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7DBT
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BU of 7dbt by Molmil
Crystal structure of catalytic domain of Anhydrobiosis-related Mn-dependent Peroxidase (AMNP) from Ramazzottius varieornatus (Mn2+-bound form)
Descriptor: AMNP/g12777, MANGANESE (II) ION
Authors:Yoshida, Y, Satoh, T, Ota, C, Tanaka, S, Horikawa, D.D, Tomita, M, Kato, K, Arakawa, K.
Deposit date:2020-10-21
Release date:2021-10-06
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.3 Å)
Cite:Time-series transcriptomic screening of factors contributing to the cross-tolerance to UV radiation and anhydrobiosis in tardigrades.
Bmc Genomics, 23, 2022
7DBU
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BU of 7dbu by Molmil
Crystal structure of catalytic domain of Anhydrobiosis-related Mn-dependent Peroxidase (AMNP) from Ramazzottius varieornatus (Zn2+-bound form)
Descriptor: AMNP/g12777, ZINC ION
Authors:Yoshida, Y, Satoh, T, Ota, C, Tanaka, S, Horikawa, D.D, Tomita, M, Kato, K, Arakawa, K.
Deposit date:2020-10-21
Release date:2021-10-06
Last modified:2022-06-15
Method:X-RAY DIFFRACTION (1.6 Å)
Cite:Time-series transcriptomic screening of factors contributing to the cross-tolerance to UV radiation and anhydrobiosis in tardigrades.
Bmc Genomics, 23, 2022
6IOY
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BU of 6ioy by Molmil
Crystal structure of Porphyromonas gingivalis acetate kinase
Descriptor: (4S)-2-METHYL-2,4-PENTANEDIOL, Acetate kinase, SULFATE ION
Authors:Kezuka, Y, Yoshida, Y, Nonaka, T.
Deposit date:2018-10-31
Release date:2019-04-24
Last modified:2023-11-22
Method:X-RAY DIFFRACTION (1.94 Å)
Cite:Characterization of the phosphotransacetylase-acetate kinase pathway for ATP production inPorphyromonas gingivalis.
J Oral Microbiol, 11, 2019
6IOX
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BU of 6iox by Molmil
Crystal structure of Porphyromonas gingivalis phosphotransacetylase in complex with acetyl-CoA
Descriptor: ACETYL COENZYME *A, Phosphotransacetylase
Authors:Kezuka, Y, Yoshida, Y, Nonaka, T.
Deposit date:2018-10-31
Release date:2019-04-24
Last modified:2023-11-22
Method:X-RAY DIFFRACTION (2.04 Å)
Cite:Characterization of the phosphotransacetylase-acetate kinase pathway for ATP production inPorphyromonas gingivalis.
J Oral Microbiol, 11, 2019
6IOW
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BU of 6iow by Molmil
Crystal structure of Porphyromonas gingivalis phosphotransacetylase
Descriptor: Phosphotransacetylase
Authors:Kezuka, Y, Yoshida, Y, Nonaka, T.
Deposit date:2018-10-31
Release date:2019-04-24
Last modified:2023-11-22
Method:X-RAY DIFFRACTION (1.7 Å)
Cite:Characterization of the phosphotransacetylase-acetate kinase pathway for ATP production inPorphyromonas gingivalis.
J Oral Microbiol, 11, 2019
3B1E
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BU of 3b1e by Molmil
Crystal structure of betaC-S lyase from Streptococcus anginosus in complex with L-serine: alpha-Aminoacrylate form
Descriptor: 2-{[(E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}prop-2-enoic acid, 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, ACETATE ION, ...
Authors:Kezuka, Y, Yoshida, Y, Nonaka, T.
Deposit date:2011-06-29
Release date:2012-06-27
Last modified:2017-10-11
Method:X-RAY DIFFRACTION (1.78 Å)
Cite:Structural insights into catalysis by beta C-S lyase from Streptococcus anginosus
Proteins, 80, 2012
3B1C
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BU of 3b1c by Molmil
Crystal structure of betaC-S lyase from Streptococcus anginosus: Internal aldimine form
Descriptor: BetaC-S lyase, GLYCEROL, PYRIDOXAL-5'-PHOSPHATE, ...
Authors:Kezuka, Y, Yoshida, Y, Nonaka, T.
