Author results

1J1O
  • Download 1j1o
  • View 1j1o
Molmil generated image of 1j1o
CRYSTAL STRUCTURE OF HYHEL-10 FV MUTANT LY50F COMPLEXED WITH HEN EGG WHITE LYSOZYME
Descriptor:lysozyme binding Ig kappa chain V23-J2 region, Ig VH,anti-lysozyme, Lysozyme C
Authors:Yokota, A., Tsumoto, K., Shiroishi, M., Kondo, H., Kumagai, I.
Deposit date:2002-12-13
Release date:2003-01-14
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:The Role of Hydrogen Bonding via Interfacial Water Molecules in Antigen-Antibody Complexation. THE HyHEL-10-HEL INTERACTION
J.BIOL.CHEM., 278, 2003
1J1P
  • Download 1j1p
  • View 1j1p
Molmil generated image of 1j1p
CRYSTAL STRUCTURE OF HYHEL-10 FV MUTANT LS91A COMPLEXED WITH HEN EGG WHITE LYSOZYME
Descriptor:lysozyme binding Ig kappa chain V23-J2 region, Ig VH,anti-lysozyme, Lysozyme C
Authors:Yokota, A., Tsumoto, K., Shiroishi, M., Kondo, H., Kumagai, I.
Deposit date:2002-12-13
Release date:2003-01-14
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:The Role of Hydrogen Bonding via Interfacial Water Molecules in Antigen-Antibody Complexation. THE HyHEL-10-HEL INTERACTION
J.BIOL.CHEM., 278, 2003
1J1X
  • Download 1j1x
  • View 1j1x
Molmil generated image of 1j1x
CRYSTAL STRUCTURE OF HYHEL-10 FV MUTANT LS93A COMPLEXED WITH HEN EGG WHITE LYSOZYME
Descriptor:lysozyme binding Ig kappa chain V23-J2 region, Ig VH,anti-lysozyme, Lysozyme C
Authors:Yokota, A., Tsumoto, K., Shiroishi, M., Kondo, H., Kumagai, I.
Deposit date:2002-12-20
Release date:2003-01-14
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:The Role of Hydrogen Bonding via Interfacial Water Molecules in Antigen-Antibody Complexation. THE HyHEL-10-HEL INTERACTION
J.BIOL.CHEM., 278, 2003
3A67
  • Download 3a67
  • View 3a67
Molmil generated image of 3a67
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
3A6B
  • Download 3a6b
  • View 3a6b
Molmil generated image of 3a6b
CRYSTAL STRUCTURE OF HYHEL-10 FV MUTANT LN32D 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:2009-08-28
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
3A6C
  • Download 3a6c
  • View 3a6c
Molmil generated image of 3a6c
CRYSTAL STRUCTURE OF HYHEL-10 FV MUTANT LN92D 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:2009-08-28
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
2E27
  • Download 2e27
  • View 2e27
Molmil generated image of 2e27
CRYSTAL STRUCTURE OF FV FRAGMENT OF ANTI-CIGUATOXIN ANTIBODY COMPLEXED WITH ABC-RING OF CIGUATOXIN
Descriptor:anti-ciguatoxin antibody, light chain, heavy chain, ...
Authors:Yokota, A., Tanaka, Y., Tsumoto, K.
Deposit date:2006-11-08
Release date:2007-11-13
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (1.7 Å)
Cite:Critical contribution of aromatic rings to specific recognition of polyether rings. The case of ciguatoxin CTX3C-ABC and its specific antibody 1C49.
J.Biol.Chem., 283, 2008
3AXK
  • Download 3axk
  • View 3axk
Molmil generated image of 3axk
STRUCTURE OF RICE RUBISCO IN COMPLEX WITH NADP(H)
Descriptor:Ribulose bisphosphate carboxylase large chain, Ribulose bisphosphate carboxylase small chain, chloroplastic, ...
Authors:Matsumura, H., Mizohata, E., Ishida, H., Kogami, A., Ueno, T., Makino, A., Inoue, T., Yokota, A., Mae, T., Kai, Y.
