2RKB
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 2rkb by Molmil](/molmil-images/mine/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
|
|
3VXF
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 3vxf by Molmil](/molmil-images/mine/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
|
|
8YTD
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 8ytd by Molmil](/molmil-images/mine/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: | 2024-07-17 | 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., 2024
|
|
8YTE
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 8yte by Molmil](/molmil-images/mine/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: | 2024-07-17 | 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., 2024
|
|
2H5L
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 2h5l by Molmil](/molmil-images/mine/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
|
|
7VNN
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 7vnn by Molmil](/molmil-images/mine/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
|
|
7VNJ
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 7vnj by Molmil](/molmil-images/mine/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
|
|
7YVQ
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 7yvq by Molmil](/molmil-images/mine/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
|
|
7YVS
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 7yvs by Molmil](/molmil-images/mine/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
|
|
1PWH
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 1pwh by Molmil](/molmil-images/mine/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
|
|
1PWE
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 1pwe by Molmil](/molmil-images/mine/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
|
|
1XWF
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 1xwf by Molmil](/molmil-images/mine/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
|
|
6KK8
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 6kk8 by Molmil](/molmil-images/mine/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
|
|
1Z9H
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 1z9h by Molmil](/molmil-images/mine/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
|
|
3VXE
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 3vxe by Molmil](/molmil-images/mine/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
|
|
2F2F
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 2f2f by Molmil](/molmil-images/mine/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
|
|
4GPG
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 4gpg by Molmil](/molmil-images/mine/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
|
|
7OZ4
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 7oz4 by Molmil](/molmil-images/mine/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
|
|
7YVW
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 7yvw by Molmil](/molmil-images/mine/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
|
|
1F3P
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 1f3p by Molmil](/molmil-images/mine/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
|
|
7YQS
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 7yqs by Molmil](/molmil-images/mine/7yqs) | Neutron structure of a L-rhamnose-alpha-1,4-D-glucuronate lyase from Fusarium oxysporum 12S, L-Rha complex | Descriptor: | 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, ACETATE ION, CALCIUM ION, ... | Authors: | Yano, N, Kondo, T, Kusaka, K, Yamada, T, Arakawa, T, Sakamoto, T, Fushinobu, S. | Deposit date: | 2022-08-08 | Release date: | 2023-08-09 | Last modified: | 2024-03-27 | Method: | NEUTRON DIFFRACTION (1.25 Å), X-RAY DIFFRACTION | Cite: | Charge neutralization and beta-elimination cleavage mechanism of family 42 L-rhamnose-alpha-1,4-D-glucuronate lyase revealed using neutron crystallography. J.Biol.Chem., 300, 2024
|
|
4L26
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 4l26 by Molmil](/molmil-images/mine/4l26) | Crystal structure of DNA duplex containing consecutive T-T mispairs (Br-derivative) | Descriptor: | DNA (5'-D(*CP*GP*(CBR)P*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: | 2024-03-20 | Method: | X-RAY DIFFRACTION (1.4 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
|
|
4L25
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 4l25 by Molmil](/molmil-images/mine/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
|
|
3OTJ
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 3otj by Molmil](/molmil-images/mine/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
|
|
4L24
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 4l24 by Molmil](/molmil-images/mine/4l24) | Crystal structure of metallo-DNA duplex containing consecutive T-Hg(II)-T base pairs | Descriptor: | DNA (5'-D(*CP*GP*CP*GP*AP*TP*TP*TP*CP*GP*CP*G)-3'), MERCURY (II) ION | Authors: | Kondo, J, Yamada, T, Hirose, C, Okamoto, I, Tanaka, Y, Ono, A. | Deposit date: | 2013-06-04 | Release date: | 2014-03-05 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.7 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
|
|