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PDB: 20 件
6ADV
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Crystal Structure Analysis of the duplex containing the S2T(2',4'-BNA/LNA)G mismatch pairs
分子名称: 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(9V9)P*GP*CP*G)-3'
著者Aoyama, H.A, Habuchi, T.H, Yamaguchi, T.Y, Obika, S.O.
登録日2018-08-02
公開日2019-03-27
最終更新日2023-11-22
実験手法X-RAY DIFFRACTION (1.96 Å)
主引用文献Hybridization and Mismatch Discrimination Abilities of 2',4'-Bridged Nucleic Acids Bearing 2-Thiothymine or 2-Selenothymine Nucleobase.
J. Org. Chem., 84, 2019
6LBW
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Crystal structure of Ag-mediated base pairs in uncanonical DNA duplex
分子名称: DNA (5'-D(*CP*GP*(CBR)P*GP*AP*(LCC)P*TP*CP*GP*CP*G)-3'), SILVER ION
著者Aoyama, H, Obika, S, Nakagawa, O.
登録日2019-11-15
公開日2020-11-18
最終更新日2024-03-27
実験手法X-RAY DIFFRACTION (1.501 Å)
主引用文献Crystallographic Structure of Novel Types of Ag I -Mediated Base Pairs in Non-canonical DNA Duplex Containing 2'-O,4'-C-Methylene Bridged Nucleic Acids.
Chemistry, 27, 2021
8HIS
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BU of 8his by Molmil
Crystal structure of DNA decamer containing GuNA[Me,tBu]
分子名称: CACODYLIC ACID, DNA (5'-D(*GP*CP*GP*TP*AP*(LR6)P*AP*CP*GP*C)-3')
著者Aoyama, H, Obika, S, Yamaguchi, T.
登録日2022-11-21
公開日2023-08-09
最終更新日2023-09-06
実験手法X-RAY DIFFRACTION (2.01 Å)
主引用文献Mechanism of the extremely high duplex-forming ability of oligonucleotides modified with N-tert-butylguanidine- or N-tert-butyl-N'- methylguanidine-bridged nucleic acids.
Nucleic Acids Res., 51, 2023
8I50
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Crystal structure of DNA octamer containing GuNA[Me,Me]
分子名称: DNA (5'-D(*GP*(OIQ)P*GP*(BRU)P*AP*CP*AP*C)-3')
著者Aoyama, H, Obika, S, Yamaguchi, T.
登録日2023-01-21
公開日2023-08-09
最終更新日2023-09-06
実験手法X-RAY DIFFRACTION (0.95 Å)
主引用文献Mechanism of the extremely high duplex-forming ability of oligonucleotides modified with N-tert-butylguanidine- or N-tert-butyl-N'- methylguanidine-bridged nucleic acids.
Nucleic Acids Res., 51, 2023
8HU5
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BU of 8hu5 by Molmil
Crystal structure of DNA octamer containing GuNA[Me,tBu]
分子名称: DNA (5'-D(*GP*(LR6)P*GP*(BRU)P*AP*CP*AP*C)-3')
著者Aoyama, H, Obika, H, Yamaguchi, T.
登録日2022-12-22
公開日2023-08-09
最終更新日2023-09-06
実験手法X-RAY DIFFRACTION (0.93 Å)
主引用文献Mechanism of the extremely high duplex-forming ability of oligonucleotides modified with N-tert-butylguanidine- or N-tert-butyl-N'- methylguanidine-bridged nucleic acids.
Nucleic Acids Res., 51, 2023
3ABM
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BU of 3abm by Molmil
Bovine heart cytochrome c oxidase at the fully oxidized state (200-s X-ray exposure dataset)
分子名称: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE, (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE, (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE, ...
著者Aoyama, H, Muramoto, K, Shinzawa-Itoh, K, Yamashita, E, Tsukihara, T, Ogura, T, Yoshikawa, S.
登録日2009-12-16
公開日2010-01-19
最終更新日2023-11-01
実験手法X-RAY DIFFRACTION (1.95 Å)
主引用文献A peroxide bridge between Fe and Cu ions in the O2 reduction site of fully oxidized cytochrome c oxidase could suppress the proton pump
Proc.Natl.Acad.Sci.USA, 106, 2009
2ZXW
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BU of 2zxw by Molmil
Bovine heart cytochrome c oxidase at the fully oxidized state (1-s X-ray exposure dataset)
分子名称: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE, (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE, (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE, ...
著者Aoyama, H, Muramoto, K, Shinzawa-Itoh, K, Hirata, K, Yamashita, E, Tsukihara, T, Ogura, T, Yoshikawa, S.
