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PDB: 79 件
6IUE
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BU of 6iue by Molmil
DNA helical wire containing Hg(II)
分子名称: DNA (5'-D(*TP*TP*TP*GP*C)-3'), MERCURY (II) ION
著者Ono, A, Kanazawa, H, Ito, H, Goto, M, Nakamura, K, Saneyoshi, H, Kondo, J.
登録日2018-11-28
公開日2019-10-16
最終更新日2024-03-27
実験手法X-RAY DIFFRACTION (1.901 Å)
主引用文献A Novel DNA Helical Wire Containing HgII-Mediated T:T and T:G Pairs.
Angew.Chem.Int.Ed.Engl., 58, 2019
3AGU
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BU of 3agu by Molmil
Hemerythrin-like domain of DcrH (semimet-R)
分子名称: CHLORO DIIRON-OXO MOIETY, Hemerythrin-like domain protein DcrH
著者Onoda, A, Okamoto, Y, Sugimoto, H, Mizohata, E, Inoue, T, Shiro, Y, Hayashi, T.
登録日2010-04-06
公開日2011-04-06
最終更新日2023-11-01
実験手法X-RAY DIFFRACTION (1.805 Å)
主引用文献Characteristics of Diiron Site with Large Cavity in Hemerythrin-like Domain of DcrH
to be published
3AGT
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Hemerythrin-like domain of DcrH (met)
分子名称: CHLORO DIIRON-OXO MOIETY, Hemerythrin-like domain protein DcrH
著者Onoda, A, Okamoto, Y, Sugimoto, H, Mizohata, E, Inoue, T, Shiro, Y, Hayashi, T.
登録日2010-04-06
公開日2011-04-06
最終更新日2023-11-01
実験手法X-RAY DIFFRACTION (1.4 Å)
主引用文献Characteristics of Diiron Site with Large Cavity in Hemerythrin-like Domain of DcrH
to be published
456D
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BU of 456d by Molmil
MOLECULAR AND CRYSTAL STRUCTURE OF D(CGCGMO6AATCCGCG): THE WATSON-CRICK TYPE N6-METHOXYADENOSINE/CYTIDINE BASE-PAIRS IN B-DNA
分子名称: DNA (5'-D(*CP*GP*CP*GP*(A47)P*AP*TP*CP*CP*GP*CP*G)-3'), MAGNESIUM ION
著者Chatake, T, Ono, A, Ueno, Y, Matsuda, A, Takenaka, A.
登録日1999-03-06
公開日2000-01-01
最終更新日2023-12-27
実験手法X-RAY DIFFRACTION (1.6 Å)
主引用文献Crystallographic studies on damaged DNAs. I. An N(6)-methoxyadenine residue forms a Watson-Crick pair with a cytosine residue in a B-DNA duplex.
J.Mol.Biol., 294, 1999
5IX7
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Crystal structure of metallo-DNA nanowire with infinite one-dimensional silver array
分子名称: DNA (5'-D(*GP*GP*AP*CP*TP*(CBR)P*GP*AP*CP*TP*CP*C)-3'), POTASSIUM ION, SILVER ION
著者Kondo, J, Tada, Y, Dairaku, T, Hattori, Y, Saneyoshi, H, Ono, A, Tanaka, Y.
登録日2016-03-23
公開日2017-07-05
最終更新日2024-03-20
実験手法X-RAY DIFFRACTION (1.398 Å)
主引用文献A metallo-DNA nanowire with uninterrupted one-dimensional silver array
Nat Chem, 9, 2017
457D
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BU of 457d by Molmil
MOLECULAR AND CRYSTAL STRUCTURE OF D(CGCGMO6AATTCGCG): N6-METHOXYADENOSINE/ THYMIDINE BASE-PAIRS IN B-DNA
分子名称: DNA (5'-D(*CP*GP*CP*GP*(A47)P*AP*TP*TP*CP*GP*CP*G)-3'), MAGNESIUM ION
著者Chatake, T, Ono, A, Ueno, Y, Matsuda, A, Takenaka, A.
登録日1999-03-06
公開日2000-01-01
最終更新日2023-12-27
実験手法X-RAY DIFFRACTION (2 Å)
主引用文献Crystallographic studies on damaged DNAs. II. N(6)-methoxyadenine can present two alternate faces for Watson-Crick base-pairing, leading to pyrimidine transition mutagenesis.
J.Mol.Biol., 294, 1999
4INJ
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BU of 4inj by Molmil
Crystal structure of the S111A mutant of member of MccF clade from Listeria monocytogenes EGD-e with product
分子名称: DI(HYDROXYETHYL)ETHER, GLYCEROL, Lmo1638 protein, ...
