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PDB: 121 件
3BNP
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Crystal Structure of the Homo sapiens Mitochondrial Ribosomal Decoding Site (A1555G Mutant)
分子名称: A site of human mitochondrial ribosome, A chain, B chain, ...
著者Kondo, J, Westhof, E.
登録日2007-12-14
公開日2008-06-24
最終更新日2024-02-21
実験手法X-RAY DIFFRACTION (2.7 Å)
主引用文献The bacterial and mitochondrial ribosomal A-site molecular switches possess different conformational substates
Nucleic Acids Res., 36, 2008
3BNT
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BU of 3bnt by Molmil
Crystal Structure of the Homo sapiens Mitochondrial Ribosomal Decoding Site in the Presence of [Co(NH3)6]Cl3 (A1555G mutant, Br-derivative)
分子名称: A site of human mitochondrial ribosome, COBALT HEXAMMINE(III), SODIUM ION
著者Kondo, J, Westhof, E.
登録日2007-12-14
公開日2008-06-24
最終更新日2024-02-21
実験手法X-RAY DIFFRACTION (2.3 Å)
主引用文献The bacterial and mitochondrial ribosomal A-site molecular switches possess different conformational substates
Nucleic Acids Res., 36, 2008
3BNN
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BU of 3bnn by Molmil
Crystal Structure of the Homo sapiens Mitochondrial Ribosomal Decoding Site
分子名称: A site of human ribosome
著者Kondo, J, Westhof, E.
登録日2007-12-14
公開日2008-06-24
最終更新日2024-02-21
実験手法X-RAY DIFFRACTION (2 Å)
主引用文献The bacterial and mitochondrial ribosomal A-site molecular switches possess different conformational substates
Nucleic Acids Res., 36, 2008
3BNS
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BU of 3bns by Molmil
Crystal Structure of the Homo sapiens Mitochondrial Ribosomal Decoding Site (A1555G mutant, Br-derivative)
分子名称: A site of human mitochondrial ribosome, chain three, chain two, ...
著者Kondo, J, Westhof, E.
登録日2007-12-14
公開日2008-06-24
最終更新日2024-02-21
実験手法X-RAY DIFFRACTION (1.9 Å)
主引用文献The bacterial and mitochondrial ribosomal A-site molecular switches possess different conformational substates
Nucleic Acids Res., 36, 2008
3BNR
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BU of 3bnr by Molmil
Crystal Structure of the Homo sapiens Mitochondrial Ribosomal Decoding Site in the presence of nonspecifically bound paromomycin (A1555G mutant, Br-derivative)
分子名称: A site of human mitochondrial ribosome, chain one, chain three, ...
著者Kondo, J, Westhof, E.
登録日2007-12-14
公開日2008-06-24
最終更新日2024-02-21
実験手法X-RAY DIFFRACTION (2.1 Å)
主引用文献The bacterial and mitochondrial ribosomal A-site molecular switches possess different conformational substates
Nucleic Acids Res., 36, 2008
3BNO
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BU of 3bno by Molmil
Crystal Structure of the Homo sapiens Mitochondrial Ribosomal Decoding Site (Br-derivative)
分子名称: A site of human mitochondrial ribosome
著者Kondo, J, Westhof, E.
登録日2007-12-14
公開日2008-06-24
最終更新日2024-02-21
実験手法X-RAY DIFFRACTION (2.35 Å)
主引用文献The bacterial and mitochondrial ribosomal A-site molecular switches possess different conformational substates
Nucleic Acids Res., 36, 2008
3BNL
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BU of 3bnl by Molmil
Crystal structure of the bacterial ribosomal decoding A site in the presence of [Co(NH3)6]Cl3
分子名称: A site of bacterial ribosome, COBALT HEXAMMINE(III)
著者Kondo, J, Westhof, E.
登録日2007-12-14
公開日2008-06-24
最終更新日2024-02-21
実験手法X-RAY DIFFRACTION (2.602 Å)
主引用文献The bacterial and mitochondrial ribosomal A-site molecular switches possess different conformational substates
Nucleic Acids Res., 36, 2008
3BNQ
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BU of 3bnq by Molmil
Crystal Structure of the Homo sapiens Mitochondrial Ribosomal Decoding Site in the Presence of SrCl2 (A1555G mutant, Br-derivative)
分子名称: A site of human mitochondrial ribosome, A chain, B chain, ...
著者Kondo, J, Westhof, E.
