4UBQ
| Crystal Structure of IMP-2 Metallo-beta-Lactamase from Acinetobacter spp. | Descriptor: | ACETATE ION, Beta-lactamase, ZINC ION | Authors: | Yamaguchi, Y, Matsueda, S, Matsunaga, K, Takashio, N, Toma-Fukai, S, Yamagata, Y, Shibata, N, Wachino, J, Shibayama, K, Arakawa, Y, Kurosaki, H. | Deposit date: | 2014-08-13 | Release date: | 2014-12-24 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.3 Å) | Cite: | Crystal structure of IMP-2 metallo-beta-lactamase from Acinetobacter spp.: comparison of active-site loop structures between IMP-1 and IMP-2. Biol.Pharm.Bull., 38, 2015
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3L6N
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7WZU
| Crystal structure of metallo-beta-lactamase IMP-6. | Descriptor: | Beta-lactamase, ZINC ION | Authors: | Yamaguchi, Y, Kurosaki, H. | Deposit date: | 2022-02-19 | Release date: | 2023-01-04 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (1.954 Å) | Cite: | Difference in the Inhibitory Effect of Thiol Compounds and Demetallation Rates from the Zn(II) Active Site of Metallo-beta-lactamases (IMP-1 and IMP-6) Associated with a Single Amino Acid Substitution. Acs Infect Dis., 9, 2023
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7DTM
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7DTN
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1WUP
| Crystal structure of metallo-beta-lactamase IMP-1 mutant (D81E) | Descriptor: | ACETIC ACID, Beta-lactamase IMP-1, ZINC ION | Authors: | Yamaguchi, Y, Yamagata, Y, Goto, M. | Deposit date: | 2004-12-08 | Release date: | 2005-03-29 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (3 Å) | Cite: | Probing the role of Asp-120(81) of metallo-beta-lactamase (IMP-1) by site-directed mutagenesis, kinetic studies, and X-ray crystallography. J.Biol.Chem., 280, 2005
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1WUO
| Crystal structure of metallo-beta-lactamase IMP-1 mutant (D81A) | Descriptor: | ACETIC ACID, Beta-lactamase IMP-1, ZINC ION | Authors: | Yamaguchi, Y, Yamagata, Y, Goto, M. | Deposit date: | 2004-12-08 | Release date: | 2005-03-29 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (2.01 Å) | Cite: | Probing the role of Asp-120(81) of metallo-beta-lactamase (IMP-1) by site-directed mutagenesis, kinetic studies, and X-ray crystallography. J.Biol.Chem., 280, 2005
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2ZJ9
| X-ray crystal structure of AmpC beta-Lactamase (AmpC(D)) from an Escherichia coli with a Tripeptide Deletion (Gly286 Ser287 Asp288) on the H10 Helix | Descriptor: | AmpC, ISOPROPYL ALCOHOL, SODIUM ION | Authors: | Yamaguchi, Y, Sato, G, Yamagata, Y, Wachino, J, Arakawa, Y, Kurosaki, H. | Deposit date: | 2008-02-29 | Release date: | 2009-03-10 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (1.7 Å) | Cite: | Structure of AmpC beta-lactamase (AmpCD) from an Escherichia coli clinical isolate with a tripeptide deletion (Gly286-Ser287-Asp288) in the H10 helix Acta Crystallogr.,Sect.F, 65, 2009
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2YZ3
| Crystallographic Investigation of Inhibition Mode of the VIM-2 Metallo-beta-lactamase from Pseudomonas aeruginosa with Mercaptocarboxylate Inhibitor | Descriptor: | (S)-2-(MERCAPTOMETHYL)-5-PHENYLPENTANOIC ACID, Metallo-beta-lactamase, SULFATE ION, ... | Authors: | Yamaguchi, Y, Yamagata, Y, Arakawa, Y, Kurosaki, H. | Deposit date: | 2007-05-02 | Release date: | 2008-03-11 | Last modified: | 2024-03-13 | Method: | X-RAY DIFFRACTION (2.3 Å) | Cite: | Crystallographic investigation of the inhibition mode of a VIM-2 metallo-beta-lactamase from Pseudomonas aeruginosa by a mercaptocarboxylate inhibitor. J.Med.Chem., 50, 2007
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2E1Q
| Crystal Structure of Human Xanthine Oxidoreductase mutant, Glu803Val | Descriptor: | 2-HYDROXYBENZOIC ACID, BICARBONATE ION, CALCIUM ION, ... | Authors: | Yamaguchi, Y, Matsumura, T, Ichida, K, Okamoto, K, Nishino, T. | Deposit date: | 2006-10-27 | Release date: | 2007-09-18 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (2.6 Å) | Cite: | Human xanthine oxidase changes its substrate specificity to aldehyde oxidase type upon mutation of amino acid residues in the active site: roles of active site residues in binding and activation of purine substrate J.Biochem.(Tokyo), 141, 2007
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2RQY
| Solution structure and dynamics of mouse ARMET | Descriptor: | Putative uncharacterized protein | Authors: | Hoseki, J, Sasakawa, H, Yamaguchi, Y, Maeda, M, Kubota, H, Kato, K, Nagata, K. | Deposit date: | 2010-01-26 | Release date: | 2010-04-21 | Last modified: | 2022-03-16 | Method: | SOLUTION NMR | Cite: | Solution structure and dynamics of mouse ARMET. Febs Lett., 584, 2010
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2KP2
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2KP1
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5GU5
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1IYF
| Solution structure of ubiquitin-like domain of human parkin | Descriptor: | parkin | Authors: | Sakata, E, Yamaguchi, Y, Kurimoto, E, Kikuchi, J, Yokoyama, S, Kawahara, H, Yokosawa, H, Hattori, N, Mizuno, Y, Tanaka, K, Kato, K, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2002-08-13 | Release date: | 2003-03-25 | Last modified: | 2023-12-27 | Method: | SOLUTION NMR | Cite: | Parkin binds the Rpn10 subunit of 26S proteasomes through its ubiquitin-like domain EMBO REP., 4, 2003
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2JZ4
| Putative 32 kDa myrosinase binding protein At3g16450.1 from Arabidopsis thaliana | Descriptor: | Jasmonate inducible protein isolog | Authors: | Takeda, N, Sugimori, N, Torizawa, T, Terauchi, T, Ono, A.M, Yagi, H, Yamaguchi, Y, Kato, K, Ikeya, T, Guntert, P, Aceti, D.J, Markley, J.L, Kainosho, M, Center for Eukaryotic Structural Genomics (CESG) | Deposit date: | 2007-12-28 | Release date: | 2008-02-19 | Last modified: | 2023-06-14 | Method: | SOLUTION NMR | Cite: | Structure of the putative 32 kDa myrosinase-binding protein from Arabidopsis (At3g16450.1) determined by SAIL-NMR. Febs J., 275, 2008
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5GZ9
| Crystal structure of catalytic domain of Protein O-mannosyl Kinase in complexes with AMP-PNP, Magnesium ions and glycopeptide | Descriptor: | MAGNESIUM ION, PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER, Protein O-mannose kinase, ... | Authors: | Nagae, M, Yamaguchi, Y. | Deposit date: | 2016-09-27 | Release date: | 2017-03-29 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.4 Å) | Cite: | 3D structural analysis of protein O-mannosyl kinase, POMK, a causative gene product of dystroglycanopathy. Genes Cells, 22, 2017
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5GZ8
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1VGN
