Author results

1VBG
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PYRUVATE PHOSPHATE DIKINASE FROM MAIZE
Descriptor:pyruvate,orthophosphate dikinase, MAGNESIUM ION, SULFATE ION
Authors:Nakanishi, T., Nakatsu, T., Matsuoka, M., Sakata, K., Kato, H., RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Deposit date:2004-02-26
Release date:2005-03-08
Last modified:2017-10-04
Method:X-RAY DIFFRACTION (2.3 Å)
Cite:Crystal structures of pyruvate phosphate dikinase from maize revealed an alternative conformation in the swiveling-domain motion
Biochemistry, 44, 2005
1VBH
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PYRUVATE PHOSPHATE DIKINASE WITH BOUND MG-PEP FROM MAIZE
Descriptor:pyruvate,orthophosphate dikinase, MAGNESIUM ION, SULFATE ION, ...
Authors:Nakanishi, T., Nakatsu, T., Matsuoka, M., Sakata, K., Kato, H., RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Deposit date:2004-02-26
Release date:2005-03-08
Last modified:2017-10-04
Method:X-RAY DIFFRACTION (2.3 Å)
Cite:Crystal structures of pyruvate phosphate dikinase from maize revealed an alternative conformation in the swiveling-domain motion
Biochemistry, 44, 2005
1WFZ
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SOLUTION STRUCTURE OF IRON-SULFUR CLUSTER PROTEIN U (ISCU)
Descriptor:nitrogen fixation cluster-like, ZINC ION
Authors:Nakanishi, T., Tomizawa, T., Koshiba, S., Inoue, M., Kigawa, T., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Deposit date:2004-05-27
Release date:2004-11-27
Last modified:2011-07-13
Method:SOLUTION NMR
Cite:Solution structure of Iron-sulfur cluster protein U (IscU)
To be Published
1V61
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SOLUTION STRUCTURE OF THE PLECKSTRIN HOMOLOGY DOMAIN OF ALPHA-PIX
Descriptor:Rac/Cdc42 guanine nucleotide exchange factor (GEF) 6
Authors:Nakanishi, T., Koshiba, S., Inoue, M., Kigawa, T., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Deposit date:2003-11-26
Release date:2004-05-26
Last modified:2011-07-13
Method:SOLUTION NMR
Cite:Solution Structure of the Pleckstrin Homology Domain of alpha-Pix
To be Published
1WFY
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SOLUTION STRUCTURE OF THE RAS-BINDING DOMAIN OF MOUSE RGS14
Descriptor:regulator of G-protein signaling 14; rap1/rap2 interacting protein
Authors:Nakanishi, T., Tochio, N., Koshiba, S., Inoue, M., Kigawa, T., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Deposit date:2004-05-27
Release date:2004-11-27
Last modified:2011-07-13
Method:SOLUTION NMR
Cite:Solution structure of the Ras-binding domain of mouse RGS14
To be Published
1WGD
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SOLUTION STRUCTURE OF THE UBL-DOMAIN OF HERP
Descriptor:Homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain member 1 protein
Authors:Nakanishi, T., Koshiba, S., Inoue, M., Kigawa, T., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Deposit date:2004-05-28
Release date:2004-11-28
Last modified:2011-07-13
Method:SOLUTION NMR
Cite:Solution structure of the Ubl-domain of Herp
To be Published
1WGE
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SOLUTION STRUCTURE OF THE MOUSE DESR1
Descriptor:Hypothetical protein 2610018L09Rik, ZINC ION
Authors:Nakanishi, T., Tochio, N., Koshiba, S., Inoue, M., Kigawa, T., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Deposit date:2004-05-28
Release date:2005-08-23
Last modified:2011-07-13
Method:SOLUTION NMR
Cite:Solution structure of the mouse DESR1
To be Published
1WH0
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SOLUTION STRUCTURE OF THE CS DOMAIN OF HUMAN USP19
Descriptor:Ubiquitin carboxyl-terminal hydrolase 19
Authors:Nakanishi, T., Tochio, N., Koshiba, S., Inoue, M., Kigawa, T., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Deposit date:2004-05-28
Release date:2004-11-28
Last modified:2011-07-13
Method:SOLUTION NMR
Cite:Solution structure of the CS domain of human USP19
To be Published
1WHD
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SOLUTION STRUCTURE OF THE PDZ DOMAIN OF RGS3
Descriptor:regulator of G-protein signaling 3
Authors:Nakanishi, T., Nemoto, N., Koshiba, S., Inoue, M., Kigawa, T., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Deposit date:2004-05-28
Release date:2004-11-28
Last modified:2011-07-13
Method:SOLUTION NMR
Cite:Solution structure of the PDZ domain of RGS3
To be Published
2EIZ
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CRYSTAL STRUCTURE OF HUMANIZED HYHEL-10 FV MUTANT(HW47Y)-HEN LYSOZYME COMPLEX
Descriptor:ANTI-LYSOZYME ANTIBODY FV REGION, Lysozyme C
Authors:Nakanishi, T., Tsumoto, K., Yokota, A., Kondo, H., Kumagai, I.
