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2ZJ9
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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, SODIUM ION, ISOPROPYL ALCOHOL
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:2011-07-13
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
1WUO
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CRYSTAL STRUCTURE OF METALLO-BETA-LACTAMASE IMP-1 MUTANT (D81A)
Descriptor:Beta-lactamase IMP-1, ZINC ION, ACETIC ACID
Authors:Yamaguchi, Y., Yamagata, Y., Goto, M.
Deposit date:2004-12-08
Release date:2005-03-29
Last modified:2014-11-12
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
1WUP
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CRYSTAL STRUCTURE OF METALLO-BETA-LACTAMASE IMP-1 MUTANT (D81E)
Descriptor:Beta-lactamase IMP-1, ZINC ION, ACETIC ACID
Authors:Yamaguchi, Y., Yamagata, Y., Goto, M.
Deposit date:2004-12-08
Release date:2005-03-29
Last modified:2017-10-11
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
2YZ3
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CRYSTALLOGRAPHIC INVESTIGATION OF INHIBITION MODE OF THE VIM-2 METALLO-BETA-LACTAMASE FROM PSEUDOMONAS AERUGINOSA WITH MERCAPTOCARBOXYLATE INHIBITOR
Descriptor:Metallo-beta-lactamase, ZINC ION, SULFATE ION, ...
Authors:Yamaguchi, Y., Yamagata, Y., Arakawa, Y., Kurosaki, H.
Deposit date:2007-05-02
Release date:2008-03-11
Last modified:2011-07-13
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
3L6N
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CRYSTAL STRUCTURE OF METALLO-BETA-LACTAMASE IND-7
Descriptor:metallo-beta-lactamase, ZINC ION, SULFATE ION
Authors:Yamaguchi, Y., Kurosaki, H., Yamagata, Y.
Deposit date:2009-12-23
Release date:2010-04-14
Last modified:2014-02-12
Method:X-RAY DIFFRACTION (1.65 Å)
Cite:Structure of metallo-beta-lactamase IND-7 from a Chryseobacterium indologenes clinical isolate at 1.65-A resolution
J.Biochem., 147, 2010
4UBQ
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CRYSTAL STRUCTURE OF IMP-2 METALLO-BETA-LACTAMASE FROM ACINETOBACTER SPP.
Descriptor:Beta-lactamase, ZINC ION, ACETATE 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:2015-05-06
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
2E1Q
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CRYSTAL STRUCTURE OF HUMAN XANTHINE OXIDOREDUCTASE MUTANT, GLU803VAL
Descriptor:Xanthine dehydrogenase/oxidase, 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:2011-07-13
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
3AVE
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CRYSTAL STRUCTURE OF THE FUCOSYLATED FC FRAGMENT FROM HUMAN IMMUNOGLOBULIN G1
Descriptor:Ig gamma-1 chain C region, N-ACETYL-D-GLUCOSAMINE, BETA-D-MANNOSE, ...
Authors:Matsumiya, S., Yamaguchi, Y., Saito, J., Nagano, M., Sasakawa, H., Otaki, S., Satoh, M., Shitara, K., Kato, K.
Deposit date:2011-03-04
Release date:2011-04-06
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (2 Å)
Cite:Corrigendum to "Structural Comparison of Fucosylated and Nonfucosylated Fc Fragments of Human Immunoglobulin G1" [J. Mol. Biol. 386/3 (2007) 767-779]
J.Mol.Biol., 408, 2011
1VGN
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STRUCTURE-BASED DESIGN OF THE IRREVERSIBLE INHIBITORS TO METALLO--LACTAMASE (IMP-1)
Descriptor:Beta-lactamase IMP-1, ZINC ION, 3-OXO-3-[(3-OXOPROPYL)SULFANYL]PROPANE-1-THIOLATE, ...
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:2011-07-13
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
2DOO
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THE STRUCTURE OF IMP-1 COMPLEXED WITH THE DETECTING REAGENT (DANSYLC4SH) BY A FLUORESCENT PROBE
Descriptor:BETA-LACTAMASE IMP-1, ZINC ION, N-[4-({[5-(DIMETHYLAMINO)-1-NAPHTHYL]SULFONYL}AMINO)BUTYL]-3-SULFANYLPROPANAMIDE
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:2011-07-13
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
5ZIB
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CRYSTAL STRUCTURE OF HUMAN GNT-V LUMINAL DOMAIN IN APO FORM
Descriptor:Alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase A, N-ACETYL-D-GLUCOSAMINE
Authors:Nagae, M., Yamaguchi, Y.