登録日2009-01-08
公開日2009-02-24
最終更新日2023-11-01
実験手法X-RAY DIFFRACTION (2.5 Å)
主引用文献A peroxide bridge between Fe and Cu ions in the O2 reduction site of fully oxidized cytochrome c oxidase could suppress the proton pump
Proc.Natl.Acad.Sci.USA, 106, 2009
3ABL
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BU of 3abl by Molmil
Bovine heart cytochrome c oxidase at the fully oxidized state (15-s X-ray exposure dataset)
分子名称: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE, (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE, (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE, ...
著者Aoyama, H, Muramoto, K, Shinzawa-Itoh, K, Yamashita, E, Tsukihara, T, Ogura, T, Yoshikawa, S.
登録日2009-12-16
公開日2010-01-19
最終更新日2023-11-01
実験手法X-RAY DIFFRACTION (2.1 Å)
主引用文献A peroxide bridge between Fe and Cu ions in the O2 reduction site of fully oxidized cytochrome c oxidase could suppress the proton pump
Proc.Natl.Acad.Sci.USA, 106, 2009
1OCC
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BU of 1occ by Molmil
STRUCTURE OF BOVINE HEART CYTOCHROME C OXIDASE AT THE FULLY OXIDIZED STATE
分子名称: COPPER (II) ION, CYTOCHROME C OXIDASE, HEME-A, ...
著者Tsukihara, T, Aoyama, H, Yamashita, E, Tomizaki, T, Yamaguchi, H, Shinzawa-Itoh, K, Nakashima, R, Yaono, R, Yoshikawa, S.
登録日1996-04-18
公開日1996-12-07
最終更新日2018-03-21
実験手法X-RAY DIFFRACTION (2.8 Å)
主引用文献The whole structure of the 13-subunit oxidized cytochrome c oxidase at 2.8 A.
Science, 272, 1996
1V55
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BU of 1v55 by Molmil
Bovine heart cytochrome c oxidase at the fully reduced state
分子名称: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE, (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE, (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE, ...
著者Tsukihara, T, Shimokata, K, Katayama, Y, Shimada, H, Muramoto, K, Aoyama, H, Mochizuki, M, Shinzawa-Itoh, K, Yamashita, E, Yao, M, Ishimura, Y, Yoshikawa, S.
登録日2003-11-21
公開日2003-12-23
最終更新日2023-12-20
実験手法X-RAY DIFFRACTION (1.9 Å)
主引用文献The low-spin heme of cytochrome c oxidase as the driving element of the proton-pumping process.
Proc.Natl.Acad.Sci.Usa, 100, 2003
1V54
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BU of 1v54 by Molmil
Bovine heart cytochrome c oxidase at the fully oxidized state
分子名称: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE, (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE, (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE, ...
著者Tsukihara, T, Shimokata, K, Katayama, Y, Shimada, H, Muramoto, K, Aoyama, H, Mochizuki, M, Shinzawa-Itoh, K, Yamashita, E, Yao, M, Ishimura, Y, Yoshikawa, S.
登録日2003-11-21
公開日2003-12-23
最終更新日2023-12-27
実験手法X-RAY DIFFRACTION (1.8 Å)
主引用文献The low-spin heme of cytochrome c oxidase as the driving element of the proton-pumping process.
Proc.Natl.Acad.Sci.Usa, 100, 2003
5AXE
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BU of 5axe by Molmil
Crystal Structure Analysis of DNA Duplexes containing sulfoamide-bridged nucleic acid (SuNA-NH)
分子名称: DNA (5'-D(*GP*CP*GP*TP*AP*(LSH)P*AP*CP*GP*C)-3')
著者Mitsuoka, Y, Aoyama, H, Kugimiya, A, Fujimura, Y, Yamamoto, T, Waki, R, Wada, F, Tahara, S, Sawamura, M, Noda, M, Hari, Y, Obika, S.
登録日2015-07-28
公開日2016-07-20
最終更新日2023-11-08
実験手法X-RAY DIFFRACTION (0.95 Å)
主引用文献Effect of an N-substituent in sulfonamide-bridged nucleic acid (SuNA) on hybridization ability and duplex structure.
Org.Biomol.Chem., 14, 2016
5AXF
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Crystal Structure Analysis of DNA Duplexes containing sulfoamide-bridged nucleic acid (SuNA-NMe)
分子名称: DNA (5'-D(*GP*CP*GP*TP*AP*(LSM)P*AP*CP*GP*C)-3')
著者Mitsuoka, Y, Aoyama, H, Kugimiya, A, Fujimura, Y, Yamamoto, T, Waki, R, Wada, F, Tahara, S, Sawamura, M, Noda, M, Hari, Y, Obika, S.
登録日2015-07-28
公開日2016-07-20
最終更新日2024-03-20
実験手法X-RAY DIFFRACTION (1.13 Å)
主引用文献Effect of an N-substituent in sulfonamide-bridged nucleic acid (SuNA) on hybridization ability and duplex structure.
Org.Biomol.Chem., 14, 2016
2EIL
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BU of 2eil by Molmil
Cadmium ion binding structure of bovine heart cytochrome C oxidase in the fully oxidized state
分子名称: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE, (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE, (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE, ...
著者Muramoto, K, Hirata, K, Shinzawa-Itoh, K, Yoko-o, S, Yamashita, E, Aoyama, H, Tsukihara, T, Yoshikawa, S.
登録日2007-03-13
公開日2007-05-29
最終更新日2023-10-25
実験手法X-RAY DIFFRACTION (2.1 Å)
主引用文献A histidine residue acting as a controlling site for dioxygen reduction and proton pumping by cytochrome c oxidase
Proc.Natl.Acad.Sci.Usa, 104, 2007
2DYR
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BU of 2dyr by Molmil
Bovine heart cytochrome C oxidase at the fully oxidized state
分子名称: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE, (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE, (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE, ...
著者Shinzawa-Itoh, K, Aoyama, H, Muramoto, K, Kurauchi, T, Mizushima, T, Yamashita, E, Tsukihara, T, Yoshikawa, S.
登録日2006-09-16
公開日2007-04-03
最終更新日2023-10-25
実験手法X-RAY DIFFRACTION (1.8 Å)
主引用文献Structures and physiological roles of 13 integral lipids of bovine heart cytochrome c oxidase
Embo J., 26, 2007
2EIN
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BU of 2ein by Molmil
Zinc ion binding structure of bovine heart cytochrome C oxidase in the fully oxidized state
分子名称: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE, (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE, (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE, ...
著者Muramoto, K, Hirata, K, Shinzawa-Itoh, K, Yoko-o, S, Yamashita, E, Aoyama, H, Tsukihara, T, Yoshikawa, S.
登録日2007-03-13
公開日2007-05-29
最終更新日2023-10-25
実験手法X-RAY DIFFRACTION (2.7 Å)
主引用文献A histidine residue acting as a controlling site for dioxygen reduction and proton pumping by cytochrome c oxidase
Proc.Natl.Acad.Sci.Usa, 104, 2007
2EIK
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BU of 2eik by Molmil
Cadmium ion binding structure of bovine heart cytochrome C oxidase in the fully reduced state
分子名称: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE, (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE, (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE, ...
著者Muramoto, K, Hirata, K, Shinzawa-Itoh, K, Yoko-O, S, Yamashita, E, Aoyama, H, Tsukihara, T, Yoshikawa, S.
登録日2007-03-13
公開日2007-05-29
最終更新日2023-10-25
実験手法X-RAY DIFFRACTION (2.1 Å)
主引用文献A histidine residue acting as a controlling site for dioxygen reduction and proton pumping by cytochrome c oxidase
Proc.Natl.Acad.Sci.Usa, 104, 2007
2EIJ
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BU of 2eij by Molmil
Bovine heart cytochrome C oxidase in the fully reduced state
分子名称: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE, (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE, (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE, ...
著者Muramoto, K, Hirata, K, Shinzawa-Itoh, K, Yoko-o, S, Yamashita, E, Aoyama, H, Tsukihara, T, Yoshikawa, S.
登録日2007-03-13
公開日2007-05-29
最終更新日2023-10-25
実験手法X-RAY DIFFRACTION (1.9 Å)
主引用文献A histidine residue acting as a controlling site for dioxygen reduction and proton pumping by cytochrome c oxidase
Proc.Natl.Acad.Sci.Usa, 104, 2007
2EIM
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BU of 2eim by Molmil
Zinc ion binding structure of bovine heart cytochrome C oxidase in the fully reduced state
分子名称: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE, (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE, (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE, ...
著者Muramoto, K, Hirata, K, Shinzawa-Itoh, K, Yoko-o, S, Yamashita, E, Aoyama, H, Tsukihara, T, Yoshikawa, S.
登録日2007-03-13
公開日2007-05-29
最終更新日2023-10-25
実験手法X-RAY DIFFRACTION (2.6 Å)
主引用文献A histidine residue acting as a controlling site for dioxygen reduction and proton pumping by cytochrome c oxidase
Proc.Natl.Acad.Sci.Usa, 104, 2007
2DYS
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Bovine heart cytochrome C oxidase modified by DCCD
分子名称: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE, (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE, (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE, ...
著者Shinzawa-Itoh, K, Aoyama, H, Muramoto, K, Kurauchi, T, Mizushima, T, Yamashita, E, Tsukihara, T, Yoshikawa, S.
登録日2006-09-16
公開日2007-04-03
最終更新日2023-10-25
実験手法X-RAY DIFFRACTION (2.2 Å)
主引用文献Structures and physiological roles of 13 integral lipids of bovine heart cytochrome c oxidase
Embo J., 26, 2007

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