8YTD
| Crystal Structure of TrkA D5 domain in complex with two different macrocyclic peptides | Descriptor: | 1,2-ETHANEDIOL, High affinity nerve growth factor receptor, Macrocyclic Peptide | Authors: | Yamada, T, Mihara, K, Ueda, T, Yamauchi, D, Shimizu, M, Ando, A, Mayumi, K, Nakata, Z, Mikamiyama, H. | Deposit date: | 2024-03-25 | Release date: | 2024-07-10 | Last modified: | 2024-07-24 | Method: | X-RAY DIFFRACTION (2.34 Å) | Cite: | Discovery and Hit to Lead Optimization of Macrocyclic Peptides as Novel Tropomyosin Receptor Kinase A Antagonists. J.Med.Chem., 67, 2024
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8YTE
| Crystal Structure of TrkA D5 domain in complex with macrocyclic peptide | Descriptor: | 1,2-ETHANEDIOL, AMINOMETHYLAMIDE, High affinity nerve growth factor receptor, ... | Authors: | Yamada, T, Mihara, K, Ueda, T, Yamauchi, D, Shimizu, M, Ando, A, Mayumi, K, Nakata, Z, Mikamiyama, H. | Deposit date: | 2024-03-25 | Release date: | 2024-07-10 | Last modified: | 2024-07-24 | Method: | X-RAY DIFFRACTION (2.26 Å) | Cite: | Discovery and Hit to Lead Optimization of Macrocyclic Peptides as Novel Tropomyosin Receptor Kinase A Antagonists. J.Med.Chem., 67, 2024
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7YVQ
| Complex structure of Clostridioides difficile binary toxin folded CDTa-bound CDTb-pore (short). | Descriptor: | ADP-ribosylating binary toxin binding subunit CdtB, ADP-ribosylating binary toxin enzymatic subunit CdtA, CALCIUM ION | Authors: | Yamada, T, Kawamoto, A, Yoshida, T, Sato, Y, Kato, T, Tsuge, H. | Deposit date: | 2022-08-19 | Release date: | 2022-10-26 | Last modified: | 2024-07-03 | Method: | ELECTRON MICROSCOPY (3.18 Å) | Cite: | Cryo-EM structures of the translocational binary toxin complex CDTa-bound CDTb-pore from Clostridioides difficile. Nat Commun, 13, 2022
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7YVS
| Complex structure of Clostridioides difficile binary toxin unfolded CDTa-bound CDTb-pore (short). | Descriptor: | ADP-ribosylating binary toxin binding subunit CdtB, ADP-ribosylating binary toxin enzymatic subunit CdtA, CALCIUM ION | Authors: | Yamada, T, Kawamoto, A, Yoshida, T, Sato, Y, Kato, T, Tsuge, H. | Deposit date: | 2022-08-19 | Release date: | 2022-10-26 | Last modified: | 2024-07-03 | Method: | ELECTRON MICROSCOPY (2.8 Å) | Cite: | Cryo-EM structures of the translocational binary toxin complex CDTa-bound CDTb-pore from Clostridioides difficile. Nat Commun, 13, 2022
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2RKB
| Serine dehydratase like-1 from human cancer cells | Descriptor: | POTASSIUM ION, PYRIDOXAL-5'-PHOSPHATE, Serine dehydratase-like | Authors: | Yamada, T, Komoto, J, Kasuya, T, Mori, H, Ogawa, H, Takusagawa, F. | Deposit date: | 2007-10-16 | Release date: | 2008-04-01 | Last modified: | 2017-10-25 | Method: | X-RAY DIFFRACTION (2.8 Å) | Cite: | A catalytic mechanism that explains a low catalytic activity of serine dehydratase like-1 from human cancer cells: Crystal structure and site-directed mutagenesis studies. Biochim.Biophys.Acta, 1780, 2008
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2H5L
| S-Adenosylhomocysteine hydrolase containing NAD and 3-deaza-D-eritadenine | Descriptor: | (2R,3R)-4-(4-AMINO-1H-IMIDAZO[4,5-C]PYRIDIN-1-YL)-2,3-DIHYDROXYBUTANOIC ACID, Adenosylhomocysteinase, NICOTINAMIDE-ADENINE-DINUCLEOTIDE | Authors: | Yamada, T, Komoto, J, Takusagawa, F. | Deposit date: | 2006-05-26 | Release date: | 2007-04-10 | Last modified: | 2024-02-14 | Method: | X-RAY DIFFRACTION (2.8 Å) | Cite: | Structure and function of eritadenine and its 3-deaza analogues: Potent inhibitors of S-adenosylhomocysteine hydrolase and hypocholesterolemic agents. Biochem.Pharm., 73, 2007