Deposit date:2018-03-14
Release date:2018-08-01
Last modified:2018-09-05
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:Structure and mechanism of cancer-associated N-acetylglucosaminyltransferase-V.
Nat Commun, 9, 2018
5ZIC
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CRYSTAL STRUCTURE OF HUMAN GNT-V LUMINAL DOMAIN IN COMPLEX WITH ACCEPTOR SUGAR
Descriptor:Alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase A, BETA-D-MANNOSE, 6-thio-alpha-D-mannopyranose, ...
Authors:Nagae, M., Yamaguchi, Y.
Deposit date:2018-03-14
Release date:2018-08-01
Last modified:2018-09-05
Method:X-RAY DIFFRACTION (2.1 Å)
Cite:Structure and mechanism of cancer-associated N-acetylglucosaminyltransferase-V.
Nat Commun, 9, 2018
1IYF
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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:2011-07-13
Method:SOLUTION NMR
Cite:Parkin binds the Rpn10 subunit of 26S proteasomes through its ubiquitin-like domain
EMBO REP., 4, 2003
1UMH
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STRUCTURAL BASIS OF SUGAR-RECOGNIZING UBIQUITIN LIGASE
Descriptor:F-box only protein 2, NICKEL (II) ION
Authors:Mizushima, T., Hirao, T., Yoshida, Y., Lee, S.J., Chiba, T., Iwai, K., Yamaguchi, Y., Kato, K., Tsukihara, T., Tanaka, K., RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Deposit date:2003-10-01
Release date:2004-04-06
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (2 Å)
Cite:Structural basis of sugar-recognizing ubiquitin ligase
NAT.STRUCT.MOL.BIOL., 11, 2004
1UMI
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STRUCTURAL BASIS OF SUGAR-RECOGNIZING UBIQUITIN LIGASE
Descriptor:F-box only protein 2, 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE, N-ACETYL-D-GLUCOSAMINE
Authors:Mizushima, T., Hirao, T., Yoshida, Y., Lee, S.J., Chiba, T., Iwai, K., Yamaguchi, Y., Kato, K., Tsukihara, T., Tanaka, K.
Deposit date:2003-10-01
Release date:2004-04-06
Last modified:2019-11-06
Method:X-RAY DIFFRACTION (2.4 Å)
Cite:Structural basis of sugar-recognizing ubiquitin ligase.
Nat.Struct.Mol.Biol., 11, 2004
1WR6
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CRYSTAL STRUCTURE OF GGA3 GAT DOMAIN IN COMPLEX WITH UBIQUITIN
Descriptor:ADP-ribosylation factor binding protein GGA3, ubiquitin
Authors:Kawasaki, M., Shiba, T., Shiba, Y., Yamaguchi, Y., Matsugaki, N., Igarashi, N., Suzuki, M., Kato, R., Kato, K., Nakayama, K., Wakatsuki, S.
Deposit date:2004-10-12
Release date:2005-06-28
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (2.6 Å)
Cite:Molecular mechanism of ubiquitin recognition by GGA3 GAT domain.
Genes Cells, 10, 2005
1WRD
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CRYSTAL STRUCTURE OF TOM1 GAT DOMAIN IN COMPLEX WITH UBIQUITIN
Descriptor:Target of Myb protein 1, Ubiquitin
Authors:Akutsu, M., Kawasaki, M., Katoh, Y., Shiba, T., Yamaguchi, Y., Kato, R., Kato, K., Nakayama, K., Wakatsuki, S.
Deposit date:2004-10-14
Release date:2005-10-11
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (1.75 Å)
Cite:Structural basis for recognition of ubiquitinated cargo by Tom1-GAT domain.
Febs Lett., 579, 2005
1WZ1
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CRYSTAL STRUCTURE OF THE FV FRAGMENT COMPLEXED WITH DANSYL-LYSINE
Descriptor:Ig light chain, Ig heavy chain, N~6~-{[5-(DIMETHYLAMINO)-1-NAPHTHYL]SULFONYL}-L-LYSINE
Authors:Nakasako, M., Oka, T., Mashumo, M., Takahashi, H., Shimada, I., Yamaguchi, Y., Kato, K., Arata, Y.
Deposit date:2005-02-21
Release date:2006-01-31
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (1.85 Å)
Cite:Conformational dynamics of complementarity-determining region H3 of an anti-dansyl Fv fragment in the presence of its hapten
J.Mol.Biol., 351, 2005
3AIH
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HUMAN OS-9 MRH DOMAIN COMPLEXED WITH ALPHA3,ALPHA6-MAN5
Descriptor:Protein OS-9, BETA-D-MANNOSE, ALPHA-D-MANNOSE
Authors:Satoh, T., Chen, Y., Hu, D., Hanashima, S., Yamamoto, K., Yamaguchi, Y.
