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2CZU
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BU of 2czu by Molmil
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:2024-03-20
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
2CZT
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BU of 2czt by Molmil
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:2021-11-10
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
2Z3I
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BU of 2z3i by Molmil
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
2Z3H
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BU of 2z3h by Molmil
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
2Z3G
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BU of 2z3g by Molmil
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
1WNI
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BU of 1wni by Molmil
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:2019-10-09
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:Crystal structure of H2-proteinase from the venom of Trimeresurus flavoviridis.
J.Biochem., 119, 1996
1WN5
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BU of 1wn5 by Molmil
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
1WN6
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BU of 1wn6 by Molmil
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
8GOI
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BU of 8goi by Molmil
23-residues Heterotetramic Antiparallel Coiled-Coil Derived From LacI
Descriptor: GLYCEROL, Lac23ys_aEE, an acidic mutant of LacI C-terminal tetramerization helix, ...
Authors:Kumasaka, T.
Deposit date:2022-08-25
Release date:2023-08-30
Method:X-RAY DIFFRACTION (1.54 Å)
Cite:Design of interchain Glu-Arg salt-bridges stabilizing heterotetrameric coiled-coil derived from Lac repressor.
To Be Published
8GOH
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BU of 8goh by Molmil
Homotetramic Antiparallel Coiled-Coil of 23-residues LacI C-terminal tetramerization helix
Descriptor: LacI C-terminal tetramerization helix, PENTAETHYLENE GLYCOL
Authors:Kumasaka, T.
Deposit date:2022-08-25
Release date:2023-08-30
Method:X-RAY DIFFRACTION (1.1 Å)
Cite:Design of interchain Glu-Arg salt-bridges stabilizing heterotetrameric coiled-coil derived from Lac repressor.
To Be Published
5B30
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BU of 5b30 by Molmil
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
5B2Z
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BU of 5b2z by Molmil
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
8GOJ
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BU of 8goj by Molmil
23-residues Heterotetramic Antiparallel Coiled-Coil Derived From LacI
Descriptor: Lac23ys_EE, an acidic mutant of LacI C-terminal tetramerization helix, Lac23ys_KK, ...
Authors:Kumasaka, T.
Deposit date:2022-08-25
Release date:2023-08-30
Method:X-RAY DIFFRACTION (1.38 Å)
Cite:Design of interchain Glu-Arg salt-bridges stabilizing heterotetrameric coiled-coil derived from Lac repressor.
To Be Published
5B4S
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BU of 5b4s by Molmil
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:2020-02-26
Method:X-RAY DIFFRACTION (1.75 Å)
Cite:Crystal structure of a family 80 chitosanase from Mitsuaria chitosanitabida
FEBS Lett., 591, 2017
3AH7
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BU of 3ah7 by Molmil
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
2Z3J
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BU of 2z3j by Molmil
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
4EFN
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BU of 4efn by Molmil
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
4EFL
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BU of 4efl by Molmil
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
4EFM
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BU of 4efm by Molmil
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
7QXK
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BU of 7qxk by Molmil
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
7QYC
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BU of 7qyc by Molmil
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
7QY4
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BU of 7qy4 by Molmil
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
3HSB
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BU of 3hsb by Molmil
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
5B42
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BU of 5b42 by Molmil
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
4XIG
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BU of 4xig by Molmil
Crystal structure of bacterial alginate ABC transporter determined through humid air and glue-coating method
Descriptor: 4-deoxy-alpha-L-erythro-hex-4-enopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid, AlgM1, AlgM2, ...
Authors:Kaneko, A, Maruyama, Y, Mizuno, N, Baba, S, Kumasaka, T, Mikami, B, Murata, K, Hashimoto, W.
Deposit date:2015-01-07
Release date:2016-01-13
Last modified:2024-03-20
Method:X-RAY DIFFRACTION (3.402 Å)
Cite:A solute-binding protein in the closed conformation induces ATP hydrolysis in a bacterial ATP-binding cassette transporter involved in the import of alginate.
J.Biol.Chem., 292, 2017

217705

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