5FB3
 
 | | Structure of glycerophosphate dehydrogenase in complex with NADPH | | Descriptor: | Glycerol-1-phosphate dehydrogenase [NAD(P)+], NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE, PYROPHOSPHATE, ... | | Authors: | Sakuraba, H, Hayashi, J, Yamamoto, K, Yoneda, K, Ohshima, T. | | Deposit date: | 2015-12-14 | | Release date: | 2016-10-12 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (2.45 Å) | | Cite: | Unique coenzyme binding mode of hyperthermophilic archaeal sn-glycerol-1-phosphate dehydrogenase from Pyrobaculum calidifontis
Proteins, 84, 2016
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3AHG
 | | H64A mutant of Phosphoketolase from Bifidobacterium Breve complexed with a tricyclic ring form of thiamine diphosphate | | Descriptor: | 1,2-ETHANEDIOL, 2-[(9aR)-2,7-dimethyl-9a,10-dihydro-5H-pyrimido[4,5-d][1,3]thiazolo[3,2-a]pyrimidin-8-yl]ethyl trihydrogen diphosphate, MAGNESIUM ION, ... | | Authors: | Suzuki, R, Katayama, T, Kim, B.-J, Wakagi, T, Shoun, H, Ashida, H, Yamamoto, K, Fushinobu, S. | | Deposit date: | 2010-04-22 | | Release date: | 2010-08-25 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Crystal Structures of phosphoketolase: thiamine diphosphate-dependent dehydration mechanism
J.Biol.Chem., 285, 2010
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3AHE
 | | Phosphoketolase from Bifidobacterium Breve complexed with dihydroxyethyl thiamine diphosphate | | Descriptor: | 1,2-ETHANEDIOL, 2-[3-[(4-AMINO-2-METHYL-5-PYRIMIDINYL)METHYL]-2-(1,2-DIHYDROXYETHYL)-4-METHYL-1,3-THIAZOL-3-IUM-5-YL]ETHYL TRIHYDROGEN DIPHOSPHATE, MAGNESIUM ION, ... | | Authors: | Suzuki, R, Katayama, T, Kim, B.-J, Wakagi, T, Shoun, H, Ashida, H, Yamamoto, K, Fushinobu, S. | | Deposit date: | 2010-04-22 | | Release date: | 2010-08-25 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Crystal Structures of phosphoketolase: thiamine diphosphate-dependent dehydration mechanism
J.Biol.Chem., 285, 2010
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3AHF
 | | Phosphoketolase from Bifidobacterium Breve complexed with inorganic phosphate | | Descriptor: | GLYCEROL, MAGNESIUM ION, PHOSPHATE ION, ... | | Authors: | Suzuki, R, Katayama, T, Kim, B.-J, Wakagi, T, Shoun, H, Ashida, H, Yamamoto, K, Fushinobu, S. | | Deposit date: | 2010-04-22 | | Release date: | 2010-08-25 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Crystal Structures of phosphoketolase: thiamine diphosphate-dependent dehydration mechanism
J.Biol.Chem., 285, 2010
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3AHH
 | | H142A mutant of Phosphoketolase from Bifidobacterium Breve complexed with acetyl thiamine diphosphate | | Descriptor: | 1,2-ETHANEDIOL, 2-ACETYL-THIAMINE DIPHOSPHATE, MAGNESIUM ION, ... | | Authors: | Suzuki, R, Katayama, T, Kim, B.-J, Wakagi, T, Shoun, H, Ashida, H, Yamamoto, K, Fushinobu, S. | | Deposit date: | 2010-04-22 | | Release date: | 2010-08-25 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Crystal Structures of phosphoketolase: thiamine diphosphate-dependent dehydration mechanism
J.Biol.Chem., 285, 2010
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3AHI
 | | H320A mutant of Phosphoketolase from Bifidobacterium Breve complexed with acetyl thiamine diphosphate | | Descriptor: | 1,2-ETHANEDIOL, 2-ACETYL-THIAMINE DIPHOSPHATE, MAGNESIUM ION, ... | | Authors: | Suzuki, R, Katayama, T, Kim, B.-J, Wakagi, T, Shoun, H, Ashida, H, Yamamoto, K, Fushinobu, S. | | Deposit date: | 2010-04-22 | | Release date: | 2010-08-25 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Crystal Structures of phosphoketolase: thiamine diphosphate-dependent dehydration mechanism
J.Biol.Chem., 285, 2010
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3AHD
 | | Phosphoketolase from Bifidobacterium Breve complexed with 2-acetyl-thiamine diphosphate | | Descriptor: | 1,2-ETHANEDIOL, 2-ACETYL-THIAMINE DIPHOSPHATE, MAGNESIUM ION, ... | | Authors: | Suzuki, R, Katayama, T, Kim, B.-J, Wakagi, T, Shoun, H, Ashida, H, Yamamoto, K, Fushinobu, S. | | Deposit date: | 2010-04-22 | | Release date: | 2010-08-25 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Crystal Structures of phosphoketolase: thiamine diphosphate-dependent dehydration mechanism
J.Biol.Chem., 285, 2010
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3AHC
 | | Resting form of Phosphoketolase from Bifidobacterium Breve | | Descriptor: | 1,2-ETHANEDIOL, MAGNESIUM ION, NONAETHYLENE GLYCOL, ... | | Authors: | Suzuki, R, Katayama, T, Kim, B.-J, Wakagi, T, Shoun, H, Ashida, H, Yamamoto, K, Fushinobu, S. | | Deposit date: | 2010-04-22 | | Release date: | 2010-08-25 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (1.7 Å) | | Cite: | Crystal Structures of phosphoketolase: thiamine diphosphate-dependent dehydration mechanism
J.Biol.Chem., 285, 2010
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3AHJ
 | | H553A mutant of Phosphoketolase from Bifidobacterium Breve | | Descriptor: | 1,2-ETHANEDIOL, MAGNESIUM ION, THIAMINE DIPHOSPHATE, ... | | Authors: | Suzuki, R, Katayama, T, Kim, B.-J, Wakagi, T, Shoun, H, Ashida, H, Yamamoto, K, Fushinobu, S. | | Deposit date: | 2010-04-22 | | Release date: | 2010-08-25 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Crystal Structures of phosphoketolase: thiamine diphosphate-dependent dehydration mechanism
J.Biol.Chem., 285, 2010
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6IQ5
 | | Crystal Structure of CYP1B1 and Inhibitor Having Azide Group | | Descriptor: | 2-(cis-4-azidocyclohexyl)-4H-naphtho[1,2-b]pyran-4-one, Cytochrome P450 1B1, PROTOPORPHYRIN IX CONTAINING FE | | Authors: | Kubo, M, Yamamoto, K, Itoh, T. | | Deposit date: | 2018-11-06 | | Release date: | 2019-01-30 | | Last modified: | 2024-03-27 | | Method: | X-RAY DIFFRACTION (3.7 Å) | | Cite: | Design and synthesis of selective CYP1B1 inhibitor via dearomatization of alpha-naphthoflavone.
Bioorg. Med. Chem., 27, 2019
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6JEY
 | | Covalent bond formation between ynone moiety of synthetic fatty acid and hPPARg-LBD | | Descriptor: | (9Z,12Z,15Z,18Z,21Z)-5-oxidanylidenetetracosa-9,12,15,18,21-pentaen-6-ynoic acid, Peroxisome proliferator-activated receptor gamma | | Authors: | Kojima, H, Yamamoto, K, Itoh, T. | | Deposit date: | 2019-02-07 | | Release date: | 2020-02-12 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Cyclization Reaction-Based Turn-on Probe for Covalent Labeling of Target Proteins.
Cell Chem Biol, 27, 2020
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2M33
 | | Solution NMR structure of full-length oxidized microsomal rabbit cytochrome b5 | | Descriptor: | Cytochrome b5, PROTOPORPHYRIN IX CONTAINING FE | | Authors: | Subramanian, V, Ahuja, S, Popovych, N, Huang, R, Le Clair, S.V, Jahr, N, Soong, R, Xu, J, Yamamoto, K, Nanga, R.P, Im, S, Waskell, L, Ramamoorthy, A. | | Deposit date: | 2013-01-08 | | Release date: | 2013-02-06 | | Last modified: | 2024-05-15 | | Method: | SOLUTION NMR | | Cite: | NMR structure of full-length mammalian cytochrome b5
To be Published
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3A4U
 | | Crystal structure of MCFD2 in complex with carbohydrate recognition domain of ERGIC-53 | | Descriptor: | CALCIUM ION, GLYCEROL, Multiple coagulation factor deficiency protein 2, ... | | Authors: | Nishio, M, Kamiya, Y, Mizushima, T, Wakatsuki, S, Sasakawa, H, Yamamoto, K, Uchiyama, S, Noda, M, McKay, A.R, Fukui, K, Hauri, H.P, Kato, K. | | Deposit date: | 2009-07-17 | | Release date: | 2010-01-05 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (1.84 Å) | | Cite: | Structural basis for the cooperative interplay between the two causative gene products of combined factor V and factor VIII deficiency.
Proc.Natl.Acad.Sci.USA, 107, 2010
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5H1E
 | | Interaction between vitamin D receptor and coactivator peptide SRC2-3 | | Descriptor: | 5-{2-[1-(5-HYDROXY-1,5-DIMETHYL-HEXYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-4-METHYLENE-CYCLOHEXANE-1,3-DIOL, Nuclear receptor coactivator 2 peptide, Vitamin D3 receptor | | Authors: | Egawa, D, Itoh, T, Kato, A, Kataoka, S, Anami, Y, Yamamoto, K. | | Deposit date: | 2016-10-08 | | Release date: | 2017-01-11 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (2.6 Å) | | Cite: | SRC2-3 binds to vitamin D receptor with high sensitivity and strong affinity
Bioorg. Med. Chem., 25, 2017
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3AY8
 | | Glutathione S-transferase unclassified 2 from Bombyx mori | | Descriptor: | GLYCEROL, Glutathione S-transferase | | Authors: | Kakuta, Y, Usuda, K, Nakashima, T, Kimura, M, Aso, Y, Yamamoto, K. | | Deposit date: | 2011-05-02 | | Release date: | 2011-09-07 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Crystallographic survey of active sites of an unclassified glutathione transferase from Bombyx mori
Biochim.Biophys.Acta, 1810, 2011
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5XPO
 | | Crystal structure of VDR-LBD complexed with 25-(hydroxyphenyl)-2-methylidene-19,26,27-trinor-25-oxo-1-hydroxyvitamin D3 | | Descriptor: | (5~{R})-5-[(1~{R},3~{a}~{S},4~{E},7~{a}~{R})-7~{a}-methyl-4-[2-[(3~{R},5~{R})-4-methylidene-3,5-bis(oxidanyl)cyclohexyl idene]ethylidene]-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-1-yl]-1-(4-hydroxyphenyl)hexan-1-one, Mediator of RNA polymerase II transcription subunit 1, Vitamin D3 receptor | | Authors: | Kato, A, Itoh, T, Yamamoto, K. | | Deposit date: | 2017-06-03 | | Release date: | 2018-06-06 | | Last modified: | 2024-03-27 | | Method: | X-RAY DIFFRACTION (2.28 Å) | | Cite: | Vitamin D Analogues with a p-Hydroxyphenyl Group at the C25 Position: Crystal Structure of Vitamin D Receptor Ligand-Binding Domain Complexed with the Ligand Explains the Mechanism Underlying Full Antagonistic Action
J. Med. Chem., 60, 2017
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3VYJ
 | | Crystal structure of C-type lectin domain of murine dendritic cell inhibitory receptor 2 (apo form) | | Descriptor: | C-type lectin domain family 4, member a4, SULFATE ION | | Authors: | Nagae, M, Yamanaka, K, Hanashima, S, Ikeda, A, Satoh, T, Matsumoto, N, Yamamoto, K, Yamaguchi, Y. | | Deposit date: | 2012-09-26 | | Release date: | 2013-10-02 | | Last modified: | 2013-12-11 | | Method: | X-RAY DIFFRACTION (2.15 Å) | | Cite: | Recognition of Bisecting N-Acetylglucosamine: STRUCTURAL BASIS FOR ASYMMETRIC INTERACTION WITH THE MOUSE LECTIN DENDRITIC CELL INHIBITORY RECEPTOR 2
J.Biol.Chem., 288, 2013
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5XPM
 | | Crystal structure of VDR-LBD complexed with 22S-Butyl-25RS-(hydroxyphenyl)-25-methoxy-2-methylidene-19,26,27-trinor-1-hydroxyvitamin D3 | | Descriptor: | (1~{R},3~{R})-5-[(2~{E})-2-[(1~{R},3~{a}~{S},7~{a}~{R})-1-[(2~{R},3~{S})-3-[(3~{S})-3-(4-hydroxyphenyl)-3-methoxy-propyl]heptan-2-yl]-7~{a}-methyl-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-4-ylidene]ethylidene]-2-methylidene-cyclohexane-1,3-diol, Mediator of RNA polymerase II transcription subunit 1, Vitamin D3 receptor | | Authors: | Kato, A, Itoh, T, Yamamoto, K. | | Deposit date: | 2017-06-03 | | Release date: | 2018-06-06 | | Last modified: | 2024-03-27 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Vitamin D Analogues with a p-Hydroxyphenyl Group at the C25 Position: Crystal Structure of Vitamin D Receptor Ligand-Binding Domain Complexed with the Ligand Explains the Mechanism Underlying Full Antagonistic Action
J. Med. Chem., 60, 2017
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5XPL
 | | Crystal structure of VDR-LBD complexed with 22S-butyl-25-hydroxyphenyl-2-methylidene-19,26,27-trinor-25-oxo-1-hydroxyvitamin D3 | | Descriptor: | (4~{S})-4-[(1~{R})-1-[(1~{R},3~{a}~{S},4~{E},7~{a}~{R})-7~{a}-methyl-4-[2-[(3~{R},5~{R})-4-methylidene-3,5-bis(oxidanyl )cyclohexylidene]ethylidene]-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-1-yl]ethyl]-1-(4-hydroxyphenyl)octan-1-one, Nuclear receptor coactivator 2, Vitamin D3 receptor | | Authors: | Kato, A, Itoh, T, Yamamoto, K. | | Deposit date: | 2017-06-03 | | Release date: | 2018-06-06 | | Last modified: | 2024-03-27 | | Method: | X-RAY DIFFRACTION (2.05 Å) | | Cite: | Vitamin D Analogues with a p-Hydroxyphenyl Group at the C25 Position: Crystal Structure of Vitamin D Receptor Ligand-Binding Domain Complexed with the Ligand Explains the Mechanism Underlying Full Antagonistic Action
J. Med. Chem., 60, 2017
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3VYK
 | | Crystal structure of C-type lectin domain of murine dendritic cell inhibitory receptor 2 in complex with N-glycan | | Descriptor: | 1,2-ETHANEDIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)][2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]methyl alpha-D-mannopyranoside, C-type lectin domain family 4, ... | | Authors: | Nagae, M, Yamanaka, K, Hanashima, S, Ikeda, A, Satoh, T, Matsumoto, N, Yamamoto, K, Yamaguchi, Y. | | Deposit date: | 2012-09-26 | | Release date: | 2013-10-02 | | Last modified: | 2020-07-29 | | Method: | X-RAY DIFFRACTION (1.5 Å) | | Cite: | Recognition of Bisecting N-Acetylglucosamine: STRUCTURAL BASIS FOR ASYMMETRIC INTERACTION WITH THE MOUSE LECTIN DENDRITIC CELL INHIBITORY RECEPTOR 2
J.Biol.Chem., 288, 2013
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5WQX
 | | Covalent bond formation of synthetic ligand with hPPARg-LBD | | Descriptor: | 2-[E-(E-2-oxidanylidenehexadec-5-enylidene)amino]ethanoic acid, Peroxisome proliferator-activated receptor gamma | | Authors: | Kojima, H, Itoh, T, Yamamoto, K. | | Deposit date: | 2016-11-29 | | Release date: | 2017-11-22 | | Last modified: | 2017-12-13 | | Method: | X-RAY DIFFRACTION (2.29 Å) | | Cite: | On-site reaction for PPAR gamma modification using a specific bifunctional ligand
Bioorg. Med. Chem., 25, 2017
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5WR1
 | | Covalent bond formation of bifunctional ligand with hPPARg-LBD | | Descriptor: | 2-[E-(E-16-azido-2-oxidanylidene-hexadec-3-enylidene)amino]ethanoic acid, Peroxisome proliferator-activated receptor gamma | | Authors: | Kojima, H, Itoh, T, Yamamoto, K. | | Deposit date: | 2016-11-29 | | Release date: | 2017-11-22 | | Last modified: | 2024-10-16 | | Method: | X-RAY DIFFRACTION (2.34 Å) | | Cite: | On-site reaction for PPAR gamma modification using a specific bifunctional ligand
Bioorg. Med. Chem., 25, 2017
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5XPP
 | | Crystal structure of VDR-LBD complexed with 25RS-(Hydroxyphenyl)-2-methylidene-19,26,27-trinor-1,25-dihydroxyvitamin D3 | | Descriptor: | (1~{R},3~{R})-5-[(2~{E})-2-[(1~{R},3~{a}~{S},7~{a}~{R})-1-[(2~{R},6~{R})-6-(4-hydroxyphenyl)-6-oxidanyl-hexan-2-yl]-7~{ a}-methyl-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-4-ylidene]ethylidene]-2-methylidene-cyclohexane-1,3-diol, Mediator of RNA polymerase II transcription subunit 1, Vitamin D3 receptor | | Authors: | Kato, A, Itoh, T, Yamamoto, K. | | Deposit date: | 2017-06-03 | | Release date: | 2018-06-06 | | Last modified: | 2024-03-27 | | Method: | X-RAY DIFFRACTION (2.85 Å) | | Cite: | Vitamin D Analogues with a p-Hydroxyphenyl Group at the C25 Position: Crystal Structure of Vitamin D Receptor Ligand-Binding Domain Complexed with the Ligand Explains the Mechanism Underlying Full Antagonistic Action
J. Med. Chem., 60, 2017
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5XPN
 | | Crystal structure of VDR-LBD complexed with 25RS-(hydroxyphenyl)-25-methoxy-2-methylidene-19,26,27-trinor-1-hydroxyvitamin D3 | | Descriptor: | (1~{R},3~{R})-5-[(2~{E})-2-[(1~{R},3~{a}~{S},7~{a}~{R})-1-[(2~{R},6~{R})-6-(4-hydroxyphenyl)-6-methoxy-hexan-2-yl]-7~{a}-methyl-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-4-ylidene]ethylidene]-2-methylidene-cyclohexane-1,3-diol, (1~{R},3~{R})-5-[(2~{E})-2-[(1~{R},3~{a}~{S},7~{a}~{R})-1-[(2~{R},6~{S})-6-(4-hydroxyphenyl)-6-methoxy-hexan-2-yl]-7~{a}-methyl-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-4-ylidene]ethylidene]-2-methylidene-cyclohexane-1,3-diol, Mediator of RNA polymerase II transcription subunit 1, ... | | Authors: | Kato, A, Itoh, T, Yamamoto, K. | | Deposit date: | 2017-06-03 | | Release date: | 2018-07-11 | | Last modified: | 2024-03-27 | | Method: | X-RAY DIFFRACTION (1.96 Å) | | Cite: | Vitamin D Analogues with a p-Hydroxyphenyl Group at the C25 Position: Crystal Structure of Vitamin D Receptor Ligand-Binding Domain Complexed with the Ligand Explains the Mechanism Underlying Full Antagonistic Action
J. Med. Chem., 60, 2017
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5WR0
 | | Huisgen cycloaddition for PPARg-LBD labeling by soaking method | | Descriptor: | (E)-N-[(3E)-2-oxo-16-(8-{6-[(trifluoroacetyl)amino]hexanoyl}-8,9-dihydro-1H-dibenzo[b,f][1,2,3]triazolo[4,5-d]azocin-1-yl)hexadec-3-en-1-ylidene]glycine, Peroxisome proliferator-activated receptor gamma | | Authors: | Kojima, H, Itoh, T, Yamamoto, K. | | Deposit date: | 2016-11-29 | | Release date: | 2017-11-22 | | Last modified: | 2017-12-13 | | Method: | X-RAY DIFFRACTION (2.85 Å) | | Cite: | On-site reaction for PPAR gamma modification using a specific bifunctional ligand
Bioorg. Med. Chem., 25, 2017
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