Deposit date:2011-06-29
Release date:2012-06-27
Last modified:2014-01-22
Method:X-RAY DIFFRACTION (1.93 Å)
Cite:Structural insights into catalysis by beta C-S lyase from Streptococcus anginosus
Proteins, 80, 2012
3B1D
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BU of 3b1d by Molmil
Crystal structure of betaC-S lyase from Streptococcus anginosus in complex with L-serine: External aldimine form
Descriptor: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, BetaC-S lyase, PYRIDOXAL-5'-PHOSPHATE, ...
Authors:Kezuka, Y, Yoshida, Y, Nonaka, T.
Deposit date:2011-06-29
Release date:2012-06-27
Last modified:2017-10-11
Method:X-RAY DIFFRACTION (1.66 Å)
Cite:Structural insights into catalysis by beta C-S lyase from Streptococcus anginosus
Proteins, 80, 2012
2RJ2
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BU of 2rj2 by Molmil
Crystal Structure of the Sugar Recognizing SCF Ubiquitin Ligase at 1.7 Resolution
Descriptor: CHLORIDE ION, F-box only protein 2, NICKEL (II) ION
Authors:Vaijayanthimala, S, Velmurugan, D, Mizushima, T, Yamane, T, Yoshida, Y, Tanaka, K.
Deposit date:2007-10-14
Release date:2008-10-14
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (1.7 Å)
Cite:Crystal Structure of the Sugar Recognizing SCF Ubiquitin Ligase at 1.7 Resolution
To be Published
2NLI
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BU of 2nli by Molmil
Crystal Structure of the complex between L-lactate oxidase and a substrate analogue at 1.59 angstrom resolution
Descriptor: FLAVIN MONONUCLEOTIDE, HYDROGEN PEROXIDE, LACTIC ACID, ...
Authors:Furuichi, M, Suzuki, N, Balasundaresan, D, Yoshida, Y, Minagawa, H, Watanabe, Y, Kaneko, H, Waga, I, Kumar, P.K.R, Mizuno, H.
Deposit date:2006-10-20
Release date:2007-10-23
Last modified:2023-11-15
Method:X-RAY DIFFRACTION (1.59 Å)
Cite:X-ray structures of Aerococcus viridans lactate oxidase and its complex with D-lactate at pH 4.5 show an alpha-hydroxyacid oxidation mechanism
J.Mol.Biol., 378, 2008
5B53
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BU of 5b53 by Molmil
Crystal structure of hydrogen sulfide-producing enzyme (Fn1055) from Fusobacterium nucleatum
Descriptor: CHLORIDE ION, Cysteine synthase, PYRIDOXAL-5'-PHOSPHATE
Authors:Kezuka, Y, Yoshida, Y, Nonaka, T.
Deposit date:2016-04-22
Release date:2017-04-26
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (2.91 Å)
Cite:Crystal structure of hydrogen sulfide-producing enzyme (Fn1055) from Fusobacterium nucleatum
To Be Published
5B55
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BU of 5b55 by Molmil
Crystal structure of hydrogen sulfide-producing enzyme (Fn1055) D232N mutant in complexed with alpha-aminoacrylate intermediate: lysine-dimethylated form
Descriptor: 2-{[(E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}prop-2-enoic acid, Cysteine synthase, DI(HYDROXYETHYL)ETHER, ...
Authors:Kezuka, Y, Yoshida, Y, Nonaka, T.
Deposit date:2016-04-22
Release date:2017-04-26
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (2.14 Å)
Cite:Structural insights into the catalytic mechanism of cysteine (hydroxyl) lyase from the hydrogen sulfide-producing oral pathogen,Fusobacterium nucleatum.
Biochem. J., 475, 2018
2ZFA
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BU of 2zfa by Molmil
Structure of Lactate Oxidase at pH4.5 from AEROCOCCUS VIRIDANS
Descriptor: 1,2-ETHANEDIOL, FLAVIN MONONUCLEOTIDE, Lactate oxidase
Authors:Furuichi, M, Balasundaresan, D, Suzuki, N, Yoshida, Y, Minagawa, H, Kaneko, H, Waga, I, Kumar, P.K.R, Mizuno, H.
