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PDB: 117 件

8JU3
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Mu phage tail fiber
分子名称: Tail fiber protein S,Tail fiber protein S'
著者Yamashita, E, Takeda, S.
登録日2023-06-24
公開日2024-02-28
最終更新日2024-09-11
実験手法X-RAY DIFFRACTION (2 Å)
主引用文献Determination of the three-dimensional structure of bacteriophage Mu(-) tail fiber and its characterization.
Virology, 593, 2024
5X1B
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CO bound cytochrome c oxidase at 20 nsec after pump laser irradiation to release CO from O2 reduction center
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Shimada, A, Kubo, M, Baba, S, Yamashita, K, Hirata, K, Ueno, G, Nomura, T, Kimura, T, Shinzawa-Itoh, K, Baba, J, Hatano, K, Eto, Y, Miyamoto, A, Murakami, H, Kumasaka, T, Owada, S, Tono, K, Yabashi, M, Yamaguchi, Y, Yanagisawa, S, Sakaguchi, M, Ogura, T, Komiya, R, Yan, J, Yamashita, E, Yamamoto, M, Ago, H, Yoshikawa, S, Tsukihara, T.
登録日2017-01-25
公開日2017-08-09
最終更新日2017-12-06
実験手法X-RAY DIFFRACTION (2.4 Å)
主引用文献A nanosecond time-resolved XFEL analysis of structural changes associated with CO release from cytochrome c oxidase.
Sci Adv, 3, 2017
5X19
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CO bound cytochrome c oxidase at 100 micro sec after pump laser irradiation to release CO from O2 reduction center
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Shimada, A, Kubo, M, Baba, S, Yamashita, K, Hirata, K, Ueno, G, Nomura, T, Kimura, T, Shinzawa-Itoh, K, Baba, J, Hatano, K, Eto, Y, Miyamoto, A, Murakami, H, Kumasaka, T, Owada, S, Tono, K, Yabashi, M, Yamaguchi, Y, Yanagisawa, S, Sakaguchi, M, Ogura, T, Komiya, R, Yan, J, Yamashita, E, Yamamoto, M, Ago, H, Yoshikawa, S, Tsukihara, T.
登録日2017-01-25
公開日2017-08-09
最終更新日2023-11-22
実験手法X-RAY DIFFRACTION (2.2 Å)
主引用文献A nanosecond time-resolved XFEL analysis of structural changes associated with CO release from cytochrome c oxidase.
Sci Adv, 3, 2017
4V60
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The structure of rat liver vault at 3.5 angstrom resolution
分子名称: Major vault protein
著者Kato, K, Zhou, Y, Tanaka, H, Yao, M, Yamashita, E, Yoshimura, M, Tsukihara, T.
登録日2008-10-24
公開日2014-07-09
最終更新日2024-04-03
実験手法X-RAY DIFFRACTION (3.5 Å)
主引用文献The structure of rat liver vault at 3.5 angstrom resolution
Science, 323, 2009
5IY5
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Electron transfer complex of cytochrome c and cytochrome c oxidase at 2.0 angstrom resolution
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Shimada, S, Baba, J, Aoe, S, Shimada, A, Yamashita, E, Tsukihara, T.
登録日2016-03-24
公開日2017-01-11
最終更新日2023-11-08
実験手法X-RAY DIFFRACTION (2 Å)
主引用文献Complex structure of cytochrome c-cytochrome c oxidase reveals a novel protein-protein interaction mode
EMBO J., 36, 2017
4I7Z
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Crystal structure of cytochrome b6f in DOPG, with disordered Rieske Iron-Sulfur Protein soluble domain
分子名称: (2R)-3-{[(R)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-2-[(6Z)-tridec-6-enoyloxy]propyl (9Z)-octadec-9-enoate, (2S)-3-(acetyloxy)-2-hydroxypropyl 6-deoxy-6-sulfo-beta-D-glucopyranoside, Apocytochrome f, ...
著者Hasan, S.S, Stofleth, J.T, Yamashita, E, Cramer, W.A.
登録日2012-12-01
公開日2013-04-17
最終更新日2024-02-28
実験手法X-RAY DIFFRACTION (2.803 Å)
主引用文献Lipid-induced conformational changes within the cytochrome b6f complex of oxygenic photosynthesis.
Biochemistry, 52, 2013
5X1F
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CO bound cytochrome c oxidase without pump laser irradiation at 278K
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Shimada, A, Kubo, M, Baba, S, Yamashita, K, Hirata, K, Ueno, G, Nomura, T, Kimura, T, Shinzawa-Itoh, K, Baba, J, Hatano, K, Eto, Y, Miyamoto, A, Murakami, H, Kumasaka, T, Owada, S, Tono, K, Yabashi, M, Yamaguchi, Y, Yanagisawa, S, Sakaguchi, M, Ogura, T, Komiya, R, Yan, J, Yamashita, E, Yamamoto, M, Ago, H, Yoshikawa, S, Tsukihara, T.
