Loading
PDBj
English日本語简体中文繁體中文한국어
✖
ﾒﾆｭｰPDBj@FacebookPDBj@TwitterPDBj@YouTubewwPDB FoundationwwPDB
RCSB PDBPDBeBMRBAdv. SearchSearch help
PDB: 23 件
6L96
DownloadVisualize
BU of 6l96 by Molmil
Structure of PPARalpha-LBD/pemafibrate/SRC1 peptide
分子名称: (2~{R})-2-[3-[[1,3-benzoxazol-2-yl-[3-(4-methoxyphenoxy)propyl]amino]methyl]phenoxy]butanoic acid, Peroxisome proliferator-activated receptor alpha, SRC1 coactivator peptide
著者Kawasaki, M, Kambe, A, Yamamoto, Y, Arulmozhira, S, Ito, S, Nakagawa, Y, Tokiwa, H, Nakano, S, Shimano, H.
登録日2019-11-08
公開日2020-01-15
最終更新日2023-11-22
実験手法X-RAY DIFFRACTION (3.2 Å)
主引用文献Elucidation of Molecular Mechanism of a Selective PPAR alpha Modulator, Pemafibrate, through Combinational Approaches of X-ray Crystallography, Thermodynamic Analysis, and First-Principle Calculations.
Int J Mol Sci, 21, 2020
4Y7P
DownloadVisualize
BU of 4y7p by Molmil
Structure of alkaline D-peptidase from Bacillus cereus
分子名称: Alkaline D-peptidase, THIOCYANATE ION
著者Nakano, S, Okazaki, S, Ishitsubo, E, Kawahara, N, Komeda, H, Tokiwa, H, Asano, Y.
登録日2015-02-15
公開日2015-10-14
最終更新日2023-11-08
実験手法X-RAY DIFFRACTION (2.1 Å)
主引用文献Structural and computational analysis of peptide recognition mechanism of class-C type penicillin binding protein, alkaline D-peptidase from Bacillus cereus DF4-B
Sci Rep, 5, 2015
6JNO
DownloadVisualize
BU of 6jno by Molmil
RXRa structure complexed with CU-6PMN
分子名称: 7-oxidanyl-2-oxidanylidene-6-(3,5,5,8,8-pentamethyl-6,7-dihydronaphthalen-2-yl)chromene-3-carboxylic acid, Retinoic acid receptor RXR-alpha
著者Kawasaki, M, Nakano, S, Motoyama, T, Yamada, S, Watanabe, M, Takamura, Y, Fujihara, M, Tokiwa, H, Kakuta, H, Ito, S.
登録日2019-03-17
公開日2019-11-20
最終更新日2023-11-22
実験手法X-RAY DIFFRACTION (2.65 Å)
主引用文献Competitive Binding Assay with an Umbelliferone-Based Fluorescent Rexinoid for Retinoid X Receptor Ligand Screening.
J.Med.Chem., 62, 2019
6JNR
DownloadVisualize
BU of 6jnr by Molmil
RXRa structure complexed with CU-6PMN and SRC1 peptide.
分子名称: 7-oxidanyl-2-oxidanylidene-6-(3,5,5,8,8-pentamethyl-6,7-dihydronaphthalen-2-yl)chromene-3-carboxylic acid, HIS-LYS-ILE-LEU-HIS-ARG-LEU-LEU-GLN, Retinoic acid receptor RXR-alpha
著者Kawasaki, M, Nakano, S, Motoyama, T, Yamada, S, Watanabe, M, Takamura, Y, Fujihara, M, Tokiwa, H, Kakuta, H, Ito, S.
登録日2019-03-18
公開日2020-03-25
最終更新日2023-11-22
実験手法X-RAY DIFFRACTION (2.3 Å)
主引用文献RXRa structure complexed with CU-6PMN and SRC1 peptide.
To Be Published
4YJF
DownloadVisualize
BU of 4yjf by Molmil
Crystal structure of DAAO(Y228L/R283G) variant (S-methylbenzylamine binding form)
分子名称: (1S)-1-phenylethanamine, D-amino-acid oxidase, FLAVIN-ADENINE DINUCLEOTIDE, ...
著者Nakano, S, Yasukawa, K, Kawahara, N, Ishitsubo, E, Tokiwa, H, Asano, Y.
登録日2015-03-03
公開日2016-04-06
最終更新日2023-11-08
実験手法X-RAY DIFFRACTION (2.2 Å)
主引用文献Crystal structure of DAAO variant
To Be Published
4YJD
DownloadVisualize
BU of 4yjd by Molmil
Crystal structure of DAAO(Y228L/R283G) variant (apo form)
分子名称: D-amino-acid oxidase, FLAVIN-ADENINE DINUCLEOTIDE, SULFATE ION
著者Nakano, S, Yasukawa, K, Kawahara, N, Ishitsubo, E, Tokiwa, H, Asano, Y.
登録日2015-03-03
公開日2016-04-06
最終更新日2023-11-08
実験手法X-RAY DIFFRACTION (2.3 Å)
主引用文献Crystal structure of DAAO variant
To Be Published
4YJH
DownloadVisualize
BU of 4yjh by Molmil
Crystal structure of DAAO(Y228L/R283G) variant (R-2-phenylpyrrolidine binding form)
分子名称: (2R)-2-phenylpyrrolidine, D-amino-acid oxidase, FLAVIN-ADENINE DINUCLEOTIDE, ...
著者Nakano, S, Yasukawa, K, Kawahara, N, Ishitsubo, E, Tokiwa, H, Asano, Y.
登録日2015-03-03
公開日2016-04-06
最終更新日2023-11-08
実験手法X-RAY DIFFRACTION (2.7 Å)
主引用文献Crystal structure of DAAO variant
To Be Published
4YJG
DownloadVisualize
BU of 4yjg by Molmil
Crystal structure of DAAO(Y228L/R283G) variant (R-3-amino 1-phenylbutane binding form)
分子名称: (2R)-4-phenylbutan-2-amine, D-amino-acid oxidase, FLAVIN-ADENINE DINUCLEOTIDE, ...
著者Nakano, S, Yasukawa, K, Kawahara, N, Ishitsubo, E, Tokiwa, H, Asano, Y.
登録日2015-03-03
公開日2016-04-06
最終更新日2023-11-08
実験手法X-RAY DIFFRACTION (2.5 Å)
主引用文献Crystal structure of DAAO variant
To Be Published
2ZMI
DownloadVisualize
BU of 2zmi by Molmil
Crystal Structure of Rat Vitamin D Receptor Bound to Adamantyl Vitamin D Analogs: Structural Basis for Vitamin D Receptor Antagonism and/or Partial Agonism
分子名称: (1R,3R,7E,17beta)-17-{(1S,2E,5R)-5-hydroxy-1-methyl-5-[(3S,5S,7S)-tricyclo[3.3.1.1~3,7~]dec-1-yl]pent-2-en-1-yl}-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol, 1,2-ETHANEDIOL, FORMIC ACID, ...
著者Nakabayashi, M, Yamada, S, Tanaka, T, Igarashi, M, Yoshimoto, N, Ikura, T, Ito, N, Makishima, M, Tokiwa, H, DeLuca, H.F, Shimizu, M.
登録日2008-04-19
公開日2008-09-02
最終更新日2024-03-13
実験手法X-RAY DIFFRACTION (1.7 Å)
主引用文献Crystal structures of rat vitamin d receptor bound to adamantyl vitamin d analogs: structural basis for vitamin d receptor antagonism and partial agonism
J.Med.Chem., 51, 2008
2ZMH
DownloadVisualize
BU of 2zmh by Molmil
Crystal Structure of Rat Vitamin D Receptor Bound to Adamantyl Vitamin D Analogs: Structural Basis for Vitamin D Receptor Antagonism and/or Partial Agonism
分子名称: (1R,3R,7E,17beta)-17-{(1R,2E,4R)-4-hydroxy-1-methyl-4-[(3S,5S,7S)-tricyclo[3.3.1.1~3,7~]dec-1-yl]but-2-en-1-yl}-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol, Mediator of RNA polymerase II transcription subunit 1, Vitamin D3 receptor
著者Nakabayashi, M, Yamada, S, Tanaka, T, Igarashi, M, Yoshimoto, N, Ikura, T, Ito, N, Makishima, M, Tokiwa, H, DeLuca, H.F, Shimizu, M.
登録日2008-04-18
公開日2008-09-02
最終更新日2024-03-13
実験手法X-RAY DIFFRACTION (2.1 Å)
主引用文献Crystal structures of rat vitamin d receptor bound to adamantyl vitamin d analogs: structural basis for vitamin d receptor antagonism and partial agonism
J.Med.Chem., 51, 2008
2ZMJ
DownloadVisualize
BU of 2zmj by Molmil
Crystal Structure of Rat Vitamin D Receptor Bound to Adamantyl Vitamin D Analogs: Structural Basis for Vitamin D Receptor Antagonism and/or Partial Agonism
分子名称: (1R,3R,7E,17beta)-17-{(1S,2E,5R)-5-hydroxy-1-methyl-6-[(3S,5S,7S)-tricyclo[3.3.1.1~3,7~]dec-1-yl]hex-2-en-1-yl}-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol, Mediator of RNA polymerase II transcription subunit 1, Vitamin D3 receptor
著者Nakabayashi, M, Yamada, S, Tanaka, T, Igarashi, M, Yoshimoto, N, Ikura, T, Ito, N, Makishima, M, Tokiwa, H, DeLuca, H.F, Shimizu, M.
登録日2008-04-19
公開日2008-09-02
最終更新日2024-03-13
実験手法X-RAY DIFFRACTION (2.35 Å)
主引用文献Crystal structures of rat vitamin d receptor bound to adamantyl vitamin d analogs: structural basis for vitamin d receptor antagonism and partial agonism
J.Med.Chem., 51, 2008
5ZQU
DownloadVisualize
BU of 5zqu by Molmil
Crystal structure of tetrameric RXRalpha-LBD complexed with partial agonist CBt-PMN
分子名称: 1-(3,5,5,8,8-pentamethyl-6,7-dihydronaphthalen-2-yl)benzotriazole-5-carboxylic acid, BROMIDE ION, Retinoic acid receptor RXR-alpha
著者Miyashita, Y, Numoto, N, Arulmozhiraja, S, Nakano, S, Matsuo, N, Shimizu, K, Kakuta, H, Ito, S, Ikura, T, Ito, N, Tokiwa, H.
登録日2018-04-20
公開日2019-02-27
最終更新日2023-11-22
実験手法X-RAY DIFFRACTION (2.60038781 Å)
主引用文献Dual conformation of the ligand induces the partial agonistic activity of retinoid X receptor alpha (RXR alpha ).
FEBS Lett., 593, 2019
3VTB
DownloadVisualize
BU of 3vtb by Molmil
Crystal structure of rat vitamin D receptor bound to a partial agonist 25-adamantyl-23-yne-19-norvitammin D ADTK1
分子名称: (1R,3R,7E,17beta)-17-{(2R,6S)-6-hydroxy-6-[(3S,5S,7S)-tricyclo[3.3.1.1~3,7~]dec-1-yl]hex-4-yn-2-yl}-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol, COACTIVATOR PEPTIDE DRIP, Vitamin D3 receptor
著者Nakabayashi, M, Kudo, T, Tokiwa, H, Makishima, M, Yamada, S, Ikura, T, Ito, N.
登録日2012-05-26
公開日2013-06-12
最終更新日2024-03-20
実験手法X-RAY DIFFRACTION (2 Å)
主引用文献Combination of Triple Bond and Adamantane Ring on the Vitamin D Side Chain Produced Partial Agonists for Vitamin D Receptor.
J.Med.Chem., 2014
3VTC
DownloadVisualize
BU of 3vtc by Molmil
Crystal structure of rat vitamin D receptor bound to a partial agonist 26-adamantyl-23-yne-19-norvitammin D ADTK3
分子名称: (1R,3R,7E,17beta)-17-{(2R,6R)-6-hydroxy-7-[(3S,5S,7S)-tricyclo[3.3.1.1~3,7~]dec-1-yl]hept-4-yn-2-yl}-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol, 1,2-ETHANEDIOL, COACTIVATOR PEPTIDE DRIP, ...
著者Nakabayashi, M, Kudo, T, Tokiwa, H, Makishima, M, Yamada, S, Ikura, T, Ito, N.
登録日2012-05-26
公開日2013-06-12
最終更新日2023-11-08
実験手法X-RAY DIFFRACTION (1.5 Å)
主引用文献Combination of Triple Bond and Adamantane Ring on the Vitamin D Side Chain Produced Partial Agonists for Vitamin D Receptor.
J.Med.Chem., 2014
3VTD
DownloadVisualize
BU of 3vtd by Molmil
Crystal structure of rat vitamin D receptor bound to a partial agonist 26-adamantyl-23-yne-19-norvitammin D ADTK4
分子名称: (1R,3R,7E,17beta)-17-{(2R,6S)-6-hydroxy-7-[(3S,5S,7S)-tricyclo[3.3.1.1~3,7~]dec-1-yl]hept-4-yn-2-yl}-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol, COACTIVATOR PEPTIDE DRIP, Vitamin D3 receptor
著者Nakabayashi, M, Kudo, T, Tokiwa, H, Makishima, M, Yamada, S, Ikura, T, Ito, N.
登録日2012-05-26
公開日2013-06-12
最終更新日2023-11-08
実験手法X-RAY DIFFRACTION (2.7 Å)
主引用文献Combination of Triple Bond and Adamantane Ring on the Vitamin D Side Chain Produced Partial Agonists for Vitamin D Receptor.
J.Med.Chem., 2014
5Y1F
DownloadVisualize
BU of 5y1f by Molmil
Monomeric L-threonine 3-dehydrogenase from metagenome database (NAD+ bound form)
分子名称: NAD dependent epimerase/dehydratase family, NICOTINAMIDE-ADENINE-DINUCLEOTIDE
著者Motoyama, T, Nakano, S, Yamamoto, Y, Tokiwa, H, Asano, Y, Ito, S.
登録日2017-07-20
公開日2017-11-15
最終更新日2023-11-22
実験手法X-RAY DIFFRACTION (1.25 Å)
主引用文献Product Release Mechanism Associated with Structural Changes in Monomeric l-Threonine 3-Dehydrogenase.
Biochemistry, 56, 2017
5Y1G
DownloadVisualize
BU of 5y1g by Molmil
Monomeric L-threonine 3-dehydrogenase from metagenome database (AKB and NADH bound form)
分子名称: 2-AMINO-3-KETOBUTYRIC ACID, NAD dependent epimerase/dehydratase family, NICOTINAMIDE-ADENINE-DINUCLEOTIDE
著者Motoyama, T, Nakano, S, Yamamoto, Y, Tokiwa, H, Asano, Y, Ito, S.
登録日2017-07-20
公開日2017-11-15
最終更新日2023-11-22
実験手法X-RAY DIFFRACTION (1.35 Å)
主引用文献Product Release Mechanism Associated with Structural Changes in Monomeric l-Threonine 3-Dehydrogenase.
Biochemistry, 56, 2017
5Y1E
DownloadVisualize
BU of 5y1e by Molmil
monomeric L-threonine 3-dehydrogenase from metagenome database (L-Ser and NAD+ bound form)
分子名称: NAD dependent epimerase/dehydratase family, NICOTINAMIDE-ADENINE-DINUCLEOTIDE, SERINE
著者Motoyama, T, Nakano, S, Yamamoto, Y, Tokiwa, H, Asano, Y, Ito, S.
登録日2017-07-20
公開日2017-11-15
最終更新日2023-11-22
実験手法X-RAY DIFFRACTION (1.9 Å)
主引用文献Product Release Mechanism Associated with Structural Changes in Monomeric l-Threonine 3-Dehydrogenase.
Biochemistry, 56, 2017
5Y1D
DownloadVisualize
BU of 5y1d by Molmil
Monomeric L-threonine 3-dehydrogenase from metagenome database (apo form)
分子名称: NAD dependent epimerase/dehydratase family
著者Motoyama, T, Nakano, S, Yamamoto, Y, Tokiwa, H, Asano, Y, Ito, S.
登録日2017-07-20
公開日2017-11-15
最終更新日2023-11-22
実験手法X-RAY DIFFRACTION (1.9 Å)
主引用文献Product Release Mechanism Associated with Structural Changes in Monomeric l-Threonine 3-Dehydrogenase.
Biochemistry, 56, 2017
5Z76
DownloadVisualize
BU of 5z76 by Molmil
Artificial L-threonine 3-dehydrogenase designed by full consensus design
分子名称: Artificial L-threonine 3-dehydrogenase
著者Nakano, S, Motoyama, T, Miyashita, Y, Ishizuka, Y, Matsuo, N, Tokiwa, H, Shinoda, S, Asano, Y, Ito, S.
登録日2018-01-27
公開日2018-08-22
最終更新日2023-11-22
実験手法X-RAY DIFFRACTION (2.8 Å)
主引用文献Benchmark Analysis of Native and Artificial NAD+-Dependent Enzymes Generated by a Sequence-Based Design Method with or without Phylogenetic Data.
Biochemistry, 57, 2018
5Z75
DownloadVisualize
BU of 5z75 by Molmil
Artificial L-threonine 3-dehydrogenase designed by ancestral sequence reconstruction.
分子名称: Artificial L-threonine 3-dehydrogenase, NICOTINAMIDE-ADENINE-DINUCLEOTIDE, NONAETHYLENE GLYCOL, ...
著者Nakano, S, Motoyama, T, Miyashita, Y, Ishizuka, Y, Matsuo, N, Tokiwa, H, Shinoda, S, Asano, Y, Ito, S.
登録日2018-01-27
公開日2018-08-22
最終更新日2023-11-22
実験手法X-RAY DIFFRACTION (2.1 Å)
主引用文献Benchmark Analysis of Native and Artificial NAD+-Dependent Enzymes Generated by a Sequence-Based Design Method with or without Phylogenetic Data.
Biochemistry, 57, 2018
3WMW
DownloadVisualize
BU of 3wmw by Molmil
GalE-like L-Threonine dehydrogenase from Cupriavidus necator (apo form)
分子名称: CALCIUM ION, NAD dependent epimerase/dehydratase
著者Nakano, S, Okazaki, S, Tokiwa, H, Asano, Y.
登録日2013-11-29
公開日2014-02-26
最終更新日2023-11-08
実験手法X-RAY DIFFRACTION (2.25 Å)
主引用文献Binding of NAD+ and L-Threonine Induces Stepwise Structural and Flexibility Changes in Cupriavidus necator L-Threonine Dehydrogenase
J.Biol.Chem., 289, 2014
3WMX
DownloadVisualize
BU of 3wmx by Molmil
GalE-like L-Threonine dehydrogenase from Cupriavidus necator (holo form)
分子名称: NAD dependent epimerase/dehydratase, NICOTINAMIDE-ADENINE-DINUCLEOTIDE, THREONINE
著者Nakano, S, Okazaki, S, Tokiwa, H, Asano, Y.
登録日2013-11-29
公開日2014-02-26
最終更新日2023-11-08
実験手法X-RAY DIFFRACTION (2.5 Å)
主引用文献Binding of NAD+ and L-Threonine Induces Stepwise Structural and Flexibility Changes in Cupriavidus necator L-Threonine Dehydrogenase
J.Biol.Chem., 289, 2014

219869

件を2024-05-15に公開中

PDB statisticsPDBj update infoContact PDBjnumon