著者Nocek, B, Tikhonov, A, Severinov, K, Joachimiak, A, Center for Structural Genomics of Infectious Diseases (CSGID)
登録日2013-01-04
公開日2013-02-20
最終更新日2023-09-20
実験手法X-RAY DIFFRACTION (2.4 Å)
主引用文献Crystal structure of the S111A mutant of member of MccF clade from Listeria monocytogenes EGD-e with product
To be Published
6IYQ
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BU of 6iyq by Molmil
Crystal structure of a DNA duplex cross-linked by 6-thioguanine-6-thioguanine disulfides
分子名称: DNA (5'-D(*CP*GP*CP*GP*AP*(S6G)P*(S6G)P*(BRU)P*CP*GP*CP*G)-3')
著者Kondo, J, Ono, A, Atsugi, T.
登録日2018-12-17
公開日2019-10-30
最終更新日2024-03-27
実験手法X-RAY DIFFRACTION (2.01 Å)
主引用文献Crystal structure of a DNA duplex cross-linked by 6-thioguanine-6-thioguanine disulfides: reversible formation and cleavage catalyzed by Cu(II) ion and glutathione
Rsc Adv, 2019
7EAY
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BU of 7eay by Molmil
DNA containing Cu(II)-mediated 4-N-carboxymethylcytosine base pairs
分子名称: COBALT (II) ION, COBALT HEXAMMINE(III), COPPER (II) ION, ...
著者Kondo, J, Terashima, A, Yoshimura, A, Tada, Y, Ono, A.
登録日2021-03-08
公開日2022-03-09
最終更新日2024-05-29
実験手法X-RAY DIFFRACTION (2.5 Å)
主引用文献DNA containing Cu(II)-mediated 4-N-carboxymethylcytosine base pairs
To Be Published
5XUV
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Crystal structure of DNA duplex containing 4-thiothymine-2Ag(I)-4-thiothymine base pairs
分子名称: DNA (5'-D(*CP*GP*CP*GP*AP*(8RO)P*(8RO)P*TP*CP*GP*CP*G)-3'), POTASSIUM ION, SILVER ION
著者Kondo, J, Sugawara, T, Saneyoshi, H, Ono, A.
登録日2017-06-26
公開日2017-09-20
最終更新日2023-11-22
実験手法X-RAY DIFFRACTION (1.9 Å)
主引用文献Crystal structure of a DNA duplex containing four Ag(i) ions in consecutive dinuclear Ag(i)-mediated base pairs: 4-thiothymine-2Ag(i)-4-thiothymine
Chem. Commun. (Camb.), 53, 2017
5AY4
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Crystal structure of RNA duplex containing C-C base pairs obtained in the presence of Hg(II)
分子名称: RNA (5'-R(*GP*GP*AP*CP*UP*(CBR)P*GP*AP*CP*UP*CP*C)-3'), SODIUM ION
著者Kondo, J, Tada, Y, Dairaku, T, Saneyoshi, H, Okamoto, I, Tanaka, Y, Ono, A.
登録日2015-08-06
公開日2015-10-21
最終更新日2023-11-08
実験手法X-RAY DIFFRACTION (1.7 Å)
主引用文献High-Resolution Crystal Structure of a Silver(I)-RNA Hybrid Duplex Containing Watson-Crick-like CSilver(I)C Metallo-Base Pairs
Angew.Chem.Int.Ed.Engl., 54, 2015
1VE8
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X-Ray analyses of oligonucleotides containing 5-formylcytosine, suggesting a structural reason for codon-anticodon recognition of mitochondrial tRNA-Met; Part 1, d(CGCGAATT(f5C)GCG)
分子名称: 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(5FC)P*GP*CP*G)-3', SODIUM ION
著者Kimura, K, Ono, A, Watanabe, K, Takenaka, A.
登録日2004-03-29
公開日2005-06-28
最終更新日2023-12-27
実験手法X-RAY DIFFRACTION (1.65 Å)
主引用文献X-Ray analyses of oligonucleotides containing 5-formylcytosine, suggest a structural reason for the codon-anticodon recognition of mitochondrial tRNA-Met
To be Published
5AY2
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Crystal structure of RNA duplex containing C-Ag(I)-C base pairs
分子名称: RNA (5'-R(*GP*GP*AP*CP*UP*(CBR)P*GP*AP*CP*UP*CP*C)-3'), SILVER ION
著者Kondo, J, Tada, Y, Dairaku, T, Saneyoshi, H, Okamoto, I, Tanaka, Y, Ono, A.
