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: | 2025-03-26 | | 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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9JSK
 | | Clostridium perfringens iota toxin pore Ib in prepore IV state | | Descriptor: | CALCIUM ION, Iota toxin component Ib | | Authors: | Yamada, T, Sugita, Y, Yoshida, T, Noda, T, Tsuge, H. | | Deposit date: | 2024-09-30 | | Release date: | 2025-05-14 | | Method: | ELECTRON MICROSCOPY (3.57 Å) | | Cite: | Step-by-Step Maturation Mechanism of Binary Toxin Pore Revealed by Cryo-EM Analysis
To Be Published
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9JSF
 | | Clostridium perfringens iota toxin pore Ib in prepore I state | | Descriptor: | CALCIUM ION, Iota toxin component Ib | | Authors: | Yamada, T, Sugita, Y, Yoshida, T, Noda, T, Tsuge, H. | | Deposit date: | 2024-09-30 | | Release date: | 2025-05-14 | | Method: | ELECTRON MICROSCOPY (3.04 Å) | | Cite: | Step-by-Step Maturation Mechanism of Binary Toxin Pore Revealed by Cryo-EM Analysis
To Be Published
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9JSG
 | | Clostridium perfringens iota toxin pore Ib in pore state | | Descriptor: | CALCIUM ION, Iota toxin component Ib | | Authors: | Yamada, T, Sugita, Y, Yoshida, T, Noda, T, Tsuge, H. | | Deposit date: | 2024-09-30 | | Release date: | 2025-05-14 | | Method: | ELECTRON MICROSCOPY (2.47 Å) | | Cite: | Step-by-Step Maturation Mechanism of Binary Toxin Pore Revealed by Cryo-EM Analysis
To Be Published
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9JSO
 | | Clostridium perfringens iota toxin pore Ib in prepore VIII state | | Descriptor: | CALCIUM ION, Iota toxin component Ib | | Authors: | Yamada, T, Sugita, Y, Yoshida, T, Noda, T, Tsuge, H. | | Deposit date: | 2024-09-30 | | Release date: | 2025-05-14 | | Method: | ELECTRON MICROSCOPY (2.9 Å) | | Cite: | Step-by-Step Maturation Mechanism of Binary Toxin Pore Revealed by Cryo-EM Analysis
To Be Published
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9JSM
 | | Clostridium perfringens iota toxin pore Ib in prepore VI state | | Descriptor: | CALCIUM ION, Iota toxin component Ib | | Authors: | Yamada, T, Sugita, Y, Yoshida, T, Noda, T, Tsuge, H. | | Deposit date: | 2024-09-30 | | Release date: | 2025-05-14 | | Method: | ELECTRON MICROSCOPY (3.73 Å) | | Cite: | Step-by-Step Maturation Mechanism of Binary Toxin Pore Revealed by Cryo-EM Analysis
To Be Published
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9JSL
 | | Clostridium perfringens iota toxin pore Ib in prepore V state | | Descriptor: | CALCIUM ION, Iota toxin component Ib | | Authors: | Yamada, T, Sugita, Y, Yoshida, T, Noda, T, Tsuge, H. | | Deposit date: | 2024-09-30 | | Release date: | 2025-05-14 | | Method: | ELECTRON MICROSCOPY (3.59 Å) | | Cite: | Step-by-Step Maturation Mechanism of Binary Toxin Pore Revealed by Cryo-EM Analysis
To Be Published
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9JSI
 | | Clostridium perfringens iota toxin pore Ib in prepore II state | | Descriptor: | CALCIUM ION, Iota toxin component Ib | | Authors: | Yamada, T, Sugita, Y, Yoshida, T, Noda, T, Tsuge, H. | | Deposit date: | 2024-09-30 | | Release date: | 2025-05-14 | | Method: | ELECTRON MICROSCOPY (3.35 Å) | | Cite: | Step-by-Step Maturation Mechanism of Binary Toxin Pore Revealed by Cryo-EM Analysis
To Be Published
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9JSN
 | | Clostridium perfringens iota toxin pore Ib in prepore VII state | | Descriptor: | CALCIUM ION, Iota toxin component Ib | | Authors: | Yamada, T, Sugita, Y, Yoshida, T, Noda, T, Tsuge, H. | | Deposit date: | 2024-09-30 | | Release date: | 2025-05-14 | | Method: | ELECTRON MICROSCOPY (3.73 Å) | | Cite: | Step-by-Step Maturation Mechanism of Binary Toxin Pore Revealed by Cryo-EM Analysis
To Be Published
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9JSH
 | | Clostridium perfringens iota toxin pore Ib in prepore III state | | Descriptor: | CALCIUM ION, Iota toxin component Ib | | Authors: | Yamada, T, Sugita, Y, Yoshida, T, Noda, T, Tsuge, H. | | Deposit date: | 2024-09-30 | | Release date: | 2025-05-14 | | Method: | ELECTRON MICROSCOPY (3.32 Å) | | Cite: | Step-by-Step Maturation Mechanism of Binary Toxin Pore Revealed by Cryo-EM Analysis
To Be Published
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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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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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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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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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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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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: | 2024-11-20 | | 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: | 2024-10-30 | | 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: | 2024-10-16 | | 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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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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7YVW
 | | NMR determination of the 2:1 binding motif structure involving cytosine flipping out for the recognition of the CGG/CGG triad DNA | | Descriptor: | 3-[3-[(7-methyl-1,8-naphthyridin-2-yl)carbamoyloxy]propylamino]propyl ~{N}-(7-methyl-1,8-naphthyridin-2-yl)carbamate, DNA (5'-D(*CP*AP*TP*TP*CP*GP*GP*TP*TP*AP*G)-3'), DNA (5'-D(*CP*TP*AP*AP*CP*GP*GP*AP*AP*TP*G)-3') | | Authors: | Furuita, K, Yamada, T, Sakurabayashi, S, Nomura, M, Kojima, C, Nakatani, K. | | Deposit date: | 2022-08-19 | | Release date: | 2023-06-14 | | Last modified: | 2024-05-15 | | Method: | SOLUTION NMR | | Cite: | NMR determination of the 2:1 binding complex of naphthyridine carbamate dimer (NCD) and CGG/CGG triad in double-stranded DNA.
Nucleic Acids Res., 50, 2022
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2PBJ
 | | GSH-heme bound microsomal prostaglandin E synthase | | Descriptor: | CHLORIDE ION, GLUTATHIONE, PROTOPORPHYRIN IX CONTAINING FE, ... | | Authors: | Takusagawa, F, Yamada, T. | | Deposit date: | 2007-03-28 | | Release date: | 2008-02-12 | | Last modified: | 2024-02-21 | | Method: | X-RAY DIFFRACTION (2.8 Å) | | Cite: | PGH2 degradation pathway catalyzed by GSH-heme complex bound microsomal prostaglandin E2 synthase type 2: the first example of a dual-function enzyme.
Biochemistry, 46, 2007
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