Deposit date:2011-04-11
Release date:2012-04-11
Last modified:2013-06-05
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:Crystal structure of rice Rubisco and implications for activation induced by positive effectors NADPH and 6-phosphogluconate
J.Mol.Biol., 422, 2012
3AXM
  • Download 3axm
  • View 3axm
Molmil generated image of 3axm
STRUCTURE OF RICE RUBISCO IN COMPLEX WITH 6PG
Descriptor:Ribulose bisphosphate carboxylase large chain, Ribulose bisphosphate carboxylase small chain, chloroplastic, ...
Authors:Matsumura, H., Mizohata, E., Ishida, H., Kogami, A., Ueno, T., Makino, A., Inoue, T., Yokota, A., Mae, T., Kai, Y.
Deposit date:2011-04-11
Release date:2012-04-11
Last modified:2013-06-05
Method:X-RAY DIFFRACTION (1.65 Å)
Cite:Crystal structure of rice Rubisco and implications for activation induced by positive effectors NADPH and 6-phosphogluconate
J.Mol.Biol., 422, 2012
1BWV
  • Download 1bwv
  • View 1bwv
Molmil generated image of 1bwv
ACTIVATED RIBULOSE 1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE (RUBISCO) COMPLEXED WITH THE REACTION INTERMEDIATE ANALOGUE 2-CARBOXYARABINITOL 1,5-BISPHOSPHATE
Descriptor:PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE), MAGNESIUM ION, 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE
Authors:Sugawara, H., Yamamoto, H., Shibata, N., Inoue, T., Miyake, C., Yokota, A., Kai, Y.
Deposit date:1998-09-29
Release date:1999-09-27
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (2.4 Å)
Cite:Crystal structure of carboxylase reaction-oriented ribulose 1, 5-bisphosphate carboxylase/oxygenase from a thermophilic red alga, Galdieria partita.
J.Biol.Chem., 274, 1999
1IC4
  • Download 1ic4
  • View 1ic4
Molmil generated image of 1ic4
CRYSTAL STRUCTURE OF HYHEL-10 FV MUTANT(HD32A)-HEN LYSOZYME COMPLEX
Descriptor:LYSOZYME BINDING IG KAPPA CHAIN, IGG1 FAB CHAIN H, LYSOZYME C
Authors:Shiroishi, M., Yokota, A., Tsumoto, K., Kondo, H., Nishimiya, Y., Horii, K., Matsushima, M., Ogasahara, K., Yutani, K., Kumagai, I.
Deposit date:2001-03-30
Release date:2001-07-18
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (2.5 Å)
Cite:Structural evidence for entropic contribution of salt bridge formation to a protein antigen-antibody interaction: the case of hen lysozyme-HyHEL-10 Fv complex.
J.Biol.Chem., 276, 2001
1IC5
  • Download 1ic5
  • View 1ic5
Molmil generated image of 1ic5
CRYSTAL STRUCTURE OF HYHEL-10 FV MUTANT(HD99A)-HEN LYSOZYME COMPLEX
Descriptor:LYSOZYME BINDING IG KAPPA CHAIN, IGG1 FAB CHAIN H, LYSOZYME C
Authors:Shiroishi, M., Yokota, A., Tsumoto, K., Kondo, H., Nishimiya, Y., Horii, K., Matsushima, M., Ogasahara, K., Yutani, K., Kumagai, I.
Deposit date:2001-03-30
Release date:2001-07-18
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (2.3 Å)
Cite:Structural evidence for entropic contribution of salt bridge formation to a protein antigen-antibody interaction: the case of hen lysozyme-HyHEL-10 Fv complex.
J.Biol.Chem., 276, 2001
1IC7
  • Download 1ic7
  • View 1ic7
Molmil generated image of 1ic7
CRYSTAL STRUCTURE OF HYHEL-10 FV MUTANT(HD32A99A)-HEN LYSOZYME COMPLEX
Descriptor:LYSOZYME BINDING IG KAPPA CHAIN, IGG1 FAB CHAIN H, LYSOZYME C
Authors:Shiroishi, M., Yokota, A., Tsumoto, K., Kