2CZU
 
 | | lipocalin-type prostaglandin D synthase | | Descriptor: | Prostaglandin-H2 D-isomerase | | Authors: | Kumasaka, T, Irikura, D, Ago, H, Aritake, K, Yamamoto, M, Inoue, T, Miyano, M, Urade, Y, Hayaishi, O, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2005-07-17 | | Release date: | 2006-10-03 | | Last modified: | 2024-10-09 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Structural basis of the catalytic mechanism operating in open-closed conformers of lipocalin type prostaglandin D synthase.
J.Biol.Chem., 284, 2009
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2CZT
 | | lipocalin-type prostaglandin D synthase | | Descriptor: | Prostaglandin-H2 D-isomerase | | Authors: | Kumasaka, T, Irikura, D, Ago, H, Aritake, K, Yamamoto, M, Inoue, T, Miyano, M, Urade, Y, Hayaishi, O, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2005-07-17 | | Release date: | 2006-10-03 | | Last modified: | 2024-10-16 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Structural basis of the catalytic mechanism operating in open-closed conformers of lipocalin type prostaglandin D synthase.
J.Biol.Chem., 284, 2009
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1WNI
 | | Crystal Structure of H2-Proteinase | | Descriptor: | Trimerelysin II, ZINC ION | | Authors: | Kumasaka, T, Yamamoto, M, Moriyama, H, Tanaka, N, Sato, M, Katsube, Y, Yamakawa, Y, Omori-Satoh, T, Iwanaga, S, Ueki, T. | | Deposit date: | 2004-08-04 | | Release date: | 2004-08-17 | | Last modified: | 2024-11-20 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Crystal structure of H2-proteinase from the venom of Trimeresurus flavoviridis.
J.Biochem., 119, 1996
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1WN5
 | | Crystal Structure of Blasticidin S Deaminase (BSD) Complexed with Cacodylic Acid | | Descriptor: | Blasticidin-S deaminase, CACODYLATE ION, ZINC ION | | Authors: | Kumasaka, T, Yamamoto, M, Furuichi, M, Nakasako, M, Kimura, M, Yamaguchi, I, Ueki, T. | | Deposit date: | 2004-07-27 | | Release date: | 2005-10-25 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Crystal structures of blasticidin S deaminase (BSD): implications for dynamic properties of catalytic zinc
J.Biol.Chem., 282, 2007
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1WN6
 | | Crystal Structure of Blasticidin S Deaminase (BSD) Complexed with Tetrahedral Intermediate of Blasticidin S | | Descriptor: | 6-(4-AMINO-4-HYDROXY-2-OXO-3,4-DIHYDRO-2H-PYRIMIDIN-1-YL)-3-[3-AMINO-5-(N-METHYL-GUANIDINO)-PENT ANOYLAMINO]-3,6-DIHYDRO-2H-PYRAN-2-CARBOXYLIC ACID, ARSENIC, Blasticidin-S deaminase, ... | | Authors: | Kumasaka, T, Yamamoto, M, Furuichi, M, Nakasako, M, Kimura, M, Yamaguchi, I, Ueki, T. | | Deposit date: | 2004-07-27 | | Release date: | 2005-10-25 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Crystal structures of blasticidin S deaminase (BSD): implications for dynamic properties of catalytic zinc
J.Biol.Chem., 282, 2007
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2Z3H
 | | Crystal structure of blasticidin S deaminase (BSD) complexed with deaminohydroxy blasticidin S | | Descriptor: | 1-(4-{[(3R)-3-AMINO-5-{[(Z)-AMINO(IMINO)METHYL](METHYL)AMINO}PENTANOYL]AMINO}-2,3,4-TRIDEOXY-D-ERYTHRO-HEX-2-ENOPYRANURONOSYL)-4-HYDROXYPYRIMIDIN-2(1H)-ONE, Blasticidin-S deaminase, ZINC ION | | Authors: | Kumasaka, T, Yamamoto, M, Furuichi, M, Nakasako, M, Kimura, M, Yamaguchi, I, Ueki, T. | | Deposit date: | 2007-06-04 | | Release date: | 2007-10-23 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (1.5 Å) | | Cite: | Crystal structures of blasticidin S deaminase (BSD): implications for dynamic properties of catalytic zinc
J.Biol.Chem., 282, 2007
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2Z3G
 | | Crystal structure of blasticidin S deaminase (BSD) | | Descriptor: | Blasticidin-S deaminase, ZINC ION, alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose | | Authors: | Kumasaka, T, Yamamoto, M, Furuichi, M, Nakasako, M, Kimura, M, Yamaguchi, I, Ueki, T. | | Deposit date: | 2007-06-04 | | Release date: | 2007-10-23 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (1.5 Å) | | Cite: | Crystal structures of blasticidin S deaminase (BSD): implications for dynamic properties of catalytic zinc
J.Biol.Chem., 282, 2007
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2Z3I
 | | Crystal structure of blasticidin S deaminase (BSD) mutant E56Q complexed with substrate | | Descriptor: | BLASTICIDIN S, Blasticidin-S deaminase, CACODYLATE ION, ... | | Authors: | Kumasaka, T, Yamamoto, M, Furuichi, M, Nakasako, M, Kimura, M, Yamaguchi, I, Ueki, T. | | Deposit date: | 2007-06-04 | | Release date: | 2007-10-23 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Crystal structures of blasticidin S deaminase (BSD): implications for dynamic properties of catalytic zinc
J.Biol.Chem., 282, 2007
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8GOH
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8GOI
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8GOJ
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5B2Z
 | | H-Ras WT in complex with GppNHp (state 2*) before structural transition by humidity control | | Descriptor: | CALCIUM ION, GTPase HRas, MAGNESIUM ION, ... | | Authors: | Kumasaka, T, Miyano, N, Baba, S, Matsumoto, S, Kataoka, T, Shima, F. | | Deposit date: | 2016-02-07 | | Release date: | 2016-06-01 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.56 Å) | | Cite: | Molecular Mechanism for Conformational Dynamics of Ras-GTP Elucidated from In-Situ Structural Transition in Crystal
Sci Rep, 6, 2016
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5B30
 | | H-Ras WT in complex with GppNHp (state 1) after structural transition by humidity control | | Descriptor: | CALCIUM ION, GTPase HRas, MAGNESIUM ION, ... | | Authors: | Kumasaka, T, Miyano, N, Baba, S, Matsumoto, S, Kataoka, T, Shima, F. | | Deposit date: | 2016-02-08 | | Release date: | 2016-06-01 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.6 Å) | | Cite: | Molecular Mechanism for Conformational Dynamics of Ras-GTP Elucidated from In-Situ Structural Transition in Crystal
Sci Rep, 6, 2016
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5B4S
 | | Crystal Structure of GH80 chitosanase from Mitsuaria chitosanitabida | | Descriptor: | Chitosanase | | Authors: | Kumasaka, T, Yorinaga, Y, Yamamoto, M, Hamada, K, Kawamukai, M. | | Deposit date: | 2016-04-19 | | Release date: | 2017-02-01 | | Last modified: | 2024-11-13 | | Method: | X-RAY DIFFRACTION (1.75 Å) | | Cite: | Crystal structure of a family 80 chitosanase from Mitsuaria chitosanitabida
FEBS Lett., 591, 2017
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3AH7
 | | Crystal structure of the ISC-like [2Fe-2S] ferredoxin (FdxB) from Pseudomonas putida JCM 20004 | | Descriptor: | CHLORIDE ION, FE2/S2 (INORGANIC) CLUSTER, SODIUM ION, ... | | Authors: | Kumasaka, T, Shimizu, N, Ohmori, D, Iwasaki, T. | | Deposit date: | 2010-04-20 | | Release date: | 2011-04-20 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Crystal structure of the ISC-like [2Fe-2S] ferredoxin (FdxB) from Pseudomonas putida JCM 20004
To be Published
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2Z3J
 | | Crystal structure of blasticidin S deaminase (BSD) R90K mutant | | Descriptor: | Blasticidin-S deaminase, CACODYLATE ION, CHLORIDE ION, ... | | Authors: | Teh, A.H, Kumasaka, T, Yamamoto, M, Furuichi, M, Nakasako, M, Kimura, M, Yamaguchi, I, Ueki, T. | | Deposit date: | 2007-06-04 | | Release date: | 2007-10-23 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (1.6 Å) | | Cite: | Crystal structures of blasticidin S deaminase (BSD): implications for dynamic properties of catalytic zinc
J.Biol.Chem., 282, 2007
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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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3HSB
 | | Crystal structure of YmaH (Hfq) from Bacillus subtilis in complex with an RNA aptamer | | Descriptor: | Protein hfq, RNA (5'-R(*AP*GP*AP*GP*AP*GP*A)-3') | | Authors: | Baba, S, Someya, T, Kumasaka, T, Kawai, G, Nakamura, K. | | Deposit date: | 2009-06-10 | | Release date: | 2010-06-23 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Crystal structure of Hfq from Bacillus subtilis in complex with SELEX-derived RNA aptamer: insight into RNA-binding properties of bacterial Hfq
Nucleic Acids Res., 40, 2012
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7QY4
 | | As isolated MSOX movie series dataset 5 (2 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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7QXK
 | | As isolated MSOX movie series dataset 1 (0.4 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: | 2022-01-26 | | 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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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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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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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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3CE1
 | | Crystal Structure of the Cu/Zn Superoxide Dismutase from Cryptococcus liquefaciens Strain N6 | | Descriptor: | ACETATE ION, COPPER (II) ION, Superoxide dismutase [Cu-Zn], ... | | Authors: | Teh, A.H, Kanamasa, S, Kajiwara, S, Kumasaka, T. | | Deposit date: | 2008-02-27 | | Release date: | 2008-08-26 | | Last modified: | 2024-10-16 | | Method: | X-RAY DIFFRACTION (1.2 Å) | | Cite: | Structure of Cu/Zn superoxide dismutase from the heavy-metal-tolerant yeast Cryptococcus liquefaciens strain N6.
Biochem.Biophys.Res.Commun., 374, 2008
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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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