登録日2017-01-25
公開日2017-08-09
最終更新日2023-11-22
実験手法X-RAY DIFFRACTION (2.2 Å)
主引用文献A nanosecond time-resolved XFEL analysis of structural changes associated with CO release from cytochrome c oxidase.
Sci Adv, 3, 2017
5WS4
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Crystal structure of tripartite-type ABC transporter MacB from Acinetobacter baumannii
分子名称: 5'-O-[(R)-HYDROXY(THIOPHOSPHONOOXY)PHOSPHORYL]ADENOSINE, Macrolide export ATP-binding/permease protein MacB
著者Murakami, S, Okada, U, Yamashita, E.
登録日2016-12-05
公開日2017-11-15
最終更新日2024-03-20
実験手法X-RAY DIFFRACTION (3.4 Å)
主引用文献Crystal structure of tripartite-type ABC transporter MacB from Acinetobacter baumannii.
Nat Commun, 8, 2017
1OCC
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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
1UKL
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Crystal structure of Importin-beta and SREBP-2 complex
分子名称: Importin beta-1 subunit, Sterol regulatory element binding protein-2
著者Lee, S.J, Sekimoto, T, Yamashita, E, Nagoshi, E, Nakagawa, A, Imamoto, N, Yoshimura, M, Sakai, H, Tsukihara, T, Yoneda, Y.
登録日2003-08-26
公開日2003-12-09
最終更新日2024-10-23
実験手法X-RAY DIFFRACTION (3 Å)
主引用文献The Structure of Importin-beta Bound to SREBP-2: Nuclear Import of a Transcription Factor
Science, 302, 2003
5C5O
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Structure of SARS-3CL protease complex with a phenyl-beta-alanyl (S,R)-N-decalin type inhibitor
分子名称: (2S)-3-(1H-imidazol-5-yl)-2-({[(3S,4aR,8aS)-2-(N-phenyl-beta-alanyl)decahydroisoquinolin-3-yl]methyl}amino)propanal, 3C-like proteinase
著者Akaji, K, Teruya, K, Shimamoto, Y, Sanjho, A, Yamashita, E, Nakagawa, A.
登録日2015-06-21
公開日2016-06-22
最終更新日2020-01-29
実験手法X-RAY DIFFRACTION (1.5 Å)
主引用文献Fused-ring structure of N-decalin as a novel scaffold for SARS 3CL protease inhibitors
to be published
2GUF
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In meso crystal structure of the cobalamin transporter, BtuB
分子名称: (4S)-2-METHYL-2,4-PENTANEDIOL, FORMIC ACID, Vitamin B12 transporter btuB, ...
著者Caffrey, M, Cherezov, V, Yamashita, E, Cramer, W.A.
登録日2006-04-29
公開日2006-12-05
最終更新日2024-02-14
実験手法X-RAY DIFFRACTION (1.95 Å)
主引用文献In Meso Structure of the Cobalamin Transporter, BtuB, at 1.95 A Resolution.
J.Mol.Biol., 364, 2006
2HI7
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Crystal structure of DsbA-DsbB-ubiquinone complex
分子名称: Disulfide bond formation protein B, Thiol:disulfide interchange protein dsbA, UBIQUINONE-1, ...
著者Inaba, K, Murakami, S, Suzuki, M, Nakagawa, A, Yamashita, E, Okada, K, Ito, K.
登録日2006-06-29
公開日2006-12-05
最終更新日2021-11-10
実験手法X-RAY DIFFRACTION (3.7 Å)
主引用文献Crystal Structure of the DsbB-DsbA Complex Reveals a Mechanism of Disulfide Bond Generation
Cell(Cambridge,Mass.), 127, 2006
1V55
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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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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
4PV1
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Cytochrome B6F structure from M. laminosus with the quinone analog inhibitor stigmatellin
分子名称: (1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate, (7R,17E)-4-HYDROXY-N,N,N,7-TETRAMETHYL-7-[(8E)-OCTADEC-8-ENOYLOXY]-10-OXO-3,5,9-TRIOXA-4-PHOSPHAHEPTACOS-17-EN-1-AMINIUM 4-OXIDE, 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL, ...
著者Hasan, S.S, Yamashita, E, Cramer, W.A.
登録日2014-03-14
公開日2014-08-20
最終更新日2024-10-16
実験手法X-RAY DIFFRACTION (3 Å)
主引用文献Traffic within the cytochrome b6f lipoprotein complex: gating of the quinone portal.
Biophys.J., 107, 2014
1WSV
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Crystal Structure of Human T-protein of Glycine Cleavage System
分子名称: Aminomethyltransferase, N-[4-({[(6S)-2-AMINO-4-HYDROXY-5-METHYL-5,6,7,8-TETRAHYDROPTERIDIN-6-YL]METHYL}AMINO)BENZOYL]-L-GLUTAMIC ACID, SULFATE ION
著者Okamura-Ikeda, K, Hosaka, H, Yoshimura, M, Yamashita, E, Toma, S, Nakagawa, A, Fujiwara, K, Motokawa, Y, Taniguchi, H.