登録日2007-12-14
公開日2008-06-24
最終更新日2024-02-21
実験手法X-RAY DIFFRACTION (2 Å)
主引用文献The bacterial and mitochondrial ribosomal A-site molecular switches possess different conformational substates
Nucleic Acids Res., 36, 2008
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
6JR4
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BU of 6jr4 by Molmil
Crystal structure of a NIR-emitting DNA-stabilized Ag16 nanocluster
分子名称: CALCIUM ION, DNA (5'-D(*CP*AP*CP*CP*TP*AP*GP*CP*GP*A)-3'), SILVER ION
著者Kondo, J, Cerretani, C, Kanazawa, H, Vosch, T.
登録日2019-04-02
公開日2019-08-28
最終更新日2024-03-27
実験手法X-RAY DIFFRACTION (1.798 Å)
主引用文献Crystal structure of a NIR-Emitting DNA-Stabilized Ag16Nanocluster.
Angew.Chem.Int.Ed.Engl., 58, 2019
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
7XLW
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BU of 7xlw by Molmil
Crystal structure of a NIR-emitting DNA-stabilized Ag16 nanocluster (G7I/G9I mutant)
分子名称: DNA (5'-D(*CP*AP*CP*CP*TP*AP*IP*CP*IP*A)-3'), SILVER ION
著者Kondo, J, Cerretani, C, Vosch, T.
登録日2022-04-23
公開日2022-07-13
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (1.89 Å)
主引用文献The effect of inosine on the spectroscopic properties and crystal structure of a NIR-emitting DNA-stabilized silver nanocluster.
Nanoscale Adv, 4, 2022
7XLV
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BU of 7xlv by Molmil
Crystal structure of a NIR-emitting DNA-stabilized Ag16 nanocluster (G7I mutant)
分子名称: (4S)-2-METHYL-2,4-PENTANEDIOL, DNA (5'-D(*CP*AP*CP*CP*TP*AP*IP*CP*GP*A)-3'), SILVER ION
著者Kondo, J, Cerretani, C, Vosch, T.
登録日2022-04-23
公開日2022-07-13
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (1.1 Å)
主引用文献The effect of inosine on the spectroscopic properties and crystal structure of a NIR-emitting DNA-stabilized silver nanocluster.
Nanoscale Adv, 4, 2022
7Y8P
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BU of 7y8p by Molmil
Crystal structure of 4'-selenoRNA duplex
分子名称: COBALT HEXAMMINE(III), RNA (5'-R(*GP*GP*AP*(IKS)P*(ILK)P*(IKS)P*GP*AP*GP*UP*CP*C)-3')
著者Kondo, J, Minakawa, N, Ohta, M, Takahashi, H, Tarashima, N.
登録日2022-06-24
公開日2023-05-03
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (1.5 Å)
主引用文献Synthesis and properties of fully-modified 4'-selenoRNA, an endonuclease-resistant RNA analog.
Bioorg.Med.Chem., 76, 2022
7YGP
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BU of 7ygp by Molmil
DNA duplex containing 5OHU-T base pairs
分子名称: COBALT (II) ION, COBALT HEXAMMINE(III), DNA (5'-D(*GP*GP*AP*CP*CP*TP*(OHU)P*GP*GP*TP*CP*C)-3')
著者Kondo, J, Torigoe, H, Arakawa, F.
登録日2022-07-12
公開日2023-05-24
最終更新日2024-05-29
実験手法X-RAY DIFFRACTION (1.997 Å)
主引用文献Specific binding of Hg 2+ to mismatched base pairs involving 5-hydroxyuracil in duplex DNA.
J.Inorg.Biochem., 241, 2023
7YGO
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BU of 7ygo by Molmil
DNA duplex containing 5OHU-Hg(II)-T base pairs
分子名称: DNA (5'-D(*GP*GP*AP*CP*CP*TP*(6HU)P*GP*GP*TP*CP*C)-3'), MERCURY (II) ION
著者Kondo, J, Torigoe, H, Arakawa, F.
登録日2022-07-12
公開日2023-05-24
最終更新日2024-05-29
実験手法X-RAY DIFFRACTION (2.403 Å)
主引用文献Specific binding of Hg 2+ to mismatched base pairs involving 5-hydroxyuracil in duplex DNA.
J.Inorg.Biochem., 241, 2023
7YVX
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BU of 7yvx by Molmil
Left-handed DNA duplex containing consecutive G-G base pairs
分子名称: COBALT (II) ION, DNA (5'-D(*CP*GP*(CBR)P*GP*GP*GP*CP*GP*CP*G)-3')
著者Kondo, J.
登録日2022-08-19
公開日2022-10-12
最終更新日2024-05-29
実験手法X-RAY DIFFRACTION (2.99 Å)
主引用文献Left-handed DNA duplex containing consecutive G-G base pairs
To Be Published
5XUV
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BU of 5xuv by Molmil
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
1UHY
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BU of 1uhy by Molmil
Crystal structure of d(GCGATAGC): the base-intercalated duplex
分子名称: 5'-D(*GP*(CBR)P*GP*AP*TP*AP*GP*C)-3', CHLORIDE ION, COBALT HEXAMMINE(III), ...
