7QYC
 
 | | As isolated MSOX movie series dataset 20 (8 MGy) of the copper nitrite reductase from Bradyrhizobium sp. ORS 375 (two-domain) | | Descriptor: | COPPER (II) ION, Copper-containing nitrite reductase, GLYCEROL, ... | | Authors: | Rose, S.L, Baba, S, Okumura, H, Antonyuk, S.V, Sasaki, D, Tosha, T, Kumasaka, T, Eady, R.R, Yamamoto, M, Hasnain, S.S. | | Deposit date: | 2022-01-27 | | Release date: | 2022-08-03 | | Last modified: | 2024-01-31 | | Method: | X-RAY DIFFRACTION (1.35 Å) | | Cite: | Single crystal spectroscopy and multiple structures from one crystal (MSOX) define catalysis in copper nitrite reductases.
Proc.Natl.Acad.Sci.USA, 119, 2022
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1ERZ
 | | CRYSTAL STRUCTURE OF N-CARBAMYL-D-AMINO ACID AMIDOHYDROLASE WITH A NOVEL CATALYTIC FRAMEWORK COMMON TO AMIDOHYDROLASES | | Descriptor: | N-CARBAMYL-D-AMINO ACID AMIDOHYDROLASE | | Authors: | Nakai, T, Hasegawa, T, Yamashita, E, Yamamoto, M, Kumasaka, T, Ueki, T, Nanba, H, Ikenaka, Y, Takahashi, S, Sato, M, Tsukihara, T. | | Deposit date: | 2000-04-06 | | Release date: | 2001-04-06 | | Last modified: | 2024-02-07 | | Method: | X-RAY DIFFRACTION (1.7 Å) | | Cite: | Crystal structure of N-carbamyl-D-amino acid amidohydrolase with a novel catalytic framework common to amidohydrolases.
Structure Fold.Des., 8, 2000
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8JNA
 | | CRAF ras-binding domain chimera, apo form | | Descriptor: | RAF proto-oncogene serine/threonine-protein kinase, CRaf | | Authors: | Kawamura, T, Kumasaka, T. | | Deposit date: | 2023-06-06 | | Release date: | 2024-06-19 | | Method: | X-RAY DIFFRACTION (1.7 Å) | | Cite: | 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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8JNB
 | | CRAF ras-binding domain chimera, ligand complex | | Descriptor: | 2-[4-[[(2S)-1-ethanoyl-3-oxidanylidene-2H-indol-2-yl]methyl]-2-methoxy-phenoxy]ethanamide, RAF proto-oncogene serine/threonine-protein kinase, CRaf | | Authors: | Kawamura, T, Kumasaka, T. | | Deposit date: | 2023-06-06 | | Release date: | 2024-06-19 | | Method: | X-RAY DIFFRACTION (1.62 Å) | | Cite: | 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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1EH1
 | | RIBOSOME RECYCLING FACTOR FROM THERMUS THERMOPHILUS | | Descriptor: | RIBOSOME RECYCLING FACTOR | | Authors: | Toyoda, T, Tin, O.F, Ito, K, Fujiwara, T, Kumasaka, T, Yamamoto, M, Garber, M.B, Nakamura, Y. | | Deposit date: | 2000-02-18 | | Release date: | 2000-11-15 | | Last modified: | 2024-02-07 | | Method: | X-RAY DIFFRACTION (2.6 Å) | | Cite: | Crystal structure combined with genetic analysis of the Thermus thermophilus ribosome recycling factor shows that a flexible hinge may act as a functional switch.
RNA, 6, 2000
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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 | | Descriptor: | (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, ... | | Authors: | 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. | | Deposit date: | 2017-01-25 | | Release date: | 2017-08-09 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | 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 | | Descriptor: | (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, ... | | Authors: | 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. | | Deposit date: | 2017-01-25 | | Release date: | 2017-08-09 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | 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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5X1B
 | | CO bound cytochrome c oxidase at 20 nsec after pump laser irradiation to release CO from O2 reduction center | | Descriptor: | (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, ... | | Authors: | 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. | | Deposit date: | 2017-01-25 | | Release date: | 2017-08-09 | | Last modified: | 2017-12-06 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | 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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4EFM
 | | Crystal structure of H-Ras G12V in complex with GppNHp (state 1) | | Descriptor: | GTPase HRas, MAGNESIUM ION, PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER | | Authors: | Muraoka, S, Shima, F, Araki, M, Inoue, T, Yoshimoto, A, Ijiri, Y, Seki, N, Tamura, A, Kumasaka, T, Yamamoto, M, Kataoka, T. | | Deposit date: | 2012-03-30 | | Release date: | 2012-05-16 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | 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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4EFN
 | | Crystal structure of H-Ras Q61L in complex with GppNHp (state 1) | | Descriptor: | GTPase HRas, MAGNESIUM ION, PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER | | Authors: | Muraoka, S, Shima, F, Araki, M, Inoue, T, Yoshimoto, A, Ijiri, Y, Seki, N, Tamura, A, Kumasaka, T, Yamamoto, M, Kataoka, T. | | Deposit date: | 2012-03-30 | | Release date: | 2012-05-16 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | 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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4EFL
 | | Crystal structure of H-Ras WT in complex with GppNHp (state 1) | | Descriptor: | GTPase HRas, MAGNESIUM ION, PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER | | Authors: | Muraoka, S, Shima, F, Araki, M, Inoue, T, Yoshimoto, A, Ijiri, Y, Seki, N, Tamura, A, Kumasaka, T, Yamamoto, M, Kataoka, T. | | Deposit date: | 2012-03-30 | | Release date: | 2012-05-16 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | 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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8IXT
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8IXU
 | | Rat Transcobalamin in Complex with Cobalamin | | Descriptor: | CHLORIDE ION, COBALAMIN, NITRATE ION, ... | | Authors: | Bokhove, M, Kumasaka, T. | | Deposit date: | 2023-04-03 | | Release date: | 2024-05-22 | | Method: | X-RAY DIFFRACTION (1.3 Å) | | Cite: | The structure of the rat vitamin B 12 transporter TC and its complex with glutathionylcobalamin.
J.Biol.Chem., 300, 2024
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8JOG
 | | solution structure of Ras Binding Domein (RBD) in C-RAF with negative allosteric modulator. | | Descriptor: | RAF proto-oncogene serine/threonine-protein kinase | | Authors: | Makino, Y, Matsumoto, S, Yoshikawa, Y, Kawamura, T, Kumasaka, T, Shima, F. | | Deposit date: | 2023-06-07 | | Release date: | 2024-06-12 | | Method: | SOLUTION NMR | | Cite: | 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 | | Descriptor: | RAF proto-oncogene serine/threonine-protein kinase | | Authors: | Makino, Y, Matsumoto, S, Yoshikawa, Y, Kawamura, T, Kumasaka, T, Shima, F. | | Deposit date: | 2023-06-07 | | Release date: | 2024-06-12 | | Method: | SOLUTION NMR | | Cite: | 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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7WB8
 | | Crystal structure of Bovine Pancreatic Trypsin in complex with 5-Methoxytryptamine at Room Temperature | | Descriptor: | 2-(5-methoxy-1H-indol-3-yl)ethanamine, CALCIUM ION, Cationic trypsin, ... | | Authors: | Sakai, N, Okumura, H, Yamamoto, M, Kumasaka, T. | | Deposit date: | 2021-12-15 | | Release date: | 2022-06-15 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.38 Å) | | Cite: | In situ crystal data-collection and ligand-screening system at SPring-8.
Acta Crystallogr.,Sect.F, 78, 2022
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7WB9
 | | Crystal structure of Bovine Pancreatic Trypsin in complex with 5-Chlorotryptamine at Room Temperature | | Descriptor: | 2-(5-chloranyl-1~{H}-indol-3-yl)ethanamine, CALCIUM ION, Cationic trypsin, ... | | Authors: | Sakai, N, Okumura, H, Yamamoto, M, Kumasaka, T. | | Deposit date: | 2021-12-15 | | Release date: | 2022-06-15 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.56 Å) | | Cite: | In situ crystal data-collection and ligand-screening system at SPring-8.
Acta Crystallogr.,Sect.F, 78, 2022
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7WB6
 | | Crystal structure of Bovine Pancreatic Trypsin in complex with 4-Bromobenzamidine at Room Temperature | | Descriptor: | 4-bromanylbenzenecarboximidamide, CALCIUM ION, Cationic trypsin, ... | | Authors: | Sakai, N, Okumura, H, Yamamoto, M, Kumasaka, T. | | Deposit date: | 2021-12-15 | | Release date: | 2022-06-15 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.48 Å) | | Cite: | In situ crystal data-collection and ligand-screening system at SPring-8.
Acta Crystallogr.,Sect.F, 78, 2022
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7WA2
 | | Crystal structure of Bovine Pancreatic Trypsin in complex with 4-Methoxybenzamidine at Room Temperature | | Descriptor: | 4-methoxybenzenecarboximidamide, CALCIUM ION, Cationic trypsin, ... | | Authors: | Sakai, N, Okumura, H, Yamamoto, M, Kumasaka, T. | | Deposit date: | 2021-12-11 | | Release date: | 2022-06-15 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.52 Å) | | Cite: | In situ crystal data-collection and ligand-screening system at SPring-8.
Acta Crystallogr.,Sect.F, 78, 2022
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7WA0
 | | Crystal structure of Bovine Pancreatic Trypsin in complex with Benzamidine at Room Temperature | | Descriptor: | BENZAMIDINE, CALCIUM ION, Cationic trypsin, ... | | Authors: | Sakai, N, Okumura, H, Yamamoto, M, Kumasaka, T. | | Deposit date: | 2021-12-11 | | Release date: | 2022-06-15 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.77 Å) | | Cite: | In situ crystal data-collection and ligand-screening system at SPring-8.
Acta Crystallogr.,Sect.F, 78, 2022
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7WBA
 | | Crystal structure of Bovine Pancreatic Trypsin in complex with Tryptamine at Room Temperature | | Descriptor: | 2-(1H-INDOL-3-YL)ETHANAMINE, CALCIUM ION, Cationic trypsin, ... | | Authors: | Sakai, N, Okumura, H, Yamamoto, M, Kumasaka, T. | | Deposit date: | 2021-12-15 | | Release date: | 2022-06-15 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.45 Å) | | Cite: | In situ crystal data-collection and ligand-screening system at SPring-8.
Acta Crystallogr.,Sect.F, 78, 2022
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7WB7
 | | Crystal structure of Bovine Pancreatic Trypsin in complex with Serotonin at Room Temperature | | Descriptor: | CALCIUM ION, Cationic trypsin, DIMETHYL SULFOXIDE, ... | | Authors: | Sakai, N, Okumura, H, Yamamoto, M, Kumasaka, T. | | Deposit date: | 2021-12-15 | | Release date: | 2022-06-15 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.45 Å) | | Cite: | In situ crystal data-collection and ligand-screening system at SPring-8.
Acta Crystallogr.,Sect.F, 78, 2022
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5X9S
 | | Crystal structure of fully modified H-Ras-GppNHp | | Descriptor: | CALCIUM ION, GTPase HRas, MAGNESIUM ION, ... | | Authors: | Matsumoto, S, Ke, H, Murashima, Y, Taniguchi-Tamura, H, Miyamoto, R, Yoshikawa, Y, Kumasaka, T, Mizohata, E, Edamatsu, H, Kataoka, T. | | Deposit date: | 2017-03-09 | | Release date: | 2017-08-30 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Structural basis for intramolecular interaction of post-translationally modified H-RasGTP prepared by protein ligation
FEBS Lett., 591, 2017
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3AHU
 | | Crystal structure of YmaH (Hfq) from Bacillus subtilis in complex with an RNA aptamer. | | Descriptor: | 5'-R(*AP*GP*AP*GP*AP*G)-3', Protein hfq | | Authors: | Baba, S, Someya, T, Kumasaka, T, Kawai, G, Nakamura, K. | | Deposit date: | 2010-04-29 | | Release date: | 2011-07-13 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Crystal structure of YmaH (Hfq) from Bacillus subtilis in complex with an RNA aptamer.
To be Published
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5B42
 | | Crystal structure of the C-terminal endonuclease domain of Aquifex aeolicus MutL. | | Descriptor: | CADMIUM ION, DI(HYDROXYETHYL)ETHER, DNA mismatch repair protein MutL | | Authors: | Fukui, K, Baba, S, Kumasaka, T, Yano, T. | | Deposit date: | 2016-03-30 | | Release date: | 2016-07-13 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (1.35 Å) | | Cite: | 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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