登録日2004-11-11
公開日2005-08-16
最終更新日2023-10-25
実験手法X-RAY DIFFRACTION (2.6 Å)
主引用文献Crystal Structure of Human T-protein of Glycine Cleavage System at 2.0A Resolution and its Implication for Understanding Non-ketotic Hyperglycinemia
J.Mol.Biol., 351, 2005
1WSR
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Crystal Structure of Human T-protein of Glycine Cleavage System
分子名称: Aminomethyltransferase, SULFATE ION
著者Okamura-Ikeda, K, Hosaka, H, Yoshimura, M, Yamashita, E, Toma, S, Nakagawa, A, Fujiwara, K, Motokawa, Y, Taniguchi, H.
登録日2004-11-10
公開日2005-08-16
最終更新日2024-03-13
実験手法X-RAY DIFFRACTION (2 Å)
主引用文献Crystal Structure of Human T-protein of Glycine Cleavage System at 2.0A Resolution and its Implication for Understanding Non-ketotic Hyperglycinemia
J.Mol.Biol., 351, 2005
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
4P76
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Cellular response to a crystal-forming protein
分子名称: Photoconvertible fluorescent protein, SODIUM ION
著者Tsutsui, H, Jinno, Y, Shoda, K, Tomita, A, Matsuda, M, Yamashita, E, Katayama, H, Nakagawa, A, Miyawaki, A.
登録日2014-03-26
公開日2015-04-29
最終更新日2024-10-23
実験手法X-RAY DIFFRACTION (2.9 Å)
主引用文献A diffraction-quality protein crystal processed as an autophagic cargo
Mol.Cell, 58, 2015
5C5N
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Structure of SARS-3CL protease complex with a phenyl-beta-alanyl (R,S)-N-decalin type inhibitor
分子名称: (2S)-3-(1H-imidazol-5-yl)-2-({[(3R,4aS,8aR)-2-(N-phenyl-beta-alanyl)decahydroisoquinolin-3-yl]methyl}amino)propanal, 3C-like proteinase
著者Akaji, K, Teruya, K, Shimamoto, Y, Sanjho, A, Yamashita, E, Nakagawa, A.
登録日2015-06-21
公開日2016-06-22
最終更新日2024-10-30
実験手法X-RAY DIFFRACTION (1.69 Å)
主引用文献Fused-ring structure of N-decalin as a novel scaffold for SARS 3CL protease inhibitors
to be published
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
1O5W
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The structure basis of specific recognitions for substrates and inhibitors of rat monoamine oxidase A
分子名称: Amine oxidase [flavin-containing] A, FLAVIN-ADENINE DINUCLEOTIDE, N-[3-(2,4-DICHLOROPHENOXY)PROPYL]-N-METHYL-N-PROP-2-YNYLAMINE
著者Ma, J, Yoshimura, M, Yamashita, E, Nakagawa, A, Ito, A, Tsukihara, T.
登録日2003-10-06
公開日2004-04-20
最終更新日2024-10-23
実験手法X-RAY DIFFRACTION (3.2 Å)
主引用文献Structure of rat monoamine oxidase a and its specific recognitions for substrates and inhibitors.
J.Mol.Biol., 338, 2004
4WY3
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Structure of SARS-3CL protease complex with a phenylbenzoyl (R,S)-N-decalin type inhibitor
分子名称: (2S)-2-({[(3R,4aS,8aR)-2-(biphenyl-4-ylcarbonyl)decahydroisoquinolin-3-yl]methyl}amino)-3-(1H-imidazol-5-yl)propanal, 3C-like proteinase
著者Akaji, K, Teruya, K, Shimamoto, Y, Sanjho, A, Yamashita, E, Nakagawa, A.
登録日2014-11-15
公開日2015-02-18
最終更新日2023-11-08
実験手法X-RAY DIFFRACTION (1.89 Å)
主引用文献Fused-ring structure of decahydroisoquinolin as a novel scaffold for SARS 3CL protease inhibitors.
Bioorg.Med.Chem., 23, 2015
1IOO
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CRYSTAL STRUCTURE OF NICOTIANA ALATA GEMETOPHYTIC SELF-INCOMPATIBILITY ASSOCIATED SF11-RNASE
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[beta-D-xylopyranose-(1-2)][alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, SF11-RNASE, beta-D-xylopyranose-(1-2)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
著者Ida, K, Sato, M, Sakiyama, F, Norioka, S, Yamamoto, M, Kumasaka, T, Yamashita, E.
登録日2001-03-26
公開日2002-05-08
最終更新日2023-12-27
実験手法X-RAY DIFFRACTION (1.55 Å)
主引用文献The 1.55 A resolution structure of Nicotiana alata S(F11)-RNase associated with gametophytic self-incompatibility.
J.Mol.Biol., 314, 2001

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