Author results

1GE9
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SOLUTION STRUCTURE OF THE RIBOSOME RECYCLING FACTOR
Descriptor:RIBOSOME RECYCLING FACTOR
Authors:Yoshida, T., Uchiyama, S., Nakano, H., Kashimori, H., Kijima, H., Ohshima, T., Saihara, Y., Ishino, T., Shimahara, T., Yoshida, T., Yokose, K., Ohkubo, T., Kaji, A., Kobayashi, Y.
Deposit date:2000-10-19
Release date:2001-05-16
Last modified:2011-07-13
Method:SOLUTION NMR
Cite:Solution structure of the ribosome recycling factor from Aquifex aeolicus.
Biochemistry, 40, 2001
5C2I
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CRYSTAL STRUCTURE OF ANABAENA SP. DYP-TYPE PEROXIDESE (ANAPX)
Descriptor:Alr1585 protein, PROTOPORPHYRIN IX CONTAINING FE, GLYCEROL, ...
Authors:Yoshida, T., Amano, Y., Tsuge, H., Sugano, Y.
Deposit date:2015-06-16
Release date:2015-12-16
Last modified:2016-01-27
Method:X-RAY DIFFRACTION (1.89 Å)
Cite:Anabaena sp. DyP-type peroxidase is a tetramer consisting of two asymmetric dimers.
Proteins, 84, 2016
5ZJ4
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GUANINE-SPECIFIC ADP-RIBOSYLTRANSFERASE
Descriptor:ADP-ribosyltransferase, (4S)-2-METHYL-2,4-PENTANEDIOL
Authors:Yoshida, T., Tsuge, H.
Deposit date:2018-03-19
Release date:2018-08-08
Last modified:2018-09-19
Method:X-RAY DIFFRACTION (1.497393 Å)
Cite:Substrate N2atom recognition mechanism in pierisin family DNA-targeting, guanine-specific ADP-ribosyltransferase ScARP.
J. Biol. Chem., 293, 2018
5ZJ5
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GUANINE-SPECIFIC ADP-RIBOSYLTRANSFERASE WITH NADH AND GDP
Descriptor:ADP-ribosyltransferase, 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE, GUANOSINE-5'-DIPHOSPHATE
Authors:Yoshida, T., Tsuge, H.
Deposit date:2018-03-19
Release date:2018-08-08
Last modified:2018-09-19
Method:X-RAY DIFFRACTION (1.568112 Å)
Cite:Substrate N2atom recognition mechanism in pierisin family DNA-targeting, guanine-specific ADP-ribosyltransferase ScARP.
J. Biol. Chem., 293, 2018
3VJK
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CRYSTAL STRUCTURE OF HUMAN DEPIPTIDYL PEPTIDASE IV (DPP-4) IN COMPLEX WITH MP-513
Descriptor:Dipeptidyl peptidase 4, {(2S,4S)-4-[4-(3-methyl-1-phenyl-1H-pyrazol-5-yl)piperazin-1-yl]pyrrolidin-2-yl}(1,3-thiazolidin-3-yl)methanone, N-ACETYL-D-GLUCOSAMINE
Authors:Akahoshi, F., Kishida, H., Miyaguchi, I., Yoshida, T., Ishii, S.
Deposit date:2011-10-24
Release date:2012-10-24
Last modified:2016-08-24
Method:X-RAY DIFFRACTION (2.49 Å)
Cite:Discovery and preclinical profile of teneligliptin (3-[(2S,4S)-4-[4-(3-methyl-1-phenyl-1H-pyrazol-5-yl)piperazin-1-yl]pyrrolidin-2-ylcarbonyl]thiazolidine): A highly potent, selective, long-lasting and orally active dipeptidyl peptidase IV inhibitor for the treatment of type 2 diabetes
Bioorg.Med.Chem., 20, 2012
3VJL
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CRYSTAL STRUCTURE OF HUMAN DEPIPTIDYL PEPTIDASE IV (DPP-4) IN COMPLEX WITH A PROLYLTHIAZOLIDINE INHIBITOR #2
Descriptor:Dipeptidyl peptidase 4, [(2S,4S)-4-{4-[1-phenyl-3-(trifluoromethyl)-1H-pyrazol-5-yl]piperidin-1-yl}pyrrolidin-2-yl](1,3-thiazolidin-3-yl)methanone, N-ACETYL-D-GLUCOSAMINE
Authors:Akahoshi, F., Kishida, H., Miyaguchi, I., Yoshida, T., Ishii, S.
Deposit date:2011-10-24
Release date:2012-10-24
Method:X-RAY DIFFRACTION (2.393 Å)
Cite:Discovery and preclinical profile of teneligliptin (3-[(2S,4S)-4-[4-(3-methyl-1-phenyl-1H-pyrazol-5-yl)piperazin-1-yl]pyrrolidin-2-ylcarbonyl]thiazolidine): A highly potent, selective, long-lasting and orally active dipeptidyl peptidase IV inhibitor for the treatment of type 2 diabetes
Bioorg.Med.Chem., 20, 2012
3AFV
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DYE-DECOLORIZING PEROXIDASE (DYP) AT 1.4 A RESOLUTION
Descriptor:DyP, PROTOPORPHYRIN IX CONTAINING FE, N-ACETYL-D-GLUCOSAMINE
Authors:Sugano, Y., Yoshida, T., Tsuge, H.
Deposit date:2010-03-11
Release date:2011-03-16
Last modified:2011-10-26
Method:X-RAY DIFFRACTION (1.4 Å)
Cite:The catalytic mechanism of dye-decolorizing peroxidase DyP may require the swinging movement of an aspartic acid residue
Febs J., 278, 2011
3MM1
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DYE-DECOLORIZING PEROXIDASE (DYP) D171N
Descriptor:DyP, PROTOPORPHYRIN IX CONTAINING FE, N-ACETYL-D-GLUCOSAMINE
Authors:Sugano, Y., Yoshida, T., Tsuge, H.
Deposit date:2010-04-19
Release date:2011-04-27
Last modified:2017-11-08
Method:X-RAY DIFFRACTION (1.42 Å)
Cite:The catalytic mechanism of dye-decolorizing peroxidase DyP may require the swinging movement of an aspartic acid residue
Febs J., 278, 2011
3MM2
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DYE-DECOLORIZING PEROXIDASE (DYP) IN COMPLEX WITH CYANIDE
Descriptor:DyP, PROTOPORPHYRIN IX CONTAINING FE, N-ACETYL-D-GLUCOSAMINE, ...
Authors:Sugano, Y., Yoshida, T., Tsuge, H.
Deposit date:2010-04-19
Release date:2011-04-27
Last modified:2017-11-08
Method:X-RAY DIFFRACTION (1.45 Å)
Cite:The catalytic mechanism of dye-decolorizing peroxidase DyP may require the swinging movement of an aspartic acid residue
Febs J., 278, 2011
3MM3
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DYE-DECOLORIZING PEROXIDASE (DYP) D171N IN COMPLEX WITH CYANIDE
Descriptor:DyP, PROTOPORPHYRIN IX CONTAINING FE, CYANIDE ION
Authors:Sugano, Y., Yoshida, T., Tsuge, H.
Deposit date:2010-04-19
Release date:2011-04-27
Last modified:2017-11-08
Method:X-RAY DIFFRACTION (1.4 Å)
Cite:The catalytic mechanism of dye-decolorizing peroxidase DyP may require the swinging movement of an aspartic acid residue
Febs J., 278, 2011
3VJM
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CRYSTAL STRUCTURE OF HUMAN DEPIPTIDYL PEPTIDASE IV (DPP-4) IN COMPLEX WITH A PROLYLTHIAZOLIDINE INHIBITOR #1
Descriptor:Dipeptidyl peptidase 4, 1,3-thiazolidin-3-yl[(2S,4S)-4-{4-[2-(trifluoromethyl)quinolin-4-yl]piperazin-1-yl}pyrrolidin-2-yl]methanone, N-ACETYL-D-GLUCOSAMINE
Authors:Akahoshi, F., Kishida, H., Miyaguchi, I., Yoshida, T., Ishii, S.
Deposit date:2011-10-24
Release date:2012-08-15
Method:X-RAY DIFFRACTION (2.1 Å)
Cite:Fused bicyclic heteroarylpiperazine-substituted l-prolylthiazolidines as highly potent DPP-4 inhibitors lacking the electrophilic nitrile group
Bioorg.Med.Chem., 20, 2012
1J1I
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CRYSTAL STRUCTURE OF A HIS-TAGGED SERINE HYDROLASE INVOLVED IN THE CARBAZOLE DEGRADATION (CARC ENZYME)
Descriptor:meta cleavage compound hydrolase
Authors:Habe, H., Morii, K., Fushinobu, S., Nam, J.W., Ayabe, Y., Yoshida, T., Wakagi, T., Yamane, H., Nojiri, H., Omori, T.
Deposit date:2002-12-05
Release date:2003-06-17
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (1.86 Å)
Cite:Crystal structure of a histidine-tagged serine hydrolase involved in the carbazole degradation (CarC enzyme).
Biochem.Biophys.Res.Commun., 303, 2003
1O5P
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SOLUTION STRUCTURE OF HOLO-NEOCARZINOSTATIN
Descriptor:Neocarzinostatin, NEOCARZINOSTATIN-CHROMOPHORE
Authors:Takashima, H., Ishino, T., Yoshida, T., Hasuda, K., Ohkubo, T., Kobayashi, Y.
Deposit date:2003-10-04
Release date:2003-10-14
Last modified:2011-07-13
Method:SOLUTION NMR
Cite:Solution NMR Structure Investigation for Releasing Mechanism of Neocarzinostatin Chromophore from the Holoprotein
J.Biol.Chem., 280, 2005
1Q2V
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CRYSTAL STRUCTURE OF THE CHAPERONIN FROM THERMOCOCCUS STRAIN KS-1 (NUCLEOTIDE-FREE FORM)
Descriptor:Thermosome alpha subunit, SULFATE ION
Authors:Shomura, Y., Yoshida, T., Iizuka, R., Yohda, M., Maruyama, T., Miki, K.
Deposit date:2003-07-26
Release date:2004-01-27
Last modified:2017-10-11
Method:X-RAY DIFFRACTION (2.4 Å)
Cite:Crystal Structures of the Group II Chaperonin from Thermococcus strain KS-1: Steric Hindrance by the Substituted Amino Acid, and Inter-subunit Rearrangement between Two Crystal Forms.
J.Mol.Biol., 335, 2004
1Q3Q
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CRYSTAL STRUCTURE OF THE CHAPERONIN FROM THERMOCOCCUS STRAIN KS-1 (TWO-POINT MUTANT COMPLEXED WITH AMP-PNP)
Descriptor:Thermosome alpha subunit, MAGNESIUM ION, PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
Authors:Shomura, Y., Yoshida, T., Iizuka, R., Maruyama, T., Yohda, M., Miki, K.
Deposit date:2003-07-31
Release date:2004-01-27
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (2.3 Å)
Cite:Crystal Structures of the Group II Chaperonin from Thermococcus strain KS-1: Steric Hindrance by the Substituted Amino Acid, and Inter-subunit Rearrangement between Two Crystal Forms.
J.Mol.Biol., 335, 2004
1Q3R
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CRYSTAL STRUCTURE OF THE CHAPERONIN FROM THERMOCOCCUS STRAIN KS-1 (NUCLEOTIDE-FREE FORM OF SINGLE MUTANT)
Descriptor:Thermosome alpha subunit, SULFATE ION
Authors:Shomura, Y., Yoshida, T., Iizuka, R., Maruyama, T., Yohda, M., Miki, K.
Deposit date:2003-07-31
Release date:2004-01-27
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (2.9 Å)
Cite:Crystal Structures of the Group II Chaperonin from Thermococcus strain KS-1: Steric Hindrance by the Substituted Amino Acid, and Inter-subunit Rearrangement between Two Crystal Forms.
J.Mol.Biol., 335, 2004
1Q3S
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CRYSTAL STRUCTURE OF THE CHAPERONIN FROM THERMOCOCCUS STRAIN KS-1 (FORMIII CRYSTAL COMPLEXED WITH ADP)
Descriptor:Thermosome alpha subunit, MAGNESIUM ION, ADENOSINE-5'-DIPHOSPHATE
Authors:Shomura, Y., Yoshida, T., Iizuka, R., Maruyama, T., Yohda, M., Miki, K.
Deposit date:2003-07-31
Release date:2004-01-27
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (3 Å)
Cite:Crystal Structures of the Group II Chaperonin from Thermococcus strain KS-1: Steric Hindrance by the Substituted Amino Acid, and Inter-subunit Rearrangement between Two Crystal Forms.
J.Mol.Biol., 335, 2004
1GDH
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CRYSTAL STRUCTURE OF A NAD-DEPENDENT D-GLYCERATE DEHYDROGENASE AT 2.4 ANGSTROMS RESOLUTION
Descriptor:D-GLYCERATE DEHYDROGENASE, SULFATE ION
Authors:Goldberg, J.D., Yoshida, T., Brick, P.
Deposit date:1993-09-22
Release date:1994-01-31
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (2.4 Å)
Cite:Crystal structure of a NAD-dependent D-glycerate dehydrogenase at 2.4 A resolution.
J.Mol.Biol., 236, 1994
1WE1
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CRYSTAL STRUCTURE OF HEME OXYGENASE-1 FROM CYANOBACTERIUM SYNECHOCYSTIS SP. PCC6803 IN COMPLEX WITH HEME
Descriptor:Heme oxygenase 1, PHOSPHATE ION, CHLORIDE ION, ...
Authors:Sugishima, M., Migita, C.T., Zhang, X., Yoshida, T., Fukuyama, K.
Deposit date:2004-05-21
Release date:2004-12-21
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (2.5 Å)
Cite:Crystal structure of heme oxygenase-1 from cyanobacterium Synechocystis sp. PCC 6803 in complex with heme
Eur.J.Biochem., 271, 2004
5YPZ
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CRYSTAL STRUCTURE OF MINOR PILIN COFB FROM CFA/III COMPLEXED WITH N-TERMINAL PEPTIDE FRAGMENT OF COFJ
Descriptor:CofB, CofJ
Authors:Oki, H., Kawahara, K., Maruno, T., Imai, T., Muroga, Y., Fukakusa, S., Iwashita, T., Kobayashi, Y., Matsuda, S., Kodama, T., Iida, T., Yoshida, T., Ohkubo, T., Nakamura, S.
Deposit date:2017-11-04
Release date:2018-06-27
Last modified:2018-07-25
Method:X-RAY DIFFRACTION (3.521 Å)
Cite:Interplay of a secreted protein with type IVb pilus for efficient enterotoxigenicEscherichia colicolonization.
Proc. Natl. Acad. Sci. U.S.A., 115, 2018
5YQ0
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CRYSTAL STRUCTURE OF SECRETED PROTEIN COFJ FROM ETEC.
Descriptor:CofJ, CALCIUM ION
Authors:Oki, H., Kawahara, K., Maruno, T., Imai, T., Muroga, Y., Fukakusa, S., Iwashita, T., Kobayashi, Y., Matsuda, S., Kodama, T., Iida, T., Yoshida, T., Ohkubo, T., Nakamura, S.
Deposit date:2017-11-04
Release date:2018-06-27
Last modified:2018-07-25
Method:X-RAY DIFFRACTION (1.76 Å)
Cite:Interplay of a secreted protein with type IVb pilus for efficient enterotoxigenicEscherichia colicolonization
Proc. Natl. Acad. Sci. U.S.A., 115, 2018
1AYG
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SOLUTION STRUCTURE OF CYTOCHROME C-552, NMR, 20 STRUCTURES
Descriptor:CYTOCHROME C-552, HEME C
Authors:Hasegawa, J., Yoshida, T., Yamazaki, T., Sambongi, Y., Yu, Y., Igarashi, Y., Kodama, T., Yamazaki, K., Hakusui, H., Kyogoku, Y., Kobayashi, Y.
Deposit date:1997-11-04
Release date:1998-11-25
Last modified:2011-07-13
Method:SOLUTION NMR
Cite:Solution structure of thermostable cytochrome c-552 from Hydrogenobacter thermophilus determined by 1H-NMR spectroscopy.
Biochemistry, 37, 1998
1IS1
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CRYSTAL STRUCTURE OF RIBOSOME RECYCLING FACTOR FROM VIBRIO PARAHAEMOLYTICUS
Descriptor:RIBOSOME RECYCLING FACTOR
Authors:Nakano, H., Yamaichi, Y., Uchiyama, S., Yoshida, T., Nishina, K., Kato, H., Ohkubo, T., Honda, T., Yamagata, Y., Kobayashi, Y.
Deposit date:2001-11-05
Release date:2003-06-17
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:Structure and binding mode of a ribosome recycling factor (RRF) from mesophilic bacterium
J.BIOL.CHEM., 278, 2003
1IY5
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SOLUTION STRUCTURE OF WILD TYPE OMSVP3
Descriptor:OMSVP3
Authors:Hemmi, H., Kumazaki, T., Yamazaki, T., Kojima, S., Yoshida, T., Kyogoku, Y., Katsu, M., Yokosawa, H., Miura, K., Kobayashi, Y.
Deposit date:2002-07-23
Release date:2003-03-11
Last modified:2011-07-13
Method:SOLUTION NMR
Cite:Inhibitory Specificity Change of Ovomucoid Third Domain of the Silver Pheasant upon Introduction of an Engineered Cys14-Cys39 Bond
BIOCHEMISTRY, 42, 2003
1IY6
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SOLUTION STRUCTURE OF OMSVP3 VARIANT, P14C/N39C
Descriptor:OMSVP3
Authors:Hemmi, H., Kumazaki, T., Yamazaki, T., Kojima, S., Yoshida, T., Kyogoku, Y., Katsu, M., Yokosawa, H., Miura, K., Kobayashi, Y.
Deposit date:2002-07-23
Release date:2003-03-11
Last modified:2011-07-13
Method:SOLUTION NMR
Cite:Inhibitory Specificity Change of Ovomucoid Third Domain of the Silver Pheasant upon Introduction of an Engineered Cys14-Cys39 Bond
BIOCHEMISTRY, 42, 2003