4EFM
 
 | | Crystal structure of H-Ras G12V in complex with GppNHp (state 1) | | 分子名称: | GTPase HRas, MAGNESIUM ION, PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER | | 著者 | Muraoka, S, Shima, F, Araki, M, Inoue, T, Yoshimoto, A, Ijiri, Y, Seki, N, Tamura, A, Kumasaka, T, Yamamoto, M, Kataoka, T. | | 登録日 | 2012-03-30 | | 公開日 | 2012-05-16 | | 最終更新日 | 2023-11-08 | | 実験手法 | X-RAY DIFFRACTION (1.9 Å) | | 主引用文献 | Crystal structures of the state 1 conformations of the GTP-bound H-Ras protein and its oncogenic G12V and Q61L mutants
Febs Lett., 586, 2012
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1VBU
 | | Crystal structure of native xylanase 10B from Thermotoga maritima | | 分子名称: | ACETIC ACID, GLYCEROL, SULFATE ION, ... | | 著者 | Ihsanawati, Kumasaka, T, Kaneko, T, Nakamura, S, Tanaka, N. | | 登録日 | 2004-03-02 | | 公開日 | 2005-06-28 | | 最終更新日 | 2023-12-27 | | 実験手法 | X-RAY DIFFRACTION (1.8 Å) | | 主引用文献 | Structural basis of the substrate subsite and the highly thermal stability of xylanase 10B from Thermotoga maritima MSB8
Proteins, 61, 2005
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1VBR
 | | Crystal structure of complex xylanase 10B from Thermotoga maritima with xylobiose | | 分子名称: | ACETIC ACID, alpha-D-xylopyranose-(1-4)-beta-D-xylopyranose, endo-1,4-beta-xylanase B | | 著者 | Ihsanawati, Kumasaka, T, Kaneko, T, Nakamura, S, Tanaka, N. | | 登録日 | 2004-03-02 | | 公開日 | 2005-06-28 | | 最終更新日 | 2023-12-27 | | 実験手法 | X-RAY DIFFRACTION (1.8 Å) | | 主引用文献 | Structural basis of the substrate subsite and the highly thermal stability of xylanase 10B from Thermotoga maritima MSB8
Proteins, 61, 2005
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5X1B
 | | 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
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5X19
 | | 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
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5X1F
 | | 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
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2HYK
 | | The crystal structure of an endo-beta-1,3-glucanase from alkaliphilic Nocardiopsis sp.strain F96 | | 分子名称: | Beta-1,3-glucanase, CALCIUM ION, ETHANOL, ... | | 著者 | Fibriansah, G, Nakamura, S, Kumasaka, T. | | 登録日 | 2006-08-07 | | 公開日 | 2007-10-02 | | 最終更新日 | 2024-03-13 | | 実験手法 | X-RAY DIFFRACTION (1.3 Å) | | 主引用文献 | The 1.3 A crystal structure of a novel endo-beta-1,3-glucanase of glycoside hydrolase family 16 from alkaliphilic Nocardiopsis sp. strain F96.
Proteins, 69, 2007
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8IXT
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8IXU
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5X9S
 | | Crystal structure of fully modified H-Ras-GppNHp | | 分子名称: | CALCIUM ION, GTPase HRas, MAGNESIUM ION, ... | | 著者 | Matsumoto, S, Ke, H, Murashima, Y, Taniguchi-Tamura, H, Miyamoto, R, Yoshikawa, Y, Kumasaka, T, Mizohata, E, Edamatsu, H, Kataoka, T. | | 登録日 | 2017-03-09 | | 公開日 | 2017-08-30 | | 最終更新日 | 2023-11-22 | | 実験手法 | X-RAY DIFFRACTION (2.5 Å) | | 主引用文献 | Structural basis for intramolecular interaction of post-translationally modified H-RasGTP prepared by protein ligation
FEBS Lett., 591, 2017
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8JOG
 | | solution structure of Ras Binding Domein (RBD) in C-RAF with negative allosteric modulator. | | 分子名称: | RAF proto-oncogene serine/threonine-protein kinase | | 著者 | Makino, Y, Matsumoto, S, Yoshikawa, Y, Kawamura, T, Kumasaka, T, Shima, F. | | 登録日 | 2023-06-07 | | 公開日 | 2024-06-12 | | 実験手法 | SOLUTION NMR | | 主引用文献 | Small-molecule RAS/RAF-binding Inhibitors Allosterically Disrupt RAF Conformation and Exert Efficacy Against Broad-spectrum RAS-driven Cancers
To Be Published
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8JOF
 | | solution-structure of Ras Binding Domain (RBD) in C-RAF | | 分子名称: | RAF proto-oncogene serine/threonine-protein kinase | | 著者 | Makino, Y, Matsumoto, S, Yoshikawa, Y, Kawamura, T, Kumasaka, T, Shima, F. | | 登録日 | 2023-06-07 | | 公開日 | 2024-06-12 | | 実験手法 | SOLUTION NMR | | 主引用文献 | Small-molecule RAS/RAF-binding Inhibitors Allosterically Disrupt RAF Conformation and Exert Efficacy Against Broad-spectrum RAS-driven Cancers
To Be Published
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1UIR
 | | Crystal Structure of Polyamine Aminopropyltransfease from Thermus thermophilus | | 分子名称: | Polyamine Aminopropyltransferase | | 著者 | Ganbe, T, Ohnuma, M, Sato, T, Kumasaka, T, Oshima, T, Tanaka, N, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | 登録日 | 2003-07-18 | | 公開日 | 2003-08-05 | | 最終更新日 | 2023-10-25 | | 実験手法 | X-RAY DIFFRACTION (2 Å) | | 主引用文献 | Crystal structures and enzymatic properties of a triamine/agmatine aminopropyltransferase from Thermus thermophilus
J.Mol.Biol., 408, 2011
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1UJ0
 | | Crystal Structure of STAM2 SH3 domain in complex with a UBPY-derived peptide | | 分子名称: | PHOSPHATE ION, deubiquitinating enzyme UBPY, signal transducing adaptor molecule (SH3 domain and ITAM motif) 2 | | 著者 | Kaneko, T, Kumasaka, T, Ganbe, T, Sato, T, Miyazawa, K, Kitamura, N, Tanaka, N. | | 登録日 | 2003-07-24 | | 公開日 | 2003-12-23 | | 最終更新日 | 2023-12-27 | | 実験手法 | X-RAY DIFFRACTION (1.7 Å) | | 主引用文献 | Structural insight into modest binding of a non-PXXP ligand to the signal transducing adaptor molecule-2 Src homology 3 domain.
J.Biol.Chem., 278, 2003
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1V3V
 | | Crystal structure of leukotriene B4 12-hydroxydehydrogenase/15-oxo-prostaglandin 13-reductase complexed with NADP and 15-oxo-PGE2 | | 分子名称: | (5E,13E)-11-HYDROXY-9,15-DIOXOPROSTA-5,13-DIEN-1-OIC ACID, CHLORIDE ION, NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE, ... | | 著者 | Hori, T, Yokomizo, T, Ago, H, Sugahara, M, Ueno, G, Yamamoto, M, Kumasaka, T, Shimizu, T, Miyano, M, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | 登録日 | 2003-11-06 | | 公開日 | 2004-07-13 | | 最終更新日 | 2023-12-27 | | 実験手法 | X-RAY DIFFRACTION (2 Å) | | 主引用文献 | Structural basis of leukotriene B4 12-hydroxydehydrogenase/15-Oxo-prostaglandin 13-reductase catalytic mechanism and a possible Src homology 3 domain binding loop
J.Biol.Chem., 279, 2004
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1V3T
 | | Crystal structure of leukotriene B4 12-hydroxydehydrogenase/15-oxo-prostaglandin 13-reductase | | 分子名称: | NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE, leukotriene b4 12-hydroxydehydrogenase/prostaglandin 15-keto reductase | | 著者 | Hori, T, Yokomizo, T, Ago, H, Sugahara, M, Ueno, G, Yamamoto, M, Kumasaka, T, Shimizu, T, Miyano, M, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | 登録日 | 2003-11-05 | | 公開日 | 2004-07-13 | | 最終更新日 | 2023-12-27 | | 実験手法 | X-RAY DIFFRACTION (2.3 Å) | | 主引用文献 | Structural basis of leukotriene B4 12-hydroxydehydrogenase/15-Oxo-prostaglandin 13-reductase catalytic mechanism and a possible Src homology 3 domain binding loop
J.Biol.Chem., 279, 2004
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5B42
 | | Crystal structure of the C-terminal endonuclease domain of Aquifex aeolicus MutL. | | 分子名称: | CADMIUM ION, DI(HYDROXYETHYL)ETHER, DNA mismatch repair protein MutL | | 著者 | Fukui, K, Baba, S, Kumasaka, T, Yano, T. | | 登録日 | 2016-03-30 | | 公開日 | 2016-07-13 | | 最終更新日 | 2024-03-20 | | 実験手法 | X-RAY DIFFRACTION (1.35 Å) | | 主引用文献 | Structural Features and Functional Dependency on beta-Clamp Define Distinct Subfamilies of Bacterial Mismatch Repair Endonuclease MutL
J.Biol.Chem., 291, 2016
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1EE8
 | | CRYSTAL STRUCTURE OF MUTM (FPG) PROTEIN FROM THERMUS THERMOPHILUS HB8 | | 分子名称: | MUTM (FPG) PROTEIN, ZINC ION | | 著者 | Sugahara, M, Mikawa, T, Kumasaka, T, Yamamoto, M, Kato, R, Fukuyama, K, Inoue, Y, Kuramitsu, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | 登録日 | 2000-01-31 | | 公開日 | 2001-01-31 | | 最終更新日 | 2024-02-07 | | 実験手法 | X-RAY DIFFRACTION (1.9 Å) | | 主引用文献 | Crystal structure of a repair enzyme of oxidatively damaged DNA, MutM (Fpg), from an extreme thermophile, Thermus thermophilus HB8.
EMBO J., 19, 2000
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2GRU
 | | Crystal structure of 2-deoxy-scyllo-inosose synthase complexed with carbaglucose-6-phosphate, NAD+ and Co2+ | | 分子名称: | (1R,2S,3S,4R)-5-METHYLENECYCLOHEXANE-1,2,3,4-TETRAOL, (4S)-2-METHYL-2,4-PENTANEDIOL, 2-deoxy-scyllo-inosose synthase, ... | | 著者 | Nango, E, Kumasaka, T. | | 登録日 | 2006-04-25 | | 公開日 | 2007-05-08 | | 最終更新日 | 2023-10-25 | | 実験手法 | X-RAY DIFFRACTION (2.15 Å) | | 主引用文献 | Structure of 2-deoxy-scyllo-inosose synthase, a key enzyme in the biosynthesis of 2-deoxystreptamine-containing aminoglycoside antibiotics, in complex with a mechanism-based inhibitor and NAD+
Proteins, 70, 2008
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5GX3
 | | Luciferin-regenerating enzyme collected with serial synchrotron rotational crystallography with accumulated dose of 6.9 MGy (6th measurement) | | 分子名称: | (4S)-2-METHYL-2,4-PENTANEDIOL, GLYCEROL, Luciferin regenerating enzyme, ... | | 著者 | Hasegawa, K, Yamashita, K, Murai, T, Nuemket, N, Hirata, K, Ueno, G, Ago, H, Nakatsu, T, Kumasaka, T, Yamamoto, M. | | 登録日 | 2016-09-15 | | 公開日 | 2017-01-04 | | 最終更新日 | 2023-11-08 | | 実験手法 | X-RAY DIFFRACTION (1.6 Å) | | 主引用文献 | Development of a dose-limiting data collection strategy for serial synchrotron rotation crystallography
