4YL4
 
 | | 1.1 Angstrom resolution X-ray Crystallographic Structure of Psudoazurin | | Descriptor: | COPPER (II) ION, GLYCEROL, Pseudoazurin | | Authors: | Yamaguchi, T, Asamura, S, Takashina, A, Unno, M, Kohzuma, T. | | Deposit date: | 2015-03-05 | | Release date: | 2016-03-09 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.1 Å) | | Cite: | X-ray crystallographic evidence for the simultaneous presence of axial and rhombic sites in cupredoxins: atomic resolution X-ray crystal structure analysis of pseudoazurin and DFT modelling
Rsc Adv, 6, 2016
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5XMO
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7CLR
 | | CryoEM structure of S.typhimurium flagellar LP ring | | Descriptor: | Flagellar L-ring protein, Flagellar P-ring protein | | Authors: | Yamaguchi, T, Makino, F, Miyata, T, Minamino, T, Kato, T, Namba, K. | | Deposit date: | 2020-07-21 | | Release date: | 2021-06-02 | | Last modified: | 2021-12-22 | | Method: | ELECTRON MICROSCOPY (3.5 Å) | | Cite: | Structure of the molecular bushing of the bacterial flagellar motor.
Nat Commun, 12, 2021
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6JY0
 | | CryoEM structure of S.typhimurium R-type straight flagellar filament made of FljB (A461V) | | Descriptor: | Flagellin | | Authors: | Yamaguchi, T, Toma, S, Terahara, N, Miyata, T, Minamino, T, Ashikara, M, Namba, K, Kato, T. | | Deposit date: | 2019-04-25 | | Release date: | 2020-02-19 | | Last modified: | 2024-03-27 | | Method: | ELECTRON MICROSCOPY (3.56 Å) | | Cite: | Structural and Functional Comparison ofSalmonellaFlagellar Filaments Composed of FljB and FliC.
Biomolecules, 10, 2020
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5Y23
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8I50
 | | Crystal structure of DNA octamer containing GuNA[Me,Me] | | Descriptor: | DNA (5'-D(*GP*(OIQ)P*GP*(BRU)P*AP*CP*AP*C)-3') | | Authors: | Aoyama, H, Obika, S, Yamaguchi, T. | | Deposit date: | 2023-01-21 | | Release date: | 2023-08-09 | | Last modified: | 2023-09-06 | | Method: | X-RAY DIFFRACTION (0.95 Å) | | Cite: | Mechanism of the extremely high duplex-forming ability of oligonucleotides modified with N-tert-butylguanidine- or N-tert-butyl-N'- methylguanidine-bridged nucleic acids.
Nucleic Acids Res., 51, 2023
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8HIS
 | | Crystal structure of DNA decamer containing GuNA[Me,tBu] | | Descriptor: | CACODYLIC ACID, DNA (5'-D(*GP*CP*GP*TP*AP*(LR6)P*AP*CP*GP*C)-3') | | Authors: | Aoyama, H, Obika, S, Yamaguchi, T. | | Deposit date: | 2022-11-21 | | Release date: | 2023-08-09 | | Last modified: | 2023-09-06 | | Method: | X-RAY DIFFRACTION (2.01 Å) | | Cite: | Mechanism of the extremely high duplex-forming ability of oligonucleotides modified with N-tert-butylguanidine- or N-tert-butyl-N'- methylguanidine-bridged nucleic acids.
Nucleic Acids Res., 51, 2023
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8HU5
 | | Crystal structure of DNA octamer containing GuNA[Me,tBu] | | Descriptor: | DNA (5'-D(*GP*(LR6)P*GP*(BRU)P*AP*CP*AP*C)-3') | | Authors: | Aoyama, H, Obika, H, Yamaguchi, T. | | Deposit date: | 2022-12-22 | | Release date: | 2023-08-09 | | Last modified: | 2023-09-06 | | Method: | X-RAY DIFFRACTION (0.93 Å) | | Cite: | Mechanism of the extremely high duplex-forming ability of oligonucleotides modified with N-tert-butylguanidine- or N-tert-butyl-N'- methylguanidine-bridged nucleic acids.
Nucleic Acids Res., 51, 2023
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5Z0X
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5YW3
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4WDU
 | | 17beta-HSD5 in complex with 4-chloro-N-(4-chlorobenzyl)-5-nitro-1H-pyrazole-3-carboxamide | | Descriptor: | 4-chloro-N-(4-chlorobenzyl)-5-nitro-1H-pyrazole-3-carboxamide, Aldo-keto reductase family 1 member C3, NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE | | Authors: | Amano, Y, Yamaguchi, T. | | Deposit date: | 2014-09-09 | | Release date: | 2015-04-15 | | Last modified: | 2022-12-14 | | Method: | X-RAY DIFFRACTION (1.7 Å) | | Cite: | Structures of complexes of type 5 17 beta-hydroxysteroid dehydrogenase with structurally diverse inhibitors: insights into the conformational changes upon inhibitor binding.