Deposit date:2010-05-14
Release date:2010-12-22
Last modified:2014-12-17
Method:X-RAY DIFFRACTION (2.1 Å)
Cite:Structural Basis for Oligosaccharide Recognition of Misfolded Glycoproteins by OS-9 in ER-Associated Degradation
Mol.Cell, 40, 2010
3APA
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CRYSTAL STRUCTURE OF HUMAN PANCREATIC SECRETORY PROTEIN ZG16P
Descriptor:Zymogen granule membrane protein 16, GLYCEROL, CHLORIDE ION
Authors:Kanagawa, M., Satoh, T., Nakano, Y., Kojima-Aikawa, K., Yamaguchi, Y.
Deposit date:2010-10-13
Release date:2010-12-08
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (1.65 Å)
Cite:Crystal structures of human secretory proteins ZG16p and ZG16b reveal a Jacalin-related beta-prism fold
Biochem.Biophys.Res.Commun., 2010
3AQG
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CRYSTAL STRUCTURE OF HUMAN PANCREATIC SECRETORY PROTEIN ZG16B
Descriptor:Zymogen granule protein 16 homolog B, PHOSPHATE ION
Authors:Kanagawa, M., Satoh, T., Nakano, Y., Kojima-Aikawa, K., Yamaguchi, Y.
Deposit date:2010-11-01
Release date:2010-12-08
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (2.75 Å)
Cite:Crystal structures of human secretory proteins ZG16p and ZG16b reveal a Jacalin-related beta-prism fold
Biochem.Biophys.Res.Commun., 2010
3AQX
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CRYSTAL STRUCTURE OF BOMBYX MORI BETA-GRP/GNBP3 N-TERMINAL DOMAIN WITH LAMINARIHEXAOSES
Descriptor:Beta-1,3-glucan-binding protein, BETA-D-GLUCOSE, GLYCEROL
Authors:Kanagawa, M., Satoh, T., Ikeda, A., Adachi, Y., Ohno, N., Yamaguchi, Y.
Deposit date:2010-11-22
Release date:2011-06-22
Last modified:2013-06-19
Method:X-RAY DIFFRACTION (2.05 Å)
Cite:Structural insights into recognition of triple-helical beta-glucans by an insect fungal receptor
J.Biol.Chem., 286, 2011
3AQY
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CRYSTAL STRUCTURE OF PLODIA INTERPUNCTELLA BETA-GRP/GNBP3 N-TERMINAL DOMAIN
Descriptor:Beta-1,3-glucan-binding protein
Authors:Kanagawa, M., Satoh, T., Ikeda, A., Adachi, Y., Ohno, N., Yamaguchi, Y.
Deposit date:2010-11-22
Release date:2011-06-22
Last modified:2013-06-19
Method:X-RAY DIFFRACTION (1.58 Å)
Cite:Structural insights into recognition of triple-helical beta-glucans by an insect fungal receptor
J.Biol.Chem., 286, 2011
3AQZ
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CRYSTAL STRUCTURE OF PLODIA INTERPUNCTELLA BETA-GRP/GNBP3 N-TERMINAL DOMAIN WITH LAMINARIHEXAOSES
Descriptor:Beta-1,3-glucan-binding protein, BETA-D-GLUCOSE
Authors:Kanagawa, M., Satoh, T., Ikeda, A., Adachi, Y., Ohno, N., Yamaguchi, Y.
Deposit date:2010-11-22
Release date:2011-06-22
Last modified:2013-06-19
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:Structural insights into recognition of triple-helical beta-glucans by an insect fungal receptor
J.Biol.Chem., 286, 2011
3VPE
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CRYSTAL STRUCTURE OF METALLO-BETA-LACTAMASE SMB-1
Descriptor:Metallo-beta-lactamase, ZINC ION, SULFATE ION, ...
Authors:Wachino, J., Yamaguchi, Y., Mori, S., Arakawa, Y., Shibayama, K.
Deposit date:2012-02-29
Release date:2013-02-13
Method:X-RAY DIFFRACTION (1.6 Å)
Cite:Structural Insights into the Subclass B3 Metallo-beta-Lactamase SMB-1 and the Mode of Inhibition by the Common Metallo- -Lactamase Inhibitor Mercaptoacetate
Antimicrob.Agents Chemother., 57, 2013