Author results

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:2011-07-13
Method:X-RAY DIFFRACTION (2.4 Å)
Cite:Structural basis of sugar-recognizing ubiquitin ligase
NAT.STRUCT.MOL.BIOL., 11, 2004
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
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
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
1WXS
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SOLUTION STRUCTURE OF UFM1, A UBIQUITIN-FOLD MODIFIER
Descriptor:Ubiquitin-fold Modifier 1
Authors:Sasakawa, H., Sakata, E., Yamaguchi, Y., Komatsu, M., Tatsumi, K., Kominami, E., Tanaka, K., Kato, K.
Deposit date:2005-02-01
Release date:2006-04-18
Last modified:2011-07-13
Method:SOLUTION NMR
Cite:Solution structure and dynamics of Ufm1, a ubiquitin-fold modifier 1
Biochem.Biophys.Res.Commun., 343, 2006
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
2D5U
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SOLUTION STRUCTURE OF THE N-TERMINAL PORTION OF THE PUB DOMAIN OF MOUSE PEPTIDE:N-GLYCANASE
Descriptor:N-glycanase 1
Authors:Sasakawa, H., Hirao, T., Yamaguchi, Y., Suzuki, T., Kato, K.
Deposit date:2005-11-06
Release date:2006-11-21
Last modified:2011-07-13
Method:SOLUTION NMR
Cite:Solution structure of the N-terminal portion of the PUB domain of mouse peptide:N-glycanase
To be Published
2DJJ
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SOLUTION STRUCTURE OF THE A' DOMAIN OF THERMOPHILIC FUNGAL PROTEIN DISULFIDE ISOMERASE
Descriptor:Protein disulfide-isomerase
Authors:Kato, K., Yamaguchi, Y.
Deposit date:2006-04-04
Release date:2006-04-25
Last modified:2011-07-13
Method:SOLUTION NMR
Cite:Solution structure of the a' domain of thermophilic fungal protein disulfide isomerase
To be Published
2DJK
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SOLUTION STRUCTURE OF THE B' DOMAIN OF THERMOPHILIC FUNGAL PROTEIN DISULFIDE ISOMERASE
Descriptor:Protein disulfide-isomerase
Authors:Kato, K., Yamaguchi, Y.
Deposit date:2006-04-04
Release date:2006-04-25
Last modified:2011-07-13
Method:SOLUTION NMR
Cite:Solution structure of the b' domain of thermophilic fungal protein disulfide isomerase
To be Published
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
2DOS
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STRUCTURAL BASIS FOR THE RECOGNITION OF LYS48-LINKED POLYUBIQUITIN CHAIN BY THE JOSEPHIN DOMAIN OF ATAXIN-3, A PUTATIVE DEUBIQUITINATING ENZYME
Descriptor:Ataxin-3
Authors:Sumiyoshi, A.
Deposit date:2006-05-03
Release date:2007-05-22
Last modified:2014-12-31
Method:SOLUTION NMR
Cite:Mode of substrate recognition by the Josephin domain of ataxin-3, which has an endo-type deubiquitinase activity.
Febs Lett., 588, 2014
2DPF
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CRYSTAL STRUCTURE OF CURCULIN1 HOMODIMER
Descriptor:Curculin, SULFATE ION
Authors:Kurimoto, E., Suzuki, M., Amemiya, E., Yamaguchi, Y., Nirasawa, S., Shimba, N., Xu, N., Kashiwagi, T., Kawai, M., Suzuki, E., Kato, K.
Deposit date:2006-05-11
Release date:2007-05-15
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (1.5 Å)
Cite:Curculin Exhibits Sweet-tasting and Taste-modifying Activities through Its Distinct Molecular Surfaces.
J.Biol.Chem., 282, 2007
2DTS
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CRYSTAL STRUCTURE OF THE DEFUCOSYLATED 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:2006-07-14
Release date:2007-03-13
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:Structural comparison of fucosylated and nonfucosylated fc fragments of human immunoglobulin g1
J.Mol.Biol., 368, 2007
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
2JZ4
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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:2011-07-13
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
2KP1
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SOLUTION STRUCTURE OF THE A' DOMAIN OF THERMOPHILIC FUNGAL PROTEIN DISULFIDE ISOMERASE
Descriptor:Protein disulfide-isomerase
Authors:Kato, K., Yamaguchi, Y., Serve, O.
Deposit date:2009-10-06
Release date:2009-10-27
Last modified:2011-07-13
Method:SOLUTION NMR
Cite:Redox-Dependent Domain Rearrangement of Protein Disulfide Isomerase Coupled with Exposure of Its Substrate-Binding Hydrophobic Surface
J.Mol.Biol., 2009
2KP2
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SOLUTION STRUCTURE OF THE B' DOMAIN OF THERMOPHILIC FUNGAL PROTEIN DISULFIDE ISOMERASE
Descriptor:Protein disulfide-isomerase
Authors:Kato, K., Yamaguchi, Y., Serve, O.
Deposit date:2009-10-06
Release date:2009-10-27
Last modified:2011-07-13
Method:SOLUTION NMR
Cite:Redox-Dependent Domain Rearrangement of Protein Disulfide Isomerase Coupled with Exposure of Its Substrate-Binding Hydrophobic Surface
J.Mol.Biol., 2009
2RJ2
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CRYSTAL STRUCTURE OF THE SUGAR RECOGNIZING SCF UBIQUITIN LIGASE AT 1.7 RESOLUTION
Descriptor:F-box only protein 2, NICKEL (II) ION, CHLORIDE ION
Authors:Vaijayanthimala, S., Velmurugan, D., Mizushima, T., Yamane, T., Yoshida, Y., Tanaka, K.
Deposit date:2007-10-14
Release date:2008-10-14
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (1.7 Å)
Cite:Crystal Structure of the Sugar Recognizing SCF Ubiquitin Ligase at 1.7 Resolution
To be Published
2RQY
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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:2011-07-13
Method:SOLUTION NMR
Cite:Solution structure and dynamics of mouse ARMET.
Febs Lett., 584, 2010
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
2ZCB
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CRYSTAL STRUCTURE OF UBIQUITIN P37A/P38A
Descriptor:Ubiquitin, ZINC ION
Authors:Kitahara, R., Tanaka, T., Sakata, E., Yamaguchi, Y., Kato, K., Yokoyama, S.
Deposit date:2007-11-08
Release date:2007-11-20
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (1.6 Å)
Cite:Crystal Structure of ubiquitin P37A/P38A
To be published