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7VNN
| Complex structure of Clostridioides difficile enzymatic component (CDTa) and binding component (CDTb) pore with long stem | Descriptor: | ADP-ribosylating binary toxin binding subunit CdtB, CALCIUM ION, CdtA | Authors: | Yamada, T, Kawamoto, A, Yoshida, T, Sato, Y, Kato, T, Tsuge, H. | Deposit date: | 2021-10-11 | Release date: | 2022-10-26 | Last modified: | 2024-06-19 | Method: | ELECTRON MICROSCOPY (2.64 Å) | Cite: | Cryo-EM structures of the translocational binary toxin complex CDTa-bound CDTb-pore from Clostridioides difficile. Nat Commun, 13, 2022
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7VNJ
| Complex structure of Clostridioides difficile enzymatic component (CDTa) and binding component (CDTb) pore with short stem | Descriptor: | ADP-ribosylating binary toxin binding subunit CdtB, ADP-ribosyltransferase enzymatic component, CALCIUM ION | Authors: | Yamada, T, Kawamoto, A, Yoshida, T, Sato, Y, Kato, T, Tsuge, H. | Deposit date: | 2021-10-11 | Release date: | 2022-10-26 | Last modified: | 2024-06-19 | Method: | ELECTRON MICROSCOPY (2.56 Å) | Cite: | Cryo-EM structures of the translocational binary toxin complex CDTa-bound CDTb-pore from Clostridioides difficile. Nat Commun, 13, 2022
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1PWH
| Rat Liver L-Serine Dehydratase- Complex with PYRIDOXYL-(O-METHYL-SERINE)-5-MONOPHOSPHATE | Descriptor: | L-serine dehydratase, N-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)-O-METHYL-L-SERINE, POTASSIUM ION | Authors: | Yamada, T, Komoto, J, Takata, Y, Ogawa, H, Takusagawa, F. | Deposit date: | 2003-07-01 | Release date: | 2003-12-02 | Last modified: | 2023-08-16 | Method: | X-RAY DIFFRACTION (2.6 Å) | Cite: | Crystal structure of serine dehydratase from rat liver. Biochemistry, 42, 2003
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1PWE
| Rat Liver L-Serine Dehydratase Apo Enzyme | Descriptor: | L-serine dehydratase | Authors: | Yamada, T, Komoto, J, Takata, Y, Ogawa, H, Takusagawa, F. | Deposit date: | 2003-07-01 | Release date: | 2003-12-02 | Last modified: | 2024-02-14 | Method: | X-RAY DIFFRACTION (2.8 Å) | Cite: | Crystal structure of serine dehydratase from rat liver. Biochemistry, 42, 2003
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6KK8
| XN joint refinement of manganese catalase from Thermus Thermophilus HB27 | Descriptor: | 1,2-ETHANEDIOL, MANGANESE (III) ION, OXYGEN ATOM, ... | Authors: | Yamada, T, Yano, N, Kusaka, K. | Deposit date: | 2019-07-24 | Release date: | 2019-09-04 | Last modified: | 2024-04-03 | Method: | NEUTRON DIFFRACTION (1.37 Å), X-RAY DIFFRACTION | Cite: | Single-crystal time-of-flight neutron Laue methods: application to manganese catalase from Thermus thermophilus HB27 J.Appl.Crystallogr., 2019
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1XWF
| K185N mutated S-adenosylhomocysteine hydrolase | Descriptor: | ADENOSINE, Adenosylhomocysteinase, NICOTINAMIDE-ADENINE-DINUCLEOTIDE | Authors: | Yamada, T, Takata, Y, Komoto, J, Gomi, T, Ogawa, H, Fujioka, M, Takusagawa, F. | Deposit date: | 2004-11-01 | Release date: | 2005-09-20 | Last modified: | 2024-02-14 | Method: | X-RAY DIFFRACTION (2.8 Å) | Cite: | Catalytic mechanism of S-adenosylhomocysteine hydrolase: Roles of His 54, Asp130, Glu155, Lys185, and Aspl89. Int.J.Biochem.Cell Biol., 37, 2005
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1Z9H