Deposit date:2007-03-14
Release date:2008-03-18
Last modified:2014-02-26
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:Critical contribution of VH-VL interaction to reshaping of an antibody: the case of humanization of anti-lysozyme antibody, HyHEL-10
Protein Sci., 17, 2008
2EKS
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CRYSTAL STRUCTURE OF HUMANIZED HYHEL-10 FV-HEN LYSOZYME COMPLEX
Descriptor:ANTI-LYSOZYME ANTIBODY FV REGION, Lysozyme C
Authors:Nakanishi, T., Tsumoto, K., Yokota, A., Kondo, H., Kumagai, I.
Deposit date:2007-03-24
Release date:2008-03-25
Last modified:2017-10-25
Method:X-RAY DIFFRACTION (2 Å)
Cite:Critical contribution of VH-VL interaction to reshaping of an antibody: the case of humanization of anti-lysozyme antibody, HyHEL-10
Protein Sci., 17, 2008
2YSS
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CRYSTAL STRUCTURE OF HUMANIZED HYHEL-10 FV MUTANT(HQ39KW47Y)-HEN LYSOZYME COMPLEX
Descriptor:ANTI-LYSOZYME ANTIBODY FV REGION, Lysozyme C
Authors:Nakanishi, T., Tsumoto, K., Yokota, A., Kondo, H., Kumagai, I.
Deposit date:2007-04-03
Release date:2008-04-08
Last modified:2017-10-25
Method:X-RAY DIFFRACTION (2.4 Å)
Cite:Critical contribution of VH-VL interaction to reshaping of an antibody: the case of humanization of anti-lysozyme antibody, HyHEL-10
Protein Sci., 17, 2008
5AYU
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CRYSTAL STRUCTURE OF HYHEL-10 FV
Descriptor:lysozyme binding Ig kappa chain V23-J2 region, Ig VH,anti-lysozyme, GLYCEROL
Authors:Nakanishi, T., Tsumoto, K., Yokota, A., Kondo, H., Kumagai, I.
Deposit date:2015-09-04
Release date:2016-09-07
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Crystal structure of HyHEL-10 Fv
To Be Published
3VVK
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AN M-LIKE REACTION STATE OF THE AZIDE-BOUND PURPLE FORM OF PHARAONIS HALORHODOPSIN
Descriptor:Halorhodopsin, RETINAL, B-NONYLGLUCOSIDE, ...
Authors:Kouyama, T., Nakanishi, T.
Deposit date:2012-07-26
Release date:2013-06-19
Method:X-RAY DIFFRACTION (2.3 Å)
Cite:Large deformation of helix F during the photoreaction cycle of Pharaonis halorhodopsin in complex with azide
Biophys.J., 104, 2013
2Z4Q
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CRYSTAL STRUCTURE OF A MURINE ANTIBODY FAB 528
Descriptor:anti egfr antibody fab, light chain, heavy chain, ...
Authors:Nakanishi, T., Tsumoto, K., Asano, R., Kondo, H., Kumagai, I.
Deposit date:2007-06-22
Release date:2007-10-30
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (2.3 Å)
Cite:Thermodynamic consequences of mutations in vernier zone residues of a humanized anti-human epidermal growth factor receptor murine antibody, 528
J.Biol.Chem., 283, 2008
3A6Q
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E13T MUTANT OF FMN-BINDING PROTEIN FROM DESULFOVIBRIO VULGARIS (MIYAZAKI F)
Descriptor:FMN-binding protein, FLAVIN MONONUCLEOTIDE, CHLORIDE ION
Authors:Nakanishi, T., Haruyama, Y., Inoue, H., Kitamura, M.
Deposit date:2009-09-08
Release date:2010-09-01
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (1.4 Å)
Cite:Effects of the disappearance of one charge on ultrafast fluorescence dynamics of the FMN binding protein.
J.Phys.Chem.B, 114, 2010
3A6R
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E13Q MUTANT OF FMN-BINDING PROTEIN FROM DESULFOVIBRIO VULGARIS (MIYAZAKI F)
Descriptor:FMN-binding protein, FLAVIN MONONUCLEOTIDE, CHLORIDE ION
Authors:Nakanishi, T., Haruyama, Y., Inoue, H., Kitamura, M.
Deposit date:2009-09-08
Release date:2010-09-01
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (1.2 Å)
Cite:Effects of the disappearance of one charge on ultrafast fluorescence dynamics of the FMN binding protein.
J.Phys.Chem.B, 114, 2010
1WJI
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SOLUTION STRUCTURE OF THE UBA DOMAIN OF HUMAN TUDOR DOMAIN CONTAINING PROTEIN 3
Descriptor:Tudor domain containing protein 3
Authors:Kamatari, Y.O., Tochio, N., Nakanishi, T., Miyamoto, K., Li, H., Kobayashi, N., Tomizawa, T., Koshiba, S., Inoue, M., Kigawa, T., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Deposit date:2004-05-29
Release date:2004-11-29
Last modified:2011-07-13
Method:SOLUTION NMR
Cite:Solution Structure of the UBA Domain of Human Tudor Domain Containing Protein 3
To be Published
3WJ4
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CRYSTAL STRUCTURE OF PPARGAMMA LIGAND BINDING DOMAIN IN COMPLEX WITH TRIBUTYLTIN
Descriptor:Peroxisome proliferator-activated receptor gamma, tributylstannanyl
Authors:Harada, S., Hiromori, Y., Fukakusa, S., Kawahara, K., Nakamura, S., Noda, M., Uchiyama, S., Fukui, K., Nishikawa, J., Nagase, H., Kobayashi, Y., Ohkubo, T., Yoshida, T., Nakanishi, T.