Deposit date:2007-12-26
Release date:2008-04-22
Last modified:2023-11-01
Method:X-RAY DIFFRACTION (1.81 Å)
Cite:X-ray structures of Aerococcus viridans lactate oxidase and its complex with D-lactate at pH 4.5 show an alpha-hydroxyacid oxidation mechanism
J.Mol.Biol., 378, 2008
1J1G
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BU of 1j1g by Molmil
Crystal structure of the RNase MC1 mutant N71S in complex with 5'-GMP
Descriptor: GUANOSINE-5'-MONOPHOSPHATE, Ribonuclease MC1
Authors:Numata, T, Suzuki, A, Kakuta, Y, Kimura, K, Yao, M, Tanaka, I, Yoshida, Y, Ueda, T, Kimura, M.
Deposit date:2002-12-04
Release date:2003-05-20
Last modified:2023-10-25
Method:X-RAY DIFFRACTION (1.6 Å)
Cite:Crystal Structures of the Ribonuclease MC1 Mutants N71T and N71S in Complex with 5'-GMP: Structural Basis for Alterations in Substrate Specificity
Biochemistry, 42, 2003
1J1F
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BU of 1j1f by Molmil
Crystal structure of the RNase MC1 mutant N71T in complex with 5'-GMP
Descriptor: GUANOSINE-5'-MONOPHOSPHATE, RIBONUCLEASE MC1
Authors:Numata, T, Suzuki, A, Kakuta, Y, Kimura, K, Yao, M, Tanaka, I, Yoshida, Y, Ueda, T, Kimura, M.
Deposit date:2002-12-03
Release date:2003-05-20
Last modified:2023-10-25
Method:X-RAY DIFFRACTION (1.6 Å)
Cite:Crystal Structures of the Ribonuclease MC1 Mutants N71T and N71S in Complex with 5'-GMP: Structural Basis for Alterations in Substrate Specificity
Biochemistry, 42, 2003
5XEM
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BU of 5xem by Molmil
Crystal structure of a hydrogen sulfide-producing enzyme (Fn1220) from Fusobacterium nucleatum in complex with L-lanthionine-PLP Schiff base
Descriptor: (2R)-2-azanyl-3-[(2R)-2-azanyl-3-oxidanyl-3-oxidanylidene-propyl]sulfanyl-propanoic acid, 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE, 2-(2-METHOXYETHOXY)ETHANOL, ...
Authors:Kezuka, Y, Yoshida, Y, Nonaka, T.
Deposit date:2017-04-05
Release date:2018-04-11
Method:X-RAY DIFFRACTION (1.84 Å)
Cite:Crystal structure of a hydrogen sulfide-producing enzyme (Fn1220) from Fusobacterium nucleatum in complex with L-lanthionine-PLP Schiff base
To Be Published
5XEO
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BU of 5xeo by Molmil
Crystal structure of a hydrogen sulfide-producing enzyme (Fn1220) from Fusobacterium nucleatum
Descriptor: ACETATE ION, CALCIUM ION, Cysteine synthase, ...
Authors:Kezuka, Y, Yoshida, Y, Nonaka, T.
Deposit date:2017-04-05
Release date:2018-04-11
Method:X-RAY DIFFRACTION (2.03 Å)
Cite:Crystal structure of a hydrogen sulfide-producing enzyme (Fn1220) from Fusobacterium nucleatum
To Be Published
5XEN
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BU of 5xen by Molmil
Crystal structure of a hydrogen sulfide-producing enzyme (Fn1220) from Fusobacterium nucleatum in complex with L-serine-PLP Schiff base
Descriptor: ACETATE ION, CALCIUM ION, Cysteine synthase, ...
Authors:Kezuka, Y, Yoshida, Y, Nonaka, T.
Deposit date:2017-04-05
Release date:2018-04-11
Method:X-RAY DIFFRACTION (1.94 Å)
Cite:Crystal structure of a hydrogen sulfide-producing enzyme (Fn1220) from Fusobacterium nucleatum in complex with L-serine-PLP Schiff base
To Be Published
5B4N
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BU of 5b4n by Molmil
Structure analysis of function associated loop mutant of substrate recognition domain of Fbs1 ubiquitin ligase
Descriptor: F-box only protein 2
Authors:Nishio, K, Yoshida, Y, Tanaka, K, Mizushima, T.