| Microsomal prostaglandin E synthase type-2 | Descriptor: | ACETATE ION, CHLORIDE ION, INDOMETHACIN, ... | Authors: | Yamada, T, Komoto, J, Watanabe, K, Ohmiya, Y, Takusagawa, F. | Deposit date: | 2005-04-02 | Release date: | 2005-05-17 | Last modified: | 2024-02-14 | Method: | X-RAY DIFFRACTION (2.6 Å) | Cite: | Crystal Structure and Possible Catalytic Mechanism of Microsomal Prostaglandin E Synthase Type 2 (mPGES-2). J.Mol.Biol., 348, 2005
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3VXF
| X/N Joint refinement of Human alpha-thrombin-Bivalirudin complex PD5 | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, BIVALIRUDIN, Thrombin heavy chain, ... | Authors: | Yamada, T, Kurihara, K, Masumi, K, Tamada, T, Tomoyori, K, Ohnishi, Y, Tanaka, I, Kuroki, R, Niimura, N. | Deposit date: | 2012-09-12 | Release date: | 2013-09-04 | Last modified: | 2020-07-29 | Method: | NEUTRON DIFFRACTION (1.602 Å), X-RAY DIFFRACTION | Cite: | Neutron and X-ray crystallographic analysis of the human alpha-thrombin-bivalirudin complex at pD 5.0: protonation states and hydration structure of the enzyme-product complex Biochim.Biophys.Acta, 1834, 2013
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3VXE
| Human alpha-thrombin-Bivalirudin complex at PD5.0 | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, BIVALIRUDIN, Thrombin heavy chain, ... | Authors: | Yamada, T, Kurihara, K, Masumi, K, Tamada, T, Tomoyori, K, Ohnishi, Y, Tanaka, I, Kuroki, R, Niimura, N. | Deposit date: | 2012-09-12 | Release date: | 2013-09-04 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.25 Å) | Cite: | Neutron and X-ray crystallographic analysis of the human alpha-thrombin-bivalirudin complex at pD 5.0: protonation states and hydration structure of the enzyme-product complex Biochim.Biophys.Acta, 1834, 2013
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2F2F
| Crystal structure of cytolethal distending toxin (CDT) from Actinobacillus actinomycetemcomitans | Descriptor: | Cytolethal distending toxin A, Cytolethal distending toxin B, cytolethal distending toxin C | Authors: | Yamada, T, Komoto, J, Saiki, K, Konishi, K, Takusagawa, F. | Deposit date: | 2005-11-16 | Release date: | 2006-03-28 | Last modified: | 2023-08-23 | Method: | X-RAY DIFFRACTION (2.4 Å) | Cite: | Variation of loop sequence alters stability of cytolethal distending toxin (CDT): crystal structure of CDT from Actinobacillus actinomycetemcomitans Protein Sci., 15, 2006
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1LZ6
| STRUCTURAL AND FUNCTIONAL ANALYSES OF THE ARG-GLY-ASP SEQUENCE INTRODUCED INTO HUMAN LYSOZYME | Descriptor: | CHLORIDE ION, HUMAN LYSOZYME | Authors: | Matsushima, M, Inaka, K, Yamada, T, Sekiguchi, K, Kikuchi, M. | Deposit date: | 1993-02-03 | Release date: | 1993-10-31 | Last modified: | 2017-11-29 | Method: | X-RAY DIFFRACTION (1.8 Å) | Cite: | Structural and functional analyses of the Arg-Gly-Asp sequence introduced into human lysozyme. J.Biol.Chem., 268, 1993
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7OZ4
| Mature capsid of bacteriophage phiRSA1 | Descriptor: | p2 family phage major capsid protein | Authors: | Effantin, G, Fujiwara, A, Kawsaki, T, Yamada, T, Schoehn, G. | Deposit date: | 2021-06-25 | Release date: | 2021-11-17 | Last modified: | 2024-07-17 | Method: | ELECTRON MICROSCOPY (3.9 Å) | Cite: | High Resolution Structure of the Mature Capsid of Ralstonia solanacearum Bacteriophage phi RSA1 by Cryo-Electron Microscopy. Int J Mol Sci, 22, 2021
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1D7Y
