4H04
| Lacto-N-biosidase from Bifidobacterium bifidum | Descriptor: | Lacto-N-biosidase, SULFATE ION, beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose | Authors: | Ito, T, Katayama, T, Wada, J, Suzuki, R, Ashida, H, Wakagi, T, Yamamoto, K, Fushinobu, S. | Deposit date: | 2012-09-07 | Release date: | 2013-03-20 | Last modified: | 2020-07-29 | Method: | X-RAY DIFFRACTION (1.8 Å) | Cite: | Crystal structures of a glycoside hydrolase family 20 lacto-N-biosidase from Bifidobacterium bifidum J.Biol.Chem., 288, 2013
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3JCJ
| Structures of ribosome-bound initiation factor 2 reveal the mechanism of subunit association | Descriptor: | 16S ribosomal RNA, 23S ribosomal RNA, 30S ribosomal protein S10, ... | Authors: | Sprink, T, Ramrath, D.J.F, Yamamoto, H, Yamamoto, K, Loerke, J, Ismer, J, Hildebrand, P.W, Scheerer, P, Buerger, J, Mielke, T, Spahn, C.M.T. | Deposit date: | 2015-12-18 | Release date: | 2016-03-09 | Last modified: | 2018-07-18 | Method: | ELECTRON MICROSCOPY (3.7 Å) | Cite: | Structures of ribosome-bound initiation factor 2 reveal the mechanism of subunit association. Sci Adv, 2, 2016
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3JCN
| Structures of ribosome-bound initiation factor 2 reveal the mechanism of subunit association: Initiation Complex I | Descriptor: | 16S ribosomal RNA, 23S ribosomal RNA, 30S ribosomal protein S10, ... | Authors: | Sprink, T, Ramrath, D.J.F, Yamamoto, H, Yamamoto, K, Loerke, J, Ismer, J, Hildebrand, P.W, Scheerer, P, Buerger, J, Mielke, T, Spahn, C.M.T. | Deposit date: | 2016-01-04 | Release date: | 2016-03-09 | Last modified: | 2018-07-18 | Method: | ELECTRON MICROSCOPY (4.6 Å) | Cite: | Structures of ribosome-bound initiation factor 2 reveal the mechanism of subunit association. Sci Adv, 2, 2016
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8I06
| Crystal structure of serine acetyltransferase from Salmonella typhimurium complexed with CoA | Descriptor: | COENZYME A, CYSTEINE, Serine acetyltransferase | Authors: | Toyomoto, T, Ono, K, Shiba, T, Momitani, K, Zhang, T, Tsutsuki, H, Ishikawa, T, Hoso, K, Hamada, K, Rahman, A, Zhong, H, Akaike, T, Yamamoto, K, Matsuoka, M, Hanaoka, K, Niidome, T, Sawa, T. | Deposit date: | 2023-01-10 | Release date: | 2023-11-22 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.5 Å) | Cite: | Alkyl gallates inhibit serine O -acetyltransferase in bacteria and enhance susceptibility of drug-resistant Gram-negative bacteria to antibiotics. Front Microbiol, 14, 2023
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8I09
| Crystal structure of serine acetyltransferase from Salmonella typhimurium complexed with butyl gallate | Descriptor: | CYSTEINE, PHOSPHATE ION, Serine acetyltransferase, ... | Authors: | Toyomoto, T, Ono, K, Shiba, T, Momitani, K, Zhang, T, Tsutsuki, H, Ishikawa, T, Hoso, K, Hamada, K, Rahman, A, Zhong, H, Akaike, T, Yamamoto, K, Matsuoka, M, Hanaoka, K, Niidome, T, Sawa, T. | Deposit date: | 2023-01-10 | Release date: | 2023-11-22 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (1.8 Å) | Cite: | Alkyl gallates inhibit serine O -acetyltransferase in bacteria and enhance susceptibility of drug-resistant Gram-negative bacteria to antibiotics. Front Microbiol, 14, 2023
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8I04
| Crystal structure of serine acetyltransferase from Salmonella typhimurium complexed with serine | Descriptor: | PHOSPHATE ION, SERINE, Serine acetyltransferase | Authors: | Toyomoto, T, Ono, K, Shiba, T, Momitani, K, Zhang, T, Tsutsuki, H, Ishikawa, T, Hoso, K, Hamada, K, Rahman, A, Zhong, H, Akaike, T, Yamamoto, K, Matsuoka, M, Hanaoka, K, Niidome, T, Sawa, T. | Deposit date: | 2023-01-10 | Release date: | 2023-11-22 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.3 Å) | Cite: | Alkyl gallates inhibit serine O -acetyltransferase in bacteria and enhance susceptibility of drug-resistant Gram-negative bacteria to antibiotics. Front Microbiol, 14, 2023
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1BKU
| EFFECTS OF GLYCOSYLATION ON THE STRUCTURE AND DYNAMICS OF EEL CALCITONIN, NMR, 10 STRUCTURES | Descriptor: | CALCITONIN | Authors: | Hashimoto, Y, Nishikido, J, Toma, K, Yamamoto, K, Haneda, K, Inazu, T, Valentine, K, Opella, S.J. | Deposit date: | 1998-07-13 | Release date: | 1999-01-13 | Last modified: | 2022-02-16 | Method: | SOLUTION NMR | Cite: | Effects of glycosylation on the structure and dynamics of eel calcitonin in micelles and lipid bilayers determined by nuclear magnetic resonance spectroscopy. Biochemistry, 38, 1999