登録日2015-08-06
公開日2015-10-21
最終更新日2024-03-20
実験手法X-RAY DIFFRACTION (1.3 Å)
主引用文献High-Resolution Crystal Structure of a Silver(I)-RNA Hybrid Duplex Containing Watson-Crick-like CSilver(I)C Metallo-Base Pairs
Angew.Chem.Int.Ed.Engl., 54, 2015
5AY3
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Crystal structure of RNA duplex containing C-C base pairs
分子名称: RNA (5'-R(*GP*GP*AP*CP*UP*(CBR)P*GP*A*CP*UP*CP*C)-3')
著者Kondo, J, Tada, Y, Dairaku, T, Saneyoshi, H, Okamoto, I, Tanaka, Y, Ono, A.
登録日2015-08-06
公開日2015-10-21
最終更新日2024-03-20
実験手法X-RAY DIFFRACTION (1.2 Å)
主引用文献High-Resolution Crystal Structure of a Silver(I)-RNA Hybrid Duplex Containing Watson-Crick-like CSilver(I)C Metallo-Base Pairs
Angew.Chem.Int.Ed.Engl., 54, 2015
7C0E
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BU of 7c0e by Molmil
Crystal structure of Azospirillum brasilense L-2-keto-3-deoxyarabonate dehydratase (2-oxobutyrate-bound form)
分子名称: L-2-keto-3-deoxyarabonate dehydratase
著者Watanabe, Y, Ono, A, Watanabe, S.
登録日2020-05-01
公開日2020-08-05
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (2.204 Å)
主引用文献Biochemical and Structural Characterization of l-2-Keto-3-deoxyarabinonate Dehydratase: A Unique Catalytic Mechanism in the Class I Aldolase Protein Superfamily.
Biochemistry, 59, 2020
7XKM
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BU of 7xkm by Molmil
Crystal structure of DNA-Ag(I) rod comprising a one-dimensional array of 11 silver ions
分子名称: DNA (5'-D(*CP*GP*CP*GP*CP*(BRU)P*CP*(BRU)P*CP*GP*CP*G)-3'), SILVER ION
著者Kondo, J, Ono, A, Atsugi, T.
登録日2022-04-20
公開日2022-07-06
最終更新日2024-05-29
実験手法X-RAY DIFFRACTION (2.79 Å)
主引用文献A Novel Ag I -DNA Rod Comprising a One-Dimensional Array of 11 Silver Ions within a Double Helical Structure.
Angew.Chem.Int.Ed.Engl., 61, 2022
4L24
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Crystal structure of metallo-DNA duplex containing consecutive T-Hg(II)-T base pairs
分子名称: DNA (5'-D(*CP*GP*CP*GP*AP*TP*TP*TP*CP*GP*CP*G)-3'), MERCURY (II) ION
著者Kondo, J, Yamada, T, Hirose, C, Okamoto, I, Tanaka, Y, Ono, A.
登録日2013-06-04
公開日2014-03-05
最終更新日2023-11-08
実験手法X-RAY DIFFRACTION (2.7 Å)
主引用文献Crystal Structure of Metallo DNA Duplex Containing Consecutive Watson-Crick-like T-Hg(II) -T Base Pairs
Angew.Chem.Int.Ed.Engl., 53, 2014
4L26
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Crystal structure of DNA duplex containing consecutive T-T mispairs (Br-derivative)
分子名称: DNA (5'-D(*CP*GP*(CBR)P*GP*AP*TP*TP*TP*CP*GP*CP*G)-3')
著者Kondo, J, Yamada, T, Hirose, C, Tanaka, Y, Ono, A.
登録日2013-06-04
公開日2014-03-05
最終更新日2024-03-20
実験手法X-RAY DIFFRACTION (1.4 Å)
主引用文献Crystal Structure of Metallo DNA Duplex Containing Consecutive Watson-Crick-like T-Hg(II) -T Base Pairs
Angew.Chem.Int.Ed.Engl., 53, 2014
4L25
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Crystal structure of DNA duplex containing consecutive T-T mispairs
分子名称: DNA (5'-D(*CP*GP*CP*GP*AP*TP*TP*TP*CP*GP*CP*G)-3')
著者Kondo, J, Yamada, T, Hirose, C, Tanaka, Y, Ono, A.
登録日2013-06-04
公開日2014-03-05
最終更新日2023-11-08
実験手法X-RAY DIFFRACTION (1.1 Å)
主引用文献Crystal Structure of Metallo DNA Duplex Containing Consecutive Watson-Crick-like T-Hg(II) -T Base Pairs
Angew.Chem.Int.Ed.Engl., 53, 2014
1EDR
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BU of 1edr by Molmil
MOLECULAR AND CRYSTAL STRUCTURE OF D(CGCGMO6AATTCGCG) AT 1.6 ANGSTROM
分子名称: 5'-D(*CP*GP*CP*GP*(A47)AP*AP*TP*TP*CP*GP*CP*G)-3', MAGNESIUM ION, SPERMINE
著者Chatake, T, Hikima, T, Ono, A, Ueno, Y, Matsuda, A, Takenaka, A.