Acta Crystallogr.,Sect.D, 71, 2015
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4WDX
 | | 17beta-HSD5 in complex with [4-(2-hydroxyethyl)piperidin-1-yl](5-methyl-1H-indol-2-yl)methanone | | Descriptor: | Aldo-keto reductase family 1 member C3, NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE, [4-(2-hydroxyethyl)piperidin-1-yl](5-methyl-1H-indol-2-yl)methanone | | Authors: | Amano, Y, Yamaguchi, T. | | Deposit date: | 2014-09-09 | | Release date: | 2015-04-15 | | Last modified: | 2022-12-14 | | Method: | X-RAY DIFFRACTION (1.64 Å) | | Cite: | Structures of complexes of type 5 17 beta-hydroxysteroid dehydrogenase with structurally diverse inhibitors: insights into the conformational changes upon inhibitor binding.
Acta Crystallogr.,Sect.D, 71, 2015
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4WDW
 | | 17beta-HSD5 in complex with 3,6-dihydropyridin-1(2H)-yl(5-methyl-1H-indol-2-yl)methanone | | Descriptor: | 3,6-dihydropyridin-1(2H)-yl(5-methyl-1H-indol-2-yl)methanone, Aldo-keto reductase family 1 member C3, NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE | | Authors: | Amano, Y, Yamaguchi, T. | | Deposit date: | 2014-09-09 | | Release date: | 2015-04-15 | | Last modified: | 2022-12-14 | | Method: | X-RAY DIFFRACTION (1.94 Å) | | Cite: | Structures of complexes of type 5 17 beta-hydroxysteroid dehydrogenase with structurally diverse inhibitors: insights into the conformational changes upon inhibitor binding.
Acta Crystallogr.,Sect.D, 71, 2015
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4WDT
 | | 17beta-HSD5 in complex with 2-nitro-5-(phenylsulfonyl)phenol | | Descriptor: | 2-nitro-5-(phenylsulfonyl)phenol, Aldo-keto reductase family 1 member C3, NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE | | Authors: | Amano, Y, Yamaguchi, T. | | Deposit date: | 2014-09-09 | | Release date: | 2015-04-15 | | Last modified: | 2022-12-14 | | Method: | X-RAY DIFFRACTION (1.5 Å) | | Cite: | Structures of complexes of type 5 17 beta-hydroxysteroid dehydrogenase with structurally diverse inhibitors: insights into the conformational changes upon inhibitor binding.
Acta Crystallogr.,Sect.D, 71, 2015
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2NVL
 | | Crystal structure of archaeal peroxiredoxin, thioredoxin peroxidase from Aeropyrum pernix K1 (sulfonic acid form) | | Descriptor: | Probable peroxiredoxin | | Authors: | Nakamura, T, Yamamoto, T, Abe, M, Matsumura, H, Hagihara, Y, Goto, T, Yamaguchi, T, Inoue, T. | | Deposit date: | 2006-11-13 | | Release date: | 2007-11-20 | | Last modified: | 2023-11-15 | | Method: | X-RAY DIFFRACTION (2.36 Å) | | Cite: | Oxidation of archaeal peroxiredoxin involves a hypervalent sulfur intermediate
Proc.Natl.Acad.Sci.Usa, 105, 2008
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4XVD
 | | 17beta-HSD5 in complex with 4-nitro-2-({4-[3-(trifluoromethyl)phenyl]piperazin-1-yl}methyl)phenol | | Descriptor: | 4-nitro-2-({4-[3-(trifluoromethyl)phenyl]piperazin-1-yl}methyl)phenol, Aldo-keto reductase family 1 member C3, NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE | | Authors: | Amano, Y, Yamaguchi, T, Niimi, T, Sakashita, H. | | Deposit date: | 2015-01-27 | | Release date: | 2015-04-15 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.81 Å) | | Cite: | Structures of complexes of type 5 17 beta-hydroxysteroid dehydrogenase with structurally diverse inhibitors: insights into the conformational changes upon inhibitor binding.