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1BZB
| GLYCOSYLATED EEL CALCITONIN | Descriptor: | PROTEIN (CALCITONIN), alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Authors: | Hashimoto, Y, Toma, K, Nishikido, J, Yamamoto, K, Haneda, K, Inazu, T, Valentine, K, Opella, S.J. | Deposit date: | 1998-10-27 | Release date: | 1998-11-11 | Last modified: | 2020-07-29 | Method: | SOLUTION NMR | Cite: | Effects of glycosylation on the structure and dynamics of eel calcitonin in micelles and lipid bilayers determined by nuclear magnetic resonance spectroscopy. Biochemistry, 38, 1999
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3UES
| Crystal structure of alpha-1,3/4-fucosidase from Bifidobacterium longum subsp. infantis complexed with deoxyfuconojirimycin | Descriptor: | (2S,3R,4S,5R)-2-METHYLPIPERIDINE-3,4,5-TRIOL, 1,2-ETHANEDIOL, Alpha-1,3/4-fucosidase, ... | Authors: | Sakurama, H, Fushinobu, S, Yoshida, E, Honda, Y, Hidaka, M, Ashida, H, Kitaoka, M, Katayama, T, Yamamoto, K, Kumagai, H. | Deposit date: | 2011-10-31 | Release date: | 2012-04-04 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (1.6 Å) | Cite: | 1,3-1,4-alpha-L-fucosynthase that specifically introduces Lewis a/x antigens into type-1/2 chains J.Biol.Chem., 287, 2012
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3UET
| Crystal structure of alpha-1,3/4-fucosidase from Bifidobacterium longum subsp. infantis D172A/E217A mutant complexed with lacto-N-fucopentaose II | Descriptor: | 1,2-ETHANEDIOL, Alpha-1,3/4-fucosidase, SODIUM ION, ... | Authors: | Sakurama, H, Fushinobu, S, Yoshida, E, Honda, Y, Hidaka, M, Ashida, H, Kitaoka, M, Katayama, T, Yamamoto, K, Kumagai, H. | Deposit date: | 2011-10-31 | Release date: | 2012-04-04 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (2.1 Å) | Cite: | 1,3-1,4-alpha-L-fucosynthase that specifically introduces Lewis a/x antigens into type-1/2 chains J.Biol.Chem., 287, 2012
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5FLX
| Mammalian 40S HCV-IRES complex | Descriptor: | 18S RRNA, 40S RIBOSOMAL PROTEIN S10, 40S RIBOSOMAL PROTEIN S11, ... | Authors: | Yamamoto, H, Collier, M, Loerke, J, Ismer, J, Schmidt, A, Hilal, T, Sprink, T, Yamamoto, K, Mielke, T, Burger, J, Shaikh, T.R, Dabrowski, M, Hildebrand, P.W, Scheerer, P, Spahn, C.M.T. | Deposit date: | 2015-10-28 | Release date: | 2015-12-23 | Last modified: | 2017-08-30 | Method: | ELECTRON MICROSCOPY (3.9 Å) | Cite: | Molecular Architecture of the Ribosome-Bound Hepatitis C Virus Internal Ribosomal Entry Site RNA. Embo J., 34, 2015
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1BYV
| GLYCOSYLATED EEL CALCITONIN | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, PROTEIN (CALCITONIN) | Authors: | Hashimoto, Y, Toma, K, Nishikido, J, Yamamoto, K, Haneda, K, Inazu, T, Valentine, K.G, Opella, S.J. | Deposit date: | 1998-10-16 | Release date: | 1998-10-28 | Last modified: | 2020-07-29 | Method: | SOLUTION NMR | Cite: | Effects of glycosylation on the structure and dynamics of eel calcitonin in micelles and lipid bilayers determined by nuclear magnetic resonance spectroscopy. Biochemistry, 38, 1999
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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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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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6J7A
| Fusion protein of heme oxygenase-1 and NADPH cytochrome P450 reductase (17aa) | Descriptor: | FLAVIN MONONUCLEOTIDE, FLAVIN-ADENINE DINUCLEOTIDE, Heme oxygenase 1,NADPH--cytochrome P450 reductase, ... | Authors: | Sugishima, M, Sato, H, Wada, K, Yamamoto, K. | Deposit date: | 2019-01-17 | Release date: | 2019-04-10 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (3.269 Å) | Cite: | Crystal structure of a NADPH-cytochrome P450 oxidoreductase (CYPOR) and heme oxygenase 1 fusion protein implies a conformational change in CYPOR upon NADPH/NADP+binding. Febs Lett., 593, 2019
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6J7I
| Fusion protein of heme oxygenase-1 and NADPH cytochrome P450 reductase (15aa) | Descriptor: | FLAVIN MONONUCLEOTIDE, FLAVIN-ADENINE DINUCLEOTIDE, Heme oxygenase 1,NADPH--cytochrome P450 reductase, ... | Authors: | Sugishima, M, Sato, H, Wada, K, Yamamoto, K. | Deposit date: | 2019-01-18 | Release date: | 2019-04-10 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (3.3 Å) | Cite: | Crystal structure of a NADPH-cytochrome P450 oxidoreductase (CYPOR) and heme oxygenase 1 fusion protein implies a conformational change in CYPOR upon NADPH/NADP+binding. Febs Lett., 593, 2019
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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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7EFN
| Crystal structure of the gastric proton pump K791S/E820D/Y340N/E936V in (BYK)E2BeF state | Descriptor: | (7R,8R,9S)-2,3-dimethyl-9-phenyl-7,8,9,10-tetrahydroimidazo[1,2-h][1,7]naphthyridine-7,8-diol, 2-acetamido-2-deoxy-beta-D-glucopyranose, MAGNESIUM ION, ... | Authors: | Abe, K, Yamamoto, K, Irie, K. | Deposit date: | 2021-03-22 | Release date: | 2021-09-01 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (3.2 Å) | Cite: | Gastric proton pump with two occluded K + engineered with sodium pump-mimetic mutations. Nat Commun, 12, 2021
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7EFM
| Crystal structure of the gastric proton pump K791S/E820D/Y340N in (BYK)E2BeF state | Descriptor: | (7R,8R,9S)-2,3-dimethyl-9-phenyl-7,8,9,10-tetrahydroimidazo[1,2-h][1,7]naphthyridine-7,8-diol, 2-acetamido-2-deoxy-beta-D-glucopyranose, MAGNESIUM ION, ... | Authors: | Abe, K, Yamamoto, K, Irie, K. | Deposit date: | 2021-03-22 | Release date: | 2021-09-01 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (3.2 Å) | Cite: | Gastric proton pump with two occluded K + engineered with sodium pump-mimetic mutations. Nat Commun, 12, 2021
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7EFL
| Crystal structure of the gastric proton pump K791S in (BYK)E2BeF state | Descriptor: | (7R,8R,9S)-2,3-dimethyl-9-phenyl-7,8,9,10-tetrahydroimidazo[1,2-h][1,7]naphthyridine-7,8-diol, 2-acetamido-2-deoxy-beta-D-glucopyranose, MAGNESIUM ION, ... | Authors: | Abe, K, Yamamoto, K, Irie, K. | Deposit date: | 2021-03-22 | Release date: | 2021-09-01 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (3.4 Å) | Cite: | Gastric proton pump with two occluded K + engineered with sodium pump-mimetic mutations. Nat Commun, 12, 2021
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2LQH
| NMR structure of FOXO3a transactivation domains (CR2C-CR3) in complex with CBP KIX domain (2b3l conformation) | Descriptor: | CREB-binding protein, Forkhead box O3 | Authors: | Wang, F, Marshall, C.B, Yamamoto, K, Li, G.B, Gasmi-Seabrook, G.M.C, Okada, H, Mak, T.W, Ikura, M. | Deposit date: | 2012-03-06 | Release date: | 2012-05-16 | Last modified: | 2024-05-15 | Method: | SOLUTION NMR | Cite: | Structures of KIX domain of CBP in complex with two FOXO3a transactivation domains reveal promiscuity and plasticity in coactivator recruitment. Proc.Natl.Acad.Sci.USA, 109, 2012
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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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2LQI
| NMR structure of FOXO3a transactivation domains (CR2C-CR3) in complex with CBP KIX domain (2l3b conformation) | Descriptor: | CREB-binding protein, Forkhead box O3 | Authors: | Wang, F, Marshall, C.B, Yamamoto, K, Li, G.B, Gasmi-Seabrook, G.M.C, Okada, H, Mak, T.W, Ikura, M. | Deposit date: | 2012-03-06 | Release date: | 2012-05-16 | Last modified: | 2024-05-15 | Method: | SOLUTION NMR | Cite: | Structures of KIX domain of CBP in complex with two FOXO3a transactivation domains reveal promiscuity and plasticity in coactivator recruitment. Proc.Natl.Acad.Sci.USA, 109, 2012
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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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6JEZ
| Covalent labeling of rVDR-LBD by turn-on fluorescent probe mediated by conjugate addition and cyclization | Descriptor: | (1R,3R)-5-(2-((1R,3aS,7aR,E)-1-((R)-6-hydroxy-6-methylheptan-2-yl)-7a-methyloctahydro-4H-inden-4-ylidene)ethylidene)-2- methylenecyclohexane-1,3-diol, 7-(diethylamino)chromen-2-one, Mediator of RNA polymerase II transcription subunit 1, ... | 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 (2.3 Å) | Cite: | Cyclization Reaction-Based Turn-on Probe for Covalent Labeling of Target Proteins. Cell Chem Biol, 27, 2020
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