Deposit date:2013-10-04
Release date:2014-10-15
Method:X-RAY DIFFRACTION (1.95 Å)
Cite:Structural basis for PPARgamma transactivation by endocrine disrupting organotin compounds
To be Published
3WJ5
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CRYSTAL STRUCTURE OF PPARGAMMA LIGAND BINDING DOMAIN IN COMPLEX WITH TRIPHENYLTIN
Descriptor:Peroxisome proliferator-activated receptor gamma, triphenylstannanyl
Authors:Harada, S., Hiromori, Y., Fukakusa, S., Kawahara, K., Nakamura, S., Noda, M., Uchiyama, S., Fukui, K., Nishikawa, J., Nagase, H., Kobayashi, Y., Ohkubo, T., Yoshida, T., Nakanishi, T.
Deposit date:2013-10-04
Release date:2014-10-15
Last modified:2019-06-12
Method:X-RAY DIFFRACTION (1.89 Å)
Cite:Structural basis for PPARgamma transactivation by endocrine disrupting organotin compounds
To be Published
2RQG
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STRUCTURE OF GSPT1/ERF3A-PABC
Descriptor:G1 to S phase transition 1, Polyadenylate-binding protein 1
Authors:Osawa, M., Nakanishi, T., Hosoda, N., Uchida, S., Hoshino, T., Katada, I., Shimada, I.
Deposit date:2009-05-08
Release date:2010-05-26
Last modified:2011-07-13
Method:SOLUTION NMR
Cite:Eukaryotic Translation Termination Factor Gspt/Erf3 Recognizes Pabp with Chemical Exchange Using Two Overlapping Motifs
To be Published
2RQH
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STRUCTURE OF GSPT1/ERF3A-PABC
Descriptor:G1 to S phase transition 1, Polyadenylate-binding protein 1
Authors:Osawa, M., Nakanishi, T., Hosoda, N., Uchida, S., Hoshino, T., Katada, I., Shimada, I.
Deposit date:2009-05-08
Release date:2010-05-26
Last modified:2011-07-13
Method:SOLUTION NMR
Cite:Eukaryotic Translation Termination Factor Gspt/Erf3 Recognizes Pabp with Chemical Exchange Using Two Overlapping Motifs
To be Published
5XEC
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HETERODIMER CONSTRUCTED FROM PA CYT C551-HT CYT C552 AND HT CYT C552-PA CYT C551 CHIMERIC PROTEINS
Descriptor:Cytochrome c-552,Cytochrome c-551, Cytochrome c-551,Cytochrome c-552, HEME C
Authors:Zhang, M., Nakanishi, T., Yamanaka, M., Nagao, S., Yanagisawa, S., Shomura, Y., Shibata, N., Ogura, T., Higuchi, Y., Hirota, S.
Deposit date:2017-04-04
Release date:2017-08-09
Last modified:2017-12-06
Method:X-RAY DIFFRACTION (1.1 Å)
Cite:Rational Design of Domain-Swapping-Based c-Type Cytochrome Heterodimers by Using Chimeric Proteins.
Chembiochem, 18, 2017
5XED
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HETERODIMER CONSTRUCTED FROM M61A PA CYT C551-HT CYT C552 AND HT CYT C552-PA CYT C551 CHIMERIC PROTEINS
Descriptor:Cytochrome c-551,Cytochrome c-552, Cytochrome c-552,Cytochrome c-551, HEME C
Authors:Zhang, M., Nakanishi, T., Yamanaka, M., Nagao, S., Yanagisawa, S., Shomura, Y., Shibata, N., Ogura, T., Higuchi, Y., Hirota, S.
Deposit date:2017-04-04
Release date:2017-08-09
Last modified:2017-12-06
Method:X-RAY DIFFRACTION (1.55 Å)
Cite:Rational Design of Domain-Swapping-Based c-Type Cytochrome Heterodimers by Using Chimeric Proteins.
Chembiochem, 18, 2017
3A67
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CRYSTAL STRUCTURE OF HYHEL-10 FV MUTANT LN31D COMPLEXED WITH HEN EGG WHITE LYSOZYME
Descriptor:Lysozyme binding ig kappa chain V23-J2 region, IG VH, anti-lysozyme, ...
Authors:Yokota, A., Tsumoto, K., Shiroishi, M., Nakanishi, T., Kondo, H., Kumagai, I.
Deposit date:2009-08-24
Release date:2009-12-22
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Contribution of asparagine residues to the stabilization of a proteinaceous antigen-antibody complex, HyHEL-10-hen egg white lysozyme
J.Biol.Chem., 285, 2010
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