登録日2000-01-28
公開日2000-02-16
最終更新日2024-02-07
実験手法X-RAY DIFFRACTION (1.6 Å)
主引用文献Crystallographic studies on damaged DNAs. II. N(6)-methoxyadenine can present two alternate faces for Watson-Crick base-pairing, leading to pyrimidine transition mutagenesis.
J.Mol.Biol., 294, 1999
1DUF
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BU of 1duf by Molmil
THE NMR STRUCTURE OF DNA DODECAMER DETERMINED IN AQUEOUS DILUTE LIQUID CRYSTALLINE PHASE
分子名称: DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')
著者Tjandra, N, Tate, S, Ono, A, Kainosho, M, Bax, A.
登録日2000-01-17
公開日2000-07-14
最終更新日2024-05-22
実験手法SOLUTION NMR
主引用文献The NMR Structure of a DNA Dodecamer in an Aqueous Dilute Liquid Crystalline Phase
J.Am.Chem.Soc., 122, 2000
2RT8
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Structure of metallo-dna in solution
分子名称: DNA (5'-D(*CP*GP*CP*GP*TP*TP*GP*TP*CP*C)-3'), DNA (5'-D(*GP*GP*AP*CP*TP*TP*CP*GP*CP*G)-3'), MERCURY (II) ION
著者Yamaguchi, H, Sebera, J, Kondo, J, Oda, S, Komuro, T, Kawamura, T, Dairaku, T, Kondo, Y, Okamoto, I, Ono, A, Burda, J.V, Kojima, C, Sychrovsky, V, Tanaka, Y.
登録日2013-06-18
公開日2014-03-05
最終更新日2024-05-15
実験手法SOLUTION NMR
主引用文献The structure of metallo-DNA with consecutive thymine-HgII-thymine base pairs explains positive entropy for the metallo base pair formation.
Nucleic Acids Res., 42, 2014
2RVP
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Solution structure of DNA Containing Metallo-Base-Pair
分子名称: DNA (5'-D(*TP*AP*AP*TP*AP*TP*AP*CP*TP*TP*AP*AP*TP*TP*A)-3'), DNA (5'-D(*TP*AP*AP*TP*TP*AP*AP*CP*TP*AP*TP*AP*TP*TP*A)-3'), SILVER ION
著者Dairaku, T, Furuita, K, Sato, H, Sebera, J, Nakashima, K, Kondo, J, Yamanaka, D, Kondo, Y, Okamoto, I, Ono, A, Sychrovsky, V, Kojima, C, Tanaka, Y.
登録日2016-03-22
公開日2016-08-31
最終更新日2024-05-15
実験手法SOLUTION NMR
主引用文献Structure Determination of an Ag(I) -Mediated Cytosine-Cytosine Base Pair within DNA Duplex in Solution with (1) H/(15) N/(109) Ag NMR Spectroscopy.
Chemistry, 22, 2016
5KP0
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Recognition and targeting mechanisms by chaperones in flagella assembly and operation
分子名称: Flagellar protein FliT,Flagellum-specific ATP synthase
著者Khanra, N.K, Rossi, P, Economou, A, Kalodimos, C.G.
登録日2016-07-01
公開日2016-08-17
最終更新日2024-05-15
実験手法SOLUTION NMR
主引用文献Recognition and targeting mechanisms by chaperones in flagellum assembly and operation.
Proc.Natl.Acad.Sci.USA, 113, 2016
8G62
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Papain-Like Protease of SARS CoV-2 in complex with remodilin NCGC 390004
分子名称: 3-methoxy-5-(1-methylpiperidin-4-yl)-N-[4-(pyrrolidine-1-sulfonyl)phenyl]benzamide, ACETATE ION, CHLORIDE ION, ...
著者Osipiuk, J, Tesar, C, Endres, M, Jedrzejczak, R, Luci, D, Kales, S, Simeonov, A, Rai, G, Drayman, N, Tay, S, Oakes, S, Rosner, M, Chen, B, Dulin, N, Solway, J, Joachimiak, A, Center for Structural Genomics of Infectious Diseases (CSGID), Center for Structural Biology of Infectious Diseases (CSBID)
登録日2023-02-14
公開日2023-02-22
最終更新日2024-05-22
実験手法X-RAY DIFFRACTION (2.17 Å)
主引用文献Papain-Like Protease of SARS CoV-2 in complex with remodilin NCGC 390004
To Be Published

 

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