J Synchrotron Radiat, 24, 2017
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5GX5
 | | Luciferin-regenerating enzyme collected with serial synchrotron rotational crystallography with accumulated dose of 26 MGy (23rd measurement) | | 分子名称: | (4S)-2-METHYL-2,4-PENTANEDIOL, GLYCEROL, Luciferin regenerating enzyme, ... | | 著者 | Hasegawa, K, Yamashita, K, Murai, T, Nuemket, N, Hirata, K, Ueno, G, Ago, H, Nakatsu, T, Kumasaka, T, Yamamoto, M. | | 登録日 | 2016-09-15 | | 公開日 | 2017-01-04 | | 最終更新日 | 2023-11-08 | | 実験手法 | X-RAY DIFFRACTION (1.6 Å) | | 主引用文献 | Development of a dose-limiting data collection strategy for serial synchrotron rotation crystallography
J Synchrotron Radiat, 24, 2017
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5GX1
 | | Luciferin-regenerating enzyme collected with serial synchrotron rotational crystallography with accumulated dose of 1.1 MGy (1st measurement) | | 分子名称: | (4S)-2-METHYL-2,4-PENTANEDIOL, GLYCEROL, Luciferin regenerating enzyme, ... | | 著者 | Hasegawa, K, Yamashita, K, Murai, T, Nuemket, N, Hirata, K, Ueno, G, Ago, H, Nakatsu, T, Kumasaka, T, Yamamoto, M. | | 登録日 | 2016-09-15 | | 公開日 | 2017-01-04 | | 最終更新日 | 2023-11-08 | | 実験手法 | X-RAY DIFFRACTION (1.6 Å) | | 主引用文献 | Development of a dose-limiting data collection strategy for serial synchrotron rotation crystallography
J Synchrotron Radiat, 24, 2017
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5GX2
 | | Luciferin-regenerating enzyme collected with serial synchrotron rotational crystallography with accumulated dose of 3.4 MGy (3rd measurement) | | 分子名称: | (4S)-2-METHYL-2,4-PENTANEDIOL, GLYCEROL, Luciferin regenerating enzyme, ... | | 著者 | Hasegawa, K, Yamashita, K, Murai, T, Nuemket, N, Hirata, K, Ueno, G, Ago, H, Nakatsu, T, Kumasaka, T, Yamamoto, M. | | 登録日 | 2016-09-15 | | 公開日 | 2017-01-04 | | 最終更新日 | 2023-11-08 | | 実験手法 | X-RAY DIFFRACTION (1.6 Å) | | 主引用文献 | Development of a dose-limiting data collection strategy for serial synchrotron rotation crystallography
J Synchrotron Radiat, 24, 2017
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5GX4
 | | Luciferin-regenerating enzyme collected with serial synchrotron rotational crystallography with accumulated dose of 14 MGy (12th measurement) | | 分子名称: | (4S)-2-METHYL-2,4-PENTANEDIOL, GLYCEROL, Luciferin regenerating enzyme, ... | | 著者 | Hasegawa, K, Yamashita, K, Murai, T, Nuemket, N, Hirata, K, Ueno, G, Ago, H, Nakatsu, T, Kumasaka, T, Yamamoto, M. | | 登録日 | 2016-09-15 | | 公開日 | 2017-01-04 | | 最終更新日 | 2023-11-08 | | 実験手法 | X-RAY DIFFRACTION (1.6 Å) | | 主引用文献 | Development of a dose-limiting data collection strategy for serial synchrotron rotation crystallography
J Synchrotron Radiat, 24, 2017
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2D2X
 | | Crystal structure of 2-deoxy-scyllo-inosose synthase | | 分子名称: | 2-deoxy-scyllo-inosose synthase, COBALT (II) ION, GLYCEROL, ... | | 著者 | Nango, E, Kumasaka, T, Tanaka, N, Kakinuma, K, Eguchi, T. | | 登録日 | 2005-09-20 | | 公開日 | 2006-10-03 | | 最終更新日 | 2011-07-13 | | 実験手法 | X-RAY DIFFRACTION (2.3 Å) | | 主引用文献 | Structure of 2-deoxy-scyllo-inosose synthase, a key enzyme in the biosynthesis of 2-deoxystreptamine-containing aminoglycoside antibiotics, in complex with a mechanism-based inhibitor and NAD+
Proteins, 70, 2008
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