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1GE9
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BU of 1ge9 by Molmil
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:2023-12-27
Method:SOLUTION NMR
Cite:Solution structure of the ribosome recycling factor from Aquifex aeolicus.
Biochemistry, 40, 2001
5C2I
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BU of 5c2i by Molmil
Crystal structure of Anabaena sp. DyP-type peroxidese (AnaPX)
Descriptor: 1,2-ETHANEDIOL, ACETIC ACID, Alr1585 protein, ...
Authors:Yoshida, T, Amano, Y, Tsuge, H, Sugano, Y.
Deposit date:2015-06-16
Release date:2015-12-16
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (1.89 Å)
Cite:Anabaena sp. DyP-type peroxidase is a tetramer consisting of two asymmetric dimers.
Proteins, 84, 2016
6KXX
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BU of 6kxx by Molmil
Human PPAR alpha ligand binding domain in complex with a synthetic agonist (compound A)
Descriptor: 1-(4-chlorophenyl)-6-methyl-3-propan-2-yl-pyrazolo[3,4-b]pyridine-4-carboxylic acid, PGC1alpha, Peroxisome proliferator-activated receptor alpha
Authors:Yoshida, T, Tachibana, K, Oki, H, Doi, M, Fukuda, S, Yuzuriha, T, Tabata, R, Ishimoto, K, Kawahara, K, Ohkubo, T, Miyachi, H, Doi, T.
Deposit date:2019-09-14
Release date:2020-05-20
Last modified:2024-03-27
Method:X-RAY DIFFRACTION (1.95 Å)
Cite:Structural Basis for PPAR alpha Activation by 1H-pyrazolo-[3,4-b]pyridine Derivatives.
Sci Rep, 10, 2020
6KXY
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BU of 6kxy by Molmil
Human PPAR alpha ligand binding domain in complex with a synthetic agonist (compound B)
Descriptor: 6-ethyl-1-(4-fluorophenyl)-3-pentan-3-yl-pyrazolo[3,4-b]pyridine-4-carboxylic acid, PGC1alpha, Peroxisome proliferator-activated receptor alpha
Authors:Yoshida, T, Tachibana, K, Oki, H, Doi, M, Fukuda, S, Yuzuriha, T, Tabata, R, Ishimoto, K, Kawahara, K, Ohkubo, T, Miyachi, H, Doi, T.
Deposit date:2019-09-14
Release date:2020-05-20
Last modified:2023-11-22
Method:X-RAY DIFFRACTION (2 Å)
Cite:Structural Basis for PPAR alpha Activation by 1H-pyrazolo-[3,4-b]pyridine Derivatives.
Sci Rep, 10, 2020
5ZJ4
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BU of 5zj4 by Molmil
Guanine-specific ADP-ribosyltransferase
Descriptor: (4S)-2-METHYL-2,4-PENTANEDIOL, ADP-ribosyltransferase
Authors:Yoshida, T, Tsuge, H.
Deposit date:2018-03-19
Release date:2018-08-08
Last modified:2023-11-22
Method:X-RAY DIFFRACTION (1.49739277 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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BU of 5zj5 by Molmil
Guanine-specific ADP-ribosyltransferase with NADH and GDP
Descriptor: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE, ADP-ribosyltransferase, GUANOSINE-5'-DIPHOSPHATE
Authors:Yoshida, T, Tsuge, H.
Deposit date:2018-03-19
Release date:2018-08-08
Last modified:2023-11-22
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
3MM2
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BU of 3mm2 by Molmil
Dye-decolorizing peroxidase (DyP) in complex with cyanide
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, CYANIDE ION, DyP, ...
Authors:Sugano, Y, Yoshida, T, Tsuge, H.
Deposit date:2010-04-19
Release date:2011-04-27
Last modified:2023-11-01
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
3MM1
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BU of 3mm1 by Molmil
Dye-decolorizing peroxidase (DyP) D171N
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, DyP, PROTOPORPHYRIN IX CONTAINING FE
Authors:Sugano, Y, Yoshida, T, Tsuge, H.
Deposit date:2010-04-19
Release date:2011-04-27
Last modified:2023-11-01
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
3MM3
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BU of 3mm3 by Molmil
Dye-decolorizing peroxidase (DyP) D171N in complex with cyanide
Descriptor: CYANIDE ION, DyP, PROTOPORPHYRIN IX CONTAINING FE
Authors:Sugano, Y, Yoshida, T, Tsuge, H.
Deposit date:2010-04-19
Release date:2011-04-27
Last modified:2023-11-01
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
3VJL
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BU of 3vjl by Molmil
Crystal structure of human depiptidyl peptidase IV (DPP-4) in complex with a prolylthiazolidine inhibitor #2
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Dipeptidyl peptidase 4, ...
Authors:Akahoshi, F, Kishida, H, Miyaguchi, I, Yoshida, T, Ishii, S.
Deposit date:2011-10-24
Release date:2012-10-24
Last modified:2023-11-08
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
3VJK
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BU of 3vjk by Molmil
Crystal structure of human depiptidyl peptidase IV (DPP-4) in complex with MP-513
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Dipeptidyl peptidase 4, ...
Authors:Akahoshi, F, Kishida, H, Miyaguchi, I, Yoshida, T, Ishii, S.
Deposit date:2011-10-24
Release date:2012-10-24
Last modified:2023-11-08
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
7CEE
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BU of 7cee by Molmil
Crystal structure of mouse neuroligin-3
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Neuroligin-3
Authors:Yamagata, A, Yoshida, T, Shiroshima, T, Maeda, A, Fukai, S.
Deposit date:2020-06-23
Release date:2021-02-24
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.763 Å)
Cite:Canonical versus non-canonical transsynaptic signaling of neuroligin 3 tunes development of sociality in mice.
Nat Commun, 12, 2021
7CEG
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BU of 7ceg by Molmil
Crystal structure of the complex between mouse PTP delta and neuroligin-3
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Isoform C of Receptor-type tyrosine-protein phosphatase delta, Neuroligin-3
Authors:Yamagata, A, Yoshida, T, Shiroshima, T, Maeda, A, Fukai, S.
Deposit date:2020-06-23
Release date:2021-02-24
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (3.85 Å)
Cite:Canonical versus non-canonical transsynaptic signaling of neuroligin 3 tunes development of sociality in mice.
Nat Commun, 12, 2021
6KLX
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BU of 6klx by Molmil
Pore structure of Iota toxin binding component (Ib)
Descriptor: CALCIUM ION, Iota toxin component Ib
Authors:Yoshida, T, Yamada, T, Kawamoto, A, Mitsuoka, K, Iwasaki, K, Tsuge, H.
Deposit date:2019-07-30
Release date:2020-01-15
Last modified:2024-03-27
Method:ELECTRON MICROSCOPY (2.9 Å)
Cite:Cryo-EM structures reveal translocational unfolding in the clostridial binary iota toxin complex.
Nat.Struct.Mol.Biol., 27, 2020
6KLO
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BU of 6klo by Molmil
Complex structure of Iota toxin enzymatic component (Ia) and binding component (Ib) pore with short stem
Descriptor: CALCIUM ION, Iota toxin component Ia, Iota toxin component Ib
Authors:Yoshida, T, Yamada, T, Kawamoto, A, Mitsuoka, K, Iwasaki, K, Tsuge, H.
Deposit date:2019-07-30
Release date:2020-01-15
Last modified:2024-03-27
Method:ELECTRON MICROSCOPY (2.8 Å)
Cite:Cryo-EM structures reveal translocational unfolding in the clostridial binary iota toxin complex.
Nat.Struct.Mol.Biol., 27, 2020
6KLW
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BU of 6klw by Molmil
Complex structure of Iota toxin enzymatic component (Ia) and binding component (Ib) pore with long stem
Descriptor: CALCIUM ION, Iota toxin component Ia, Iota toxin component Ib
Authors:Yoshida, T, Yamada, T, Kawamoto, A, Mitsuoka, K, Iwasaki, K, Tsuge, H.
Deposit date:2019-07-30
Release date:2020-01-15
Last modified:2024-03-27
Method:ELECTRON MICROSCOPY (2.9 Å)
Cite:Cryo-EM structures reveal translocational unfolding in the clostridial binary iota toxin complex.
Nat.Struct.Mol.Biol., 27, 2020
3VJM
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BU of 3vjm by Molmil
Crystal structure of human depiptidyl peptidase IV (DPP-4) in complex with a prolylthiazolidine inhibitor #1
Descriptor: 1,3-thiazolidin-3-yl[(2S,4S)-4-{4-[2-(trifluoromethyl)quinolin-4-yl]piperazin-1-yl}pyrrolidin-2-yl]methanone, 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:Akahoshi, F, Kishida, H, Miyaguchi, I, Yoshida, T, Ishii, S.
Deposit date:2011-10-24
Release date:2012-08-15
Last modified:2023-11-08
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
3AFV
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BU of 3afv by Molmil
Dye-decolorizing peroxidase (DyP) at 1.4 A resolution
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, DyP, PROTOPORPHYRIN IX CONTAINING FE
Authors:Sugano, Y, Yoshida, T, Tsuge, H.
Deposit date:2010-03-11
Release date:2011-03-16
Last modified:2023-11-01
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
2KTD
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BU of 2ktd by Molmil
Solution structure of mouse lipocalin-type prostaglandin D synthase / substrate analog (U-46619) complex
Descriptor: (5Z)-7-{(1R,4S,5S,6R)-6-[(1E,3S)-3-hydroxyoct-1-en-1-yl]-2-oxabicyclo[2.2.1]hept-5-yl}hept-5-enoic acid, Prostaglandin-H2 D-isomerase
Authors:Shimamoto, S, Maruo, H, Yoshida, T, Kato, N, Ohkubo, T.
Deposit date:2010-01-27
Release date:2011-02-02
Last modified:2024-05-01
Method:SOLUTION NMR
Cite:Solution Structure of Lipocalin-type Prostaglandin D synthase / Substrate analog complex reveals Open-Closed Conformational Change required for Substrate Recognition
To be Published
2LAA
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BU of 2laa by Molmil
Solution Strucuture of the CBM25-1 of beta/alpha-amylase from Paenibacillus polymyxa
Descriptor: Beta/alpha-amylase
Authors:Horibe, I, Nishimura, S, Takahashi, R, Ohkubo, T, Yoshida, T.
Deposit date:2011-03-09
Release date:2012-04-04
Last modified:2024-05-01
Method:SOLUTION NMR
Cite:A functional and structural analysis of tundem family 25 carbohydrate-binding modules from Paenibacillus polymyxa beta/alpha-amylase
To be Published
1AYG
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BU of 1ayg by Molmil
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:2022-02-16
Method:SOLUTION NMR
Cite:Solution structure of thermostable cytochrome c-552 from Hydrogenobacter thermophilus determined by 1H-NMR spectroscopy.
Biochemistry, 37, 1998
4XSH
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BU of 4xsh by Molmil
The complex structure of C3cer exoenzyme and GTP bound RhoA (NADH-bound state)
Descriptor: 1,2-ETHANEDIOL, 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE, 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE, ...
Authors:Toda, A, Tsurumura, T, Yoshida, T, Tsuge, H.
Deposit date:2015-01-22
Release date:2015-06-24
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (2.5 Å)
Cite:Rho GTPase Recognition by C3 Exoenzyme Based on C3-RhoA Complex Structure.
J.Biol.Chem., 290, 2015
4XSG
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BU of 4xsg by Molmil
The complex structure of C3cer exoenzyme and GTP bound RhoA (NADH-free state)
Descriptor: 1,2-ETHANEDIOL, 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE, ADP-ribosyltransferase, ...
Authors:Toda, A, Tsurumura, T, Yoshida, T, Tsuge, H.
Deposit date:2015-01-22
Release date:2015-06-24
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Rho GTPase Recognition by C3 Exoenzyme Based on C3-RhoA Complex Structure.
J.Biol.Chem., 290, 2015
1GDH
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BU of 1gdh by Molmil
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:2024-02-07
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
5D47
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BU of 5d47 by Molmil
Crystal Structure of FABP4 in complex with 3-[5-cyclopropyl-3-(3-methoxypyridin-4-yl)-2-phenyl-1H-indol-1-yl] propanoic acid
Descriptor: 3-[5-cyclopropyl-3-(3-methoxypyridin-4-yl)-2-phenyl-1H-indol-1-yl]propanoic acid, Fatty acid-binding protein, adipocyte
Authors:Tagami, U, Takahashi, K, Igarashi, S, Ejima, C, Yoshida, T, Takeshita, S, Miyanaga, W, Sugiki, M, Tokumasu, M, Hatanaka, T, Kashiwagi, T, Ishikawa, K, Miyano, H, Mizukoshi, T.
Deposit date:2015-08-07
Release date:2016-06-22
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (1.7 Å)
Cite:Interaction Analysis of FABP4 Inhibitors by X-ray Crystallography and Fragment Molecular Orbital Analysis
Acs Med.Chem.Lett., 7, 2016

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