著者Kondo, J, Umeda, S.I, Fujita, K, Sunami, T, Takenaka, A.
登録日2003-07-13
公開日2004-02-03
最終更新日2023-12-27
実験手法X-RAY DIFFRACTION (1.7 Å)
主引用文献X-ray analyses of d(GCGAXAGC) containing G and T at X: the base-intercalated duplex is still stable even in point mutants at the fifth residue.
J.Synchrotron Radiat., 11, 2004
1UHX
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BU of 1uhx by Molmil
Crystal structure of d(GCGAGAGC): the base-intercalated duplex
分子名称: 5'-D(*GP*(CBR)P*GP*AP*GP*AP*GP*C)-3', CHLORIDE ION, COBALT HEXAMMINE(III), ...
著者Kondo, J, Umeda, S.I, Fujita, K, Sunami, T, Takenaka, A.
登録日2003-07-13
公開日2004-02-03
最終更新日2023-12-27
実験手法X-RAY DIFFRACTION (2 Å)
主引用文献X-ray analyses of d(GCGAXAGC) containing G and T at X: the base-intercalated duplex is still stable even in point mutants at the fifth residue.
J.Synchrotron Radiat., 11, 2004
4P3U
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BU of 4p3u by Molmil
Crystal structure of the bacterial A1408U-mutant ribosomal decoding site (C2 form 1)
分子名称: 5'-R(*UP*UP*GP*CP*GP*UP*CP*UP*CP*GP*(5BU)P*CP*GP*AP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3'
著者Kondo, J, Koganei, M.
登録日2014-03-10
公開日2016-05-04
最終更新日2023-12-27
実験手法X-RAY DIFFRACTION (3 Å)
主引用文献Crystal structure of the bacterial A1408U-mutant ribosomal decoding site (C2 form 1)
To Be Published
4P3S
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Crystal structure of the bacterial A1408C-mutant ribosomal decoding site in complex with geneticin
分子名称: 5'-R(*UP*UP*GP*CP*GP*UP*CP*CP*CP*GP*(5BU)P*CP*GP*AP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3', GENETICIN
著者Kondo, J, Koganei, M.
登録日2014-03-10
公開日2016-05-04
最終更新日2023-12-27
実験手法X-RAY DIFFRACTION (2.3 Å)
主引用文献Crystal structure of the bacterial A1408C-mutant ribosomal decoding site in complex with geneticin
To Be Published
4P3T
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BU of 4p3t by Molmil
Crystal structure of the bacterial A1408C-mutant ribosomal decoding site
分子名称: 5'-D(*UP*UP*GP*CP*GP*UP*CP*CP*CP*GP*(5BU)P*CP*GP*AP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3'
著者Kondo, J, Koganei, M.
登録日2014-03-10
公開日2016-05-04
最終更新日2023-12-27
実験手法X-RAY DIFFRACTION (1.6 Å)
主引用文献Crystal structure of the bacterial A1408C-mutant ribosomal decoding site
To Be Published
4P43
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Crystal structure of the bacterial A1408U-mutant ribosomal decoding site (C2 form 2)
分子名称: 5'-R(*UP*UP*GP*CP*GP*UP*CP*UP*CP*GP*UP*CP*GP*AP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3', CALCIUM ION, SODIUM ION
著者Kondo, J, Koganei, M.
登録日2014-03-11
公開日2016-05-04
最終更新日2023-12-27
実験手法X-RAY DIFFRACTION (2 Å)
主引用文献Crystal structure of the bacterial A1408U-mutant ribosomal decoding site (C2 form 2)
To Be Published
4P20
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Crystal structures of the bacterial ribosomal decoding site complexed with amikacin
分子名称: (2S)-N-[(1R,2S,3S,4R,5S)-4-[(2R,3R,4S,5S,6R)-6-(aminomethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-5-azanyl-2-[(2S,3R,4S,5S ,6R)-4-azanyl-6-(hydroxymethyl)-3,5-bis(oxidanyl)oxan-2-yl]oxy-3-oxidanyl-cyclohexyl]-4-azanyl-2-oxidanyl-butanamide, 5'-R(*UP*UP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*C)-3'
著者Kondo, J, Francois, B, Russell, R.J.M, Murray, J.B, Westhof, E.
登録日2014-02-28
公開日2014-05-07
最終更新日2023-12-27
実験手法X-RAY DIFFRACTION (2.7 Å)
主引用文献Crystal structure of the bacterial ribosomal decoding site complexed with amikacin containing the gamma-amino-alpha-hydroxybutyryl (haba) group.
Biochimie, 88, 2006

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