| CRYSTAL STRUCTURE OF NADH-DEPENDENT FERREDOXIN REDUCTASE, BPHA4 | Descriptor: | FERREDOXIN REDUCTASE, FLAVIN-ADENINE DINUCLEOTIDE | Authors: | Senda, T, Yamada, T, Sakurai, N, Kubota, M, Nishizaki, T, Masai, E, Fukuda, M, Mitsui, Y. | Deposit date: | 1999-10-21 | Release date: | 2000-12-20 | Last modified: | 2024-02-07 | Method: | X-RAY DIFFRACTION (2.1 Å) | Cite: | Crystal structure of NADH-dependent ferredoxin reductase component in biphenyl dioxygenase. J.Mol.Biol., 304, 2000
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6L9C
| Neutron structure of copper amine oxidase from Arthrobacter glibiformis at pD 7.4 | Descriptor: | COPPER (II) ION, Phenylethylamine oxidase, SODIUM ION | Authors: | Murakawa, T, Kurihara, K, Shoji, M, Shibazaki, C, Sunami, T, Tamada, T, Yano, N, Yamada, T, Kusaka, K, Suzuki, M, Shigeta, Y, Kuroki, R, Hayashi, H, Yano, Y, Tanizawa, K, Adachi, M, Okajima, T. | Deposit date: | 2019-11-08 | Release date: | 2020-04-29 | Last modified: | 2023-11-22 | Method: | NEUTRON DIFFRACTION (1.14 Å), X-RAY DIFFRACTION | Cite: | Neutron crystallography of copper amine oxidase reveals keto/enolate interconversion of the quinone cofactor and unusual proton sharing. Proc.Natl.Acad.Sci.USA, 117, 2020
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3OTJ
| A Crystal Structure of Trypsin Complexed with BPTI (Bovine Pancreatic Trypsin Inhibitor) by X-ray/Neutron Joint Refinement | Descriptor: | CALCIUM ION, Cationic trypsin, Pancreatic trypsin inhibitor, ... | Authors: | Kawamura, K, Yamada, T, Kurihara, K, Tamada, T, Kuroki, R, Tanaka, I, Takahashi, H, Niimura, N. | Deposit date: | 2010-09-12 | Release date: | 2011-01-26 | Last modified: | 2017-11-08 | Method: | NEUTRON DIFFRACTION (2.15 Å), X-RAY DIFFRACTION | Cite: | X-ray and neutron protein crystallographic analysis of the trypsin-BPTI complex. Acta Crystallogr.,Sect.D, 67, 2011
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4GPG
| X/N joint refinement of Achromobacter Lyticus Protease I free form at pD8.0 | Descriptor: | Protease 1 | Authors: | Ohnishi, Y, Yamada, T, Kurihara, K, Tanaka, I, Sakiyama, F, Masaki, T, Niimura, N. | Deposit date: | 2012-08-21 | Release date: | 2013-09-11 | Last modified: | 2023-11-08 | Method: | NEUTRON DIFFRACTION (1.895 Å), X-RAY DIFFRACTION | Cite: | Neutron and X-ray crystallographic analysis of Achromobacter protease I at pD 8.0: protonation states and hydration structure in the free-form. Biochim.Biophys.Acta, 1834, 2013
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6KLO
| 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
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1F3P
| FERREDOXIN REDUCTASE (BPHA4)-NADH COMPLEX | Descriptor: | FERREDOXIN REDUCTASE, FLAVIN-ADENINE DINUCLEOTIDE, NICOTINAMIDE-ADENINE-DINUCLEOTIDE | Authors: | Senda, T, Yamada, T, Sakurai, N, Kubota, M, Nishizaki, T, Masai, E, Fukuda, M, Mitsuidagger, Y. | Deposit date: | 2000-06-06 | Release date: | 2001-06-06 | Last modified: | 2024-03-13 | Method: | X-RAY DIFFRACTION (2.4 Å) | Cite: | Crystal structure of NADH-dependent ferredoxin reductase component in biphenyl dioxygenase. J.Mol.Biol., 304, 2000
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4L25
| Crystal structure of DNA duplex containing consecutive T-T mispairs | Descriptor: | DNA (5'-D(*CP*GP*CP*GP*AP*TP*TP*TP*CP*GP*CP*G)-3') | Authors: | Kondo, J, Yamada, T, Hirose, C, Tanaka, Y, Ono, A. | Deposit date: | 2013-06-04 | Release date: | 2014-03-05 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.1 Å) | Cite: | Crystal Structure of Metallo DNA Duplex Containing Consecutive Watson-Crick-like T-Hg(II) -T Base Pairs Angew.Chem.Int.Ed.Engl., 53, 2014
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