| Structure-based design of the irreversible inhibitors to metallo--lactamase (IMP-1) | Descriptor: | 3-OXO-3-[(3-OXOPROPYL)SULFANYL]PROPANE-1-THIOLATE, ACETIC ACID, Beta-lactamase IMP-1, ... | Authors: | Kurosaki, H, Yamaguchi, Y, Higashi, T, Soga, K, Matsueda, S, Misumi, S, Yamagata, Y, Arakawa, Y, Goto, M. | Deposit date: | 2004-04-27 | Release date: | 2005-06-21 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (2.63 Å) | Cite: | Irreversible Inhibition of Metallo-beta-lactamase (IMP-1) by 3-(3-Mercaptopropionylsulfanyl)propionic Acid Pentafluorophenyl Ester Angew.Chem.Int.Ed.Engl., 44, 2005
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7DCZ
| Crystal Structure of BACE1 in complex with N-{3-[(4S)-2-amino-4-methyl-4H-1,3-thiazin-4-yl]-4- fluorophenyl}-5-cyanopyridine-2-carboxamide | Descriptor: | Beta-secretase 1, GLYCEROL, IODIDE ION, ... | Authors: | Koriyama, Y, Hori, A, Ito, H, Yonezawa, S, Baba, Y, Tanimoto, N, Ueno, T, Yamamoto, S, Yamamoto, T, Asada, N, Morimoto, K, Einaru, S, Sakai, K, Kanazu, T, Matsuda, A, Yamaguchi, Y, Oguma, T, Timmers, M, Tritsmans, L, Kusakabe, K.I, Kato, A, Sakaguchi, G. | Deposit date: | 2020-10-27 | Release date: | 2021-03-10 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.3 Å) | Cite: | Discovery of Atabecestat (JNJ-54861911): A Thiazine-Based beta-Amyloid Precursor Protein Cleaving Enzyme 1 Inhibitor Advanced to the Phase 2b/3 EARLY Clinical Trial. J.Med.Chem., 64, 2021
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2DOO
| The structure of IMP-1 complexed with the detecting reagent (DansylC4SH) by a fluorescent probe | Descriptor: | BETA-LACTAMASE IMP-1, N-[4-({[5-(DIMETHYLAMINO)-1-NAPHTHYL]SULFONYL}AMINO)BUTYL]-3-SULFANYLPROPANAMIDE, ZINC ION | Authors: | Kurosaki, H, Yamaguchi, Y, Yasuzawa, H, Jin, W, Yamagata, Y, Arakawa, Y. | Deposit date: | 2006-05-01 | Release date: | 2006-11-28 | Last modified: | 2024-03-13 | Method: | X-RAY DIFFRACTION (2.43 Å) | Cite: | Probing, inhibition, and crystallographic characterization of metallo-beta-lactamase (IMP-1) with fluorescent agents containing dansyl and thiol groups Chemmedchem, 1, 2006
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5ZIC
| Crystal structure of human GnT-V luminal domain in complex with acceptor sugar | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-6-thio-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose, Alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase A | Authors: | Nagae, M, Yamaguchi, Y. | Deposit date: | 2018-03-14 | Release date: | 2018-08-01 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2.1 Å) | Cite: | Structure and mechanism of cancer-associated N-acetylglucosaminyltransferase-V. Nat Commun, 9, 2018
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5ZIB
| Crystal structure of human GnT-V luminal domain in apo form | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, Alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase A | Authors: | Nagae, M, Yamaguchi, Y. | Deposit date: | 2018-03-14 | Release date: | 2018-08-01 | Last modified: | 2020-07-29 | Method: | X-RAY DIFFRACTION (1.9 Å) | Cite: | Structure and mechanism of cancer-associated N-acetylglucosaminyltransferase-V. Nat Commun, 9, 2018
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5AV7
| Crystal structure of Calsepa lectin in complex with bisected glycan | Descriptor: | 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, Lectin | Authors: | Nagae, M, Yamaguchi, Y. | Deposit date: | 2015-06-12 | Release date: | 2016-04-27 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.85 Å) | Cite: | Atomic visualization of a flipped-back conformation of bisected glycans bound to specific lectins Sci Rep, 6, 2016
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5AVA
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