Acta Crystallogr.,Sect.D, 71, 2015
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4XVE
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5D9B
 | | Luciferin-regenerating enzyme solved by SIRAS using XFEL (refined against native data) | | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, Luciferin regenerating enzyme, MAGNESIUM ION | | Authors: | Yamashita, K, Pan, D, Okuda, T, Murai, T, Kodan, A, Yamaguchi, T, Gomi, K, Kajiyama, N, Kato, H, Ago, H, Yamamoto, M, Nakatsu, T. | | Deposit date: | 2015-08-18 | | Release date: | 2015-09-23 | | Last modified: | 2023-09-06 | | Method: | X-RAY DIFFRACTION (1.5 Å) | | Cite: | An isomorphous replacement method for efficient de novo phasing for serial femtosecond crystallography.
Sci Rep, 5, 2015
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5D9D
 | | Luciferin-regenerating enzyme solved by SAD using synchrotron radiation at room temperature | | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, Luciferin regenerating enzyme, MAGNESIUM ION, ... | | Authors: | Yamashita, K, Pan, D, Okuda, T, Murai, T, Kodan, A, Yamaguchi, T, Gomi, K, Kajiyama, N, Kato, H, Ago, H, Yamamoto, M, Nakatsu, T. | | Deposit date: | 2015-08-18 | | Release date: | 2015-09-23 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (1.701 Å) | | Cite: | An isomorphous replacement method for efficient de novo phasing for serial femtosecond crystallography.
Sci Rep, 5, 2015
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5D9C
 | | Luciferin-regenerating enzyme solved by SIRAS using XFEL (refined against Hg derivative data) | | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, Luciferin regenerating enzyme, MAGNESIUM ION, ... | | Authors: | Yamashita, K, Pan, D, Okuda, T, Murai, T, Kodan, A, Yamaguchi, T, Gomi, K, Kajiyama, N, Kato, H, Ago, H, Yamamoto, M, Nakatsu, T. | | Deposit date: | 2015-08-18 | | Release date: | 2015-09-23 | | Last modified: | 2023-09-06 | | Method: | X-RAY DIFFRACTION (1.6 Å) | | Cite: | An isomorphous replacement method for efficient de novo phasing for serial femtosecond crystallography.
Sci Rep, 5, 2015
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5WV4
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5XJE
 | | Crystal structure of fucosylated IgG1 Fc complexed with bis-glycosylated soluble form of Fc gamma receptor IIIa | | Descriptor: | CHLORIDE ION, Immunoglobulin gamma-1 heavy chain, Low affinity immunoglobulin gamma Fc region receptor III-A, ... | | Authors: | Sakae, Y, Satoh, T, Yagi, H, Yanaka, S, Yamaguchi, T, Isoda, Y, Iida, S, Okamoto, Y, Kato, K. | | Deposit date: | 2017-05-01 | | Release date: | 2017-11-01 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | Conformational effects of N-glycan core fucosylation of immunoglobulin G Fc region on its interaction with Fc gamma receptor IIIa.
Sci Rep, 7, 2017
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5XFV
 | | Crystal structures of FMN-bound form of dihydroorotate dehydrogenase from Trypanosoma brucei | | Descriptor: | Dihydroorotate dehydrogenase (fumarate), FLAVIN MONONUCLEOTIDE, MALONATE ION | | Authors: | Kubota, T, Tani, O, Yamaguchi, T, Namatame, I, Sakashita, H, Furukawa, K, Yamasaki, K. | | Deposit date: | 2017-04-11 | | Release date: | 2018-04-25 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.79 Å) | | Cite: | Crystal structures of FMN-bound and FMN-free forms of dihydroorotate dehydrogenase fromTrypanosoma brucei.
FEBS Open Bio, 8, 2018
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5DKZ
 | | Crystal structure of glucosidase II alpha subunit (alpha3-Glc2-bound from) | | Descriptor: | Alpha glucosidase-like protein, alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose | | Authors: | Satoh, T, Toshimori, T, Yan, G, Yamaguchi, T, Kato, K. | | Deposit date: | 2015-09-04 | | Release date: | 2016-01-27 | | Last modified: | 2020-07-29 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | Structural basis for two-step glucose trimming by glucosidase II involved in ER glycoprotein quality control.
Sci Rep, 6, 2016
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5DKX
 | | Crystal structure of glucosidase II alpha subunit (Tris-bound from) | | Descriptor: | 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, Alpha glucosidase-like protein, CHLORIDE ION | | Authors: | Satoh, T, Toshimori, T, Yan, G, Yamaguchi, T, Kato, K. | | Deposit date: | 2015-09-04 | | Release date: | 2016-01-27 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (1.4 Å) | | Cite: | Structural basis for two-step glucose trimming by glucosidase II involved in ER glycoprotein quality control.
Sci Rep, 6, 2016
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