Deposit date:2016-04-06
Release date:2016-09-14
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (2.3 Å)
Cite:Structural analysis of a function-associated loop mutant of the substrate-recognition domain of Fbs1 ubiquitin ligase
Acta Crystallogr.,Sect.F, 72, 2016
1UMI
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BU of 1umi by Molmil
Structural basis of sugar-recognizing ubiquitin ligase
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose, F-box only protein 2
Authors:Mizushima, T, Hirao, T, Yoshida, Y, Lee, S.J, Chiba, T, Iwai, K, Yamaguchi, Y, Kato, K, Tsukihara, T, Tanaka, K.
Deposit date:2003-10-01
Release date:2004-04-06
Last modified:2023-12-27
Method:X-RAY DIFFRACTION (2.4 Å)
Cite:Structural basis of sugar-recognizing ubiquitin ligase.
Nat.Struct.Mol.Biol., 11, 2004
1UMH
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BU of 1umh by Molmil
Structural basis of sugar-recognizing ubiquitin ligase
Descriptor: F-box only protein 2, NICKEL (II) ION
Authors:Mizushima, T, Hirao, T, Yoshida, Y, Lee, S.J, Chiba, T, Iwai, K, Yamaguchi, Y, Kato, K, Tsukihara, T, Tanaka, K, RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Deposit date:2003-10-01
Release date:2004-04-06
Last modified:2023-12-27
Method:X-RAY DIFFRACTION (2 Å)
Cite:Structural basis of sugar-recognizing ubiquitin ligase
NAT.STRUCT.MOL.BIOL., 11, 2004
5Z5C
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BU of 5z5c by Molmil
Crystal structure of hydrogen sulfide-producing enzyme (Fn1055) from Fusobacterium nucleatum: lysine-dimethylated form
Descriptor: CHLORIDE ION, Cysteine synthase, PYRIDOXAL-5'-PHOSPHATE
Authors:Kezuka, Y, Yoshida, Y, Nonaka, T.
Deposit date:2018-01-17
Release date:2018-02-14
Last modified:2018-03-07
Method:X-RAY DIFFRACTION (2.07 Å)
Cite:Structural insights into the catalytic mechanism of cysteine (hydroxyl) lyase from the hydrogen sulfide-producing oral pathogen,
Biochem. J., 475, 2018
2D35
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BU of 2d35 by Molmil
Solution structure of Cell Division Reactivation Factor, CedA
Descriptor: Cell division activator cedA
Authors:Abe, Y, Watanabe, N, Matsuda, Y, Yoshida, Y, Katayama, T, Ueda, T.
Deposit date:2005-09-26
Release date:2006-12-12
Last modified:2022-03-09
Method:SOLUTION NMR
Cite:Structural Analysis and Molecular Interaction of Cell Division Reactivation Factor, CedA from Escherichia coli
To be Published
2E33
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BU of 2e33 by Molmil
Structural basis for selection of glycosylated substrate by SCFFbs1 ubiquitin ligase
Descriptor: F-box only protein 2, Ribonuclease pancreatic, alpha-D-mannopyranose-(1-3)-[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
Authors:Mizushima, T, Yoshida, Y, Kumanomidou, T, Hasegawa, Y, Yamane, T, Tanaka, K.
Deposit date:2006-11-20
Release date:2007-03-20
Last modified:2023-10-25
Method:X-RAY DIFFRACTION (2.7 Å)
Cite:Structural basis for the selection of glycosylated substrates by SCFFbs1 ubiquitin ligase
Proc.Natl.Acad.Sci.Usa, 104, 2007
2E31
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BU of 2e31 by Molmil
Structural basis for selection of glycosylated substrate by SCFFbs1 ubiquitin ligase
Descriptor: F-box only protein 2, S-phase kinase-associated protein 1A
Authors:Mizushima, T, Yoshida, Y, Kumanomidou, T, Hasegawa, Y, Yamane, T, Tanaka, K.
Deposit date:2006-11-20
Release date:2007-03-20
Last modified:2023-10-25
Method:X-RAY DIFFRACTION (2.4 Å)
Cite:Structural basis for the selection of glycosylated substrates by SCFFbs1 ubiquitin ligase
Proc.Natl.Acad.Sci.Usa, 104, 2007

 

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