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PDB: 108 件
2EIJ
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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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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
1WDW
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Structural basis of mutual activation of the tryptophan synthase a2b2 complex from a hyperthermophile, Pyrococcus furiosus
分子名称: PYRIDOXAL-5'-PHOSPHATE, Tryptophan synthase alpha chain, Tryptophan synthase beta chain 1
著者Lee, S.J, Ogasahara, K, Ma, J, Nishio, K, Ishida, M, Yamagata, Y, Tsukihara, T, Yutani, K, RIKEN Structural Genomics/Proteomics Initiative (RSGI)
登録日2004-05-19
公開日2005-07-12
最終更新日2023-10-25
実験手法X-RAY DIFFRACTION (3 Å)
主引用文献Conformational Changes in the Tryptophan Synthase from a Hyperthermophile upon alpha(2)beta(2) Complex Formation: Crystal Structure of the Complex
Biochemistry, 44, 2005
1WRU
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Structure of central hub elucidated by X-ray analysis of gene product 44; baseplate component of bacteriophage Mu
分子名称: 43 kDa tail protein
著者Kondou, Y, Kitazawa, D, Takeda, S, Yamashita, E, Mizuguchi, M, Kawano, K, Tsukihara, T.
登録日2004-10-27
公開日2005-09-20
最終更新日2024-03-13
実験手法X-RAY DIFFRACTION (2.1 Å)
主引用文献Structure of central hub elucidated by X-ray analysis of gene product 44; baseplate component of bacteriophage Mu
To be Published
2D1O
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Stromelysin-1 (MMP-3) complexed to a hydroxamic acid inhibitor
分子名称: CALCIUM ION, SM-25453, Stromelysin-1, ...
著者Kohno, T, Hochigai, H, Yamashita, E, Tsukihara, T, Kanaoka, M.
登録日2005-08-30
公開日2006-06-27
最終更新日2023-10-25
実験手法X-RAY DIFFRACTION (2.02 Å)
主引用文献Crystal structures of the catalytic domain of human stromelysin-1 (MMP-3) and collagenase-3 (MMP-13) with a hydroxamic acid inhibitor SM-25453
Biochem.Biophys.Res.Commun., 344, 2006
2D1N
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Collagenase-3 (MMP-13) complexed to a hydroxamic acid inhibitor
分子名称: CALCIUM ION, Collagenase 3, SM-25453, ...
著者Kohno, T, Hochigai, H, Yamashita, E, Tsukihara, T, Kanaoka, M.
登録日2005-08-29
公開日2006-06-27
最終更新日2023-10-25
実験手法X-RAY DIFFRACTION (2.37 Å)
主引用文献Crystal structures of the catalytic domain of human stromelysin-1 (MMP-3) and collagenase-3 (MMP-13) with a hydroxamic acid inhibitor SM-25453
Biochem.Biophys.Res.Commun., 344, 2006
2E0Z
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Crystal structure of virus-like particle from Pyrococcus furiosus
分子名称: Virus-like particle
著者Akita, F, Chong, K.T, Tanaka, H, Yamashita, E, Miyazaki, N, Nakaishi, Y, Namba, K, Ono, Y, Suzuki, M, Tsukihara, T, Nakagawa, A.
登録日2006-10-16
公開日2007-04-17
最終更新日2024-03-13
実験手法X-RAY DIFFRACTION (3.6 Å)
主引用文献The Crystal Structure of a Virus-like Particle from the Hyperthermophilic Archaeon Pyrococcus furiosus Provides Insight into the Evolution of Viruses
J.Mol.Biol., 368, 2007
1X0G
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Crystal Structure of IscA with the [2Fe-2S] cluster
分子名称: FE2/S2 (INORGANIC) CLUSTER, IscA, SODIUM ION
著者Morimoto, K, Yamashita, E, Kondou, Y, Lee, S.J, Tsukihara, T, Nakai, M.
登録日2005-03-22
公開日2006-06-06
最終更新日2024-03-13
実験手法X-RAY DIFFRACTION (2.5 Å)
主引用文献The Asymmetric IscA Homodimer with an Exposed [2Fe-2S] Cluster Suggests the Structural Basis of the Fe-S Cluster Biosynthetic Scaffold.
J.Mol.Biol., 360, 2006
3ASO
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Bovine heart cytochrome C oxidase in the fully oxidized state measured at 0.9 angstrom wavelength
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Suga, M, Yano, N, Muramoto, K, Shinzawa-Itoh, K, Maeda, T, Yamashita, E, Tsukihara, T, Yoshikawa, S.
登録日2010-12-17
公開日2011-08-03
最終更新日2023-11-01
実験手法X-RAY DIFFRACTION (2.3 Å)
主引用文献Distinguishing between Cl- and O2(2-) as the bridging element between Fe3+ and Cu2+ in resting-oxidized cytochrome c oxidase
Acta Crystallogr.,Sect.D, 67, 2011
2DH6
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Crystal structure of E. coli Apo-TrpB
分子名称: SULFATE ION, tryptophan synthase beta subunit
著者Nishio, K, Morimoto, Y, Ogasahara, K, Yasuoka, N, Yutani, K, Tsukihara, T, RIKEN Structural Genomics/Proteomics Initiative (RSGI)
登録日2006-03-23
公開日2007-04-24
最終更新日2023-10-25
実験手法X-RAY DIFFRACTION (3 Å)
主引用文献Large conformational changes in the Escherichia coli tryptophan synthase beta(2) subunit upon pyridoxal 5'-phosphate binding
Febs J., 277, 2010
2DH5
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Crystal structure of E. coli Holo-TrpB
分子名称: GLYCEROL, PYRIDOXAL-5'-PHOSPHATE, SULFATE ION, ...
著者Nishio, K, Morimoto, Y, Ogasahara, K, Yutani, K, Tsukihara, T, RIKEN Structural Genomics/Proteomics Initiative (RSGI)
登録日2006-03-23
公開日2007-04-24
最終更新日2023-10-25
実験手法X-RAY DIFFRACTION (2.9 Å)
主引用文献Large conformational changes in the Escherichia coli tryptophan synthase beta(2) subunit upon pyridoxal 5'-phosphate binding
Febs J., 277, 2010
3AG1
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Bovine Heart Cytochrome c Oxidase in the Carbon Monoxide-bound Fully Reduced State at 280 K
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, Ohta, K, Shinzawa-Itoh, K, Kanda, K, Taniguchi, M, Nabekura, H, Yamashita, E, Tsukihara, T, Yoshikawa, S.
登録日2010-03-19
公開日2010-04-28
最終更新日2023-11-01
実験手法X-RAY DIFFRACTION (2.2 Å)
主引用文献Bovine cytochrome c oxidase structures enable O2 reduction with minimization of reactive oxygens and provide a proton-pumping gate
Proc.Natl.Acad.Sci.USA, 107, 2010
2ZAH
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X-ray structure of Melon necrotic spot virus
分子名称: CALCIUM ION, Coat protein, UNKNOWN ATOM OR ION
著者Wada, Y, Tsukihara, T, Omura, T.
登録日2007-10-05
公開日2008-10-07
最終更新日2023-11-01
実験手法X-RAY DIFFRACTION (2.81 Å)
主引用文献X-ray structure of Melon necrotic spot virus
Acta Crystallogr.,Sect.F, 64, 2008
3ABK
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Bovine heart cytochrome c oxidase at the NO-bound fully reduced state (50K)
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Ohta, K, Muramoto, K, Shinzawa-Itoh, K, Yamashita, E, Yoshikawa, S, Tsukihara, T.
登録日2009-12-16
公開日2010-03-09
最終更新日2023-11-01
実験手法X-RAY DIFFRACTION (2 Å)
主引用文献X-ray structure of the NO-bound Cu(B) in bovine cytochrome c oxidase
Acta Crystallogr.,Sect.F, 66, 2010
3ABM
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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
2ZZQ
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Crystal structure analysis of the HEV capsid protein, PORF2
分子名称: Protein ORF3, Capsid protein
著者Miyazaki, N, Xing, L, Wang, C.-Y, Li, T.-C, Takeda, N, Higashiura, A, Nakagawa, A, Tsukihara, T, Miyamura, T, Cheng, R.H.
登録日2009-02-23
公開日2010-03-09
最終更新日2024-03-13
実験手法X-RAY DIFFRACTION (3.81 Å)
主引用文献Role of protein domain-modularity in designating capsid assembly and antigenicity
To be Published
2ZXW
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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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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
3ASN
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Bovine heart cytochrome C oxidase in the fully oxidized state measured at 1.7470 angstrom wavelength
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Suga, M, Yano, N, Muramoto, K, Shinzawa-Itoh, K, Maeda, T, Yamashita, E, Tsukihara, T, Yoshikawa, S.
登録日2010-12-17
公開日2011-08-03
最終更新日2023-11-01
実験手法X-RAY DIFFRACTION (3 Å)
主引用文献Distinguishing between Cl- and O2(2-) as the bridging element between Fe3+ and Cu2+ in resting-oxidized cytochrome c oxidase
Acta Crystallogr.,Sect.D, 67, 2011
3AG4
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Bovine Heart Cytochrome c Oxidase in the Cyanide Ion-bound Fully Reduced State at 100 K
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, Ohta, K, Shinzawa-Itoh, K, Kanda, K, Taniguchi, M, Nabekura, H, Yamashita, E, Tsukihara, T, Yoshikawa, S.
登録日2010-03-19
公開日2010-04-28
最終更新日2023-11-01
実験手法X-RAY DIFFRACTION (2.05 Å)
主引用文献Bovine cytochrome c oxidase structures enable O2 reduction with minimization of reactive oxygens and provide a proton-pumping gate
Proc.Natl.Acad.Sci.USA, 107, 2010
2ZUH
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Crystal Structure of Camphor-soaked Ferric Cytochrome P450cam Mutant (D297A)
分子名称: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, CAMPHOR, Camphor 5-monooxygenase, ...
著者Sakurai, K, Harada, K, Shimada, H, Shimokata, K, Hayashi, T, Tsukihara, T.
登録日2008-10-18
公開日2009-10-20
最終更新日2023-11-01
実験手法X-RAY DIFFRACTION (1.55 Å)
主引用文献Crystal Structure of Camphor-soaked Ferric Cytochrome P450cam Mutant
to be published
2ZUI
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Crystal Structure of Camphor-soaked Ferric Cytochrome P450cam Mutant (D297N)
分子名称: CAMPHOR, Camphor 5-monooxygenase, POTASSIUM ION, ...
著者Sakurai, K, Harada, K, Shimada, H, Shimokata, K, Hayashi, T, Tsukihara, T.
登録日2008-10-18
公開日2009-10-20
最終更新日2023-11-01
実験手法X-RAY DIFFRACTION (1.5 Å)
主引用文献Crystal Structure of Camphor-soaked Ferric Cytochrome P450cam Mutant
TO BE PUBLISHED
2ZUJ
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Crystal Structure of Camphor-soaked Ferric Cytochrome P450cam Mutant(D297L)
分子名称: CAMPHOR, Camphor 5-monooxygenase, POTASSIUM ION, ...
著者Sakurai, K, Harada, K, Shimada, H, Shimokata, K, Hayashi, T, Tsukihara, T.
登録日2008-10-18
公開日2009-10-20
最終更新日2023-11-01
実験手法X-RAY DIFFRACTION (1.6 Å)
主引用文献Crystal Structure of Camphor-soaked Ferric Cytochrome P450cam Mutant
to be published
2ZWU
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Crystal Structure of Camphor Soaked Ferric Cytochrome P450cam
分子名称: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, CAMPHOR, Camphor 5-monooxygenase, ...
著者Sakurai, K, Shimada, H, Hayashi, T, Tsukihara, T.
登録日2008-12-18
公開日2009-02-17
最終更新日2023-11-01
実験手法X-RAY DIFFRACTION (1.3 Å)
主引用文献Substrate binding induces structural changes in cytochrome P450cam
Acta Crystallogr.,Sect.F, 65, 2009
2ZWT
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Crystal Structure of Ferric Cytochrome P450cam
分子名称: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, CAMPHOR, Camphor 5-monooxygenase, ...
著者Sakurai, K, Shimada, H, Hayashi, T, Tsukihara, T.
登録日2008-12-18
公開日2009-02-17
最終更新日2023-11-01
実験手法X-RAY DIFFRACTION (1.35 Å)
主引用文献Substrate binding induces structural changes in cytochrome P450cam
Acta Crystallogr.,Sect.F, 65, 2009

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