by oxidation of the Cys86 to cysteine sulfinic aicd
To Be Published
7DC0
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BU of 7dc0 by Molmil
Crystal structure of glycan-free Pseudomonas taiwanensis lectin
分子名称: Lectin, SULFATE ION
著者Oda, K, Matoba, Y.
登録日2020-10-23
公開日2021-04-28
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (1.88 Å)
主引用文献Lectins engineered to favor a glycan-binding conformation have enhanced antiviral activity.
J.Biol.Chem., 296, 2021
7DC4
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BU of 7dc4 by Molmil
Crystal structure of glycan-bound Pseudomonas taiwanensis lectin
分子名称: Lectin, SULFATE ION, alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose
著者Oda, K, Matoba, Y.
登録日2020-10-23
公開日2021-04-28
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (0.95 Å)
主引用文献Lectins engineered to favor a glycan-binding conformation have enhanced antiviral activity.
J.Biol.Chem., 296, 2021
7CIT
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BU of 7cit by Molmil
Crystal structure of tyrosinase from Streptomyces castaneoglobisporus in complex with the caddie protein obtained by soaking in the solution containing Cu(II) and hydroxylamine for 24 h
分子名称: COPPER (II) ION, HYDROGEN PEROXIDE, MelC, ...
著者Oda, K, Matoba, Y.
登録日2020-07-08
公開日2021-06-16
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (1.5 Å)
主引用文献The basicity of an active-site water molecule discriminates between tyrosinase and catechol oxidase activity.
Int.J.Biol.Macromol., 183, 2021
7CIY
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BU of 7ciy by Molmil
Crystal structure of N191G-mutated tyrosinase from Streptomyces castaneoglobisporus in complex with the caddie protein obtained by soaking in the solution containing Cu(II) and hydroxylamine for 24 h
分子名称: COPPER (II) ION, HYDROGEN PEROXIDE, MelC, ...
著者Oda, K, Matoba, Y.
登録日2020-07-08
公開日2021-06-16
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (1.47 Å)
主引用文献The basicity of an active-site water molecule discriminates between tyrosinase and catechol oxidase activity.
Int.J.Biol.Macromol., 183, 2021
7VDY
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BU of 7vdy by Molmil
Crystal structure of O-ureidoserine racemase
分子名称: O-ureido-serine racemase, SULFATE ION
著者Oda, K, Matoba, Y.
登録日2021-09-07
公開日2021-12-15
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (2.12 Å)
主引用文献Crystal structure of O-ureidoserine racemase found in the d-cycloserine biosynthetic pathway.
Proteins, 90, 2022
7EUN
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BU of 7eun by Molmil
Crystal structure of N(omega)-hydroxy-L-arginine hydrolase in complex with ABH
分子名称: 2(S)-AMINO-6-BORONOHEXANOIC ACID, MAGNESIUM ION, MANGANESE (II) ION, ...
著者Oda, K, Matoba, Y.
登録日2021-05-18
公開日2022-05-18
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (1.28 Å)
主引用文献Catalytic mechanism of DcsB: Arginase framework used for hydrolyzing its inhibitor.
Protein Sci., 31, 2022
7EUQ
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BU of 7euq by Molmil
Crystal structure of C86H-Y124N-G126H-H196S mutant of N(omega)-hydroxy-L-arginine hydrolase
分子名称: MAGNESIUM ION, MANGANESE (II) ION, N(omega)-hydroxy-L-arginine amidinohydrolase
著者Oda, K, Matoba, Y.
登録日2021-05-18
公開日2022-05-18
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (1.8 Å)
主引用文献Catalytic mechanism of DcsB: Arginase framework used for hydrolyzing its inhibitor.
Protein Sci., 31, 2022
7EUL
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BU of 7eul by Molmil
Crystal structure of C86H-H196S mutant of N(omega)-hydroxy-L-arginine hydrolase
分子名称: MAGNESIUM ION, MANGANESE (II) ION, N(omega)-hydroxy-L-arginine amidinohydrolase
著者Oda, K, Matoba, Y.
登録日2021-05-18
公開日2022-05-18
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (1.45 Å)
主引用文献Catalytic mechanism of DcsB: Arginase framework used for hydrolyzing its inhibitor.
Protein Sci., 31, 2022
7EUK
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Crystal structure of N(omega)-hydroxy-L-arginine hydrolase in complex with L-Orn
分子名称: L-ornithine, MAGNESIUM ION, MANGANESE (II) ION, ...
著者Oda, K, Matoba, Y.
登録日2021-05-18
公開日2022-05-18
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (1.4 Å)
主引用文献Catalytic mechanism of DcsB: Arginase framework used for hydrolyzing its inhibitor.
Protein Sci., 31, 2022
3VX7
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BU of 3vx7 by Molmil
Crystal structure of Kluyveromyces marxianus Atg7NTD-Atg10 complex
分子名称: E1, E2
著者Yamaguchi, M, Matoba, K, Sawada, R, Fujioka, Y, Nakatogawa, H, Yamamoto, H, Kobashigawa, Y, Hoshida, H, Akada, R, Ohsumi, Y, Noda, N.N, Inagaki, F.
登録日2012-09-11
公開日2012-11-14
最終更新日2023-11-08
実験手法X-RAY DIFFRACTION (3.2 Å)
主引用文献Noncanonical recognition and UBL loading of distinct E2s by autophagy-essential Atg7.
Nat.Struct.Mol.Biol., 19, 2012
3VX6
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Crystal structure of Kluyveromyces marxianus Atg7NTD
分子名称: E1
著者Yamaguchi, M, Matoba, K, Sawada, R, Fujioka, Y, Nakatogawa, H, Yamamoto, H, Kobashigawa, Y, Hoshida, H, Akada, R, Ohsumi, Y, Noda, N.N, Inagaki, F.
登録日2012-09-11
公開日2012-11-14
最終更新日2023-11-08
実験手法X-RAY DIFFRACTION (2.6 Å)
主引用文献Noncanonical recognition and UBL loading of distinct E2s by autophagy-essential Atg7.
Nat.Struct.Mol.Biol., 19, 2012
3WJ4
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BU of 3wj4 by Molmil
Crystal structure of PPARgamma ligand binding domain in complex with tributyltin
分子名称: Peroxisome proliferator-activated receptor gamma, tributylstannanyl
著者Harada, S, Hiromori, Y, Fukakusa, S, Kawahara, K, Nakamura, S, Noda, M, Uchiyama, S, Fukui, K, Nishikawa, J, Nagase, H, Kobayashi, Y, Ohkubo, T, Yoshida, T, Nakanishi, T.
登録日2013-10-04
公開日2014-10-15
最終更新日2024-03-20
実験手法X-RAY DIFFRACTION (1.95 Å)
主引用文献Structural basis for PPARgamma transactivation by endocrine disrupting organotin compounds
To be Published
3WJ5
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Crystal structure of PPARgamma ligand binding domain in complex with triphenyltin
分子名称: Peroxisome proliferator-activated receptor gamma, triphenylstannanyl
著者Harada, S, Hiromori, Y, Fukakusa, S, Kawahara, K, Nakamura, S, Noda, M, Uchiyama, S, Fukui, K, Nishikawa, J, Nagase, H, Kobayashi, Y, Ohkubo, T, Yoshida, T, Nakanishi, T.
登録日2013-10-04
公開日2014-10-15
最終更新日2024-03-20
実験手法X-RAY DIFFRACTION (1.89 Å)
主引用文献Structural basis for PPARgamma transactivation by endocrine disrupting organotin compounds
To be Published
3VOR
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Crystal Structure Analysis of the CofA
分子名称: CFA/III pilin
著者Fukakusa, S, Kawahara, K, Nakamura, S, Iwasita, T, Baba, S, Nishimura, M, Kobayashi, Y, Honda, T, Iida, T, Taniguchi, T, Ohkubo, T.
登録日2012-02-06
公開日2012-09-26
最終更新日2013-07-31
実験手法X-RAY DIFFRACTION (0.9 Å)
主引用文献Structure of the CFA/III major pilin subunit CofA from human enterotoxigenic Escherichia coli determined at 0.90 A resolution by sulfur-SAD phasing
Acta Crystallogr.,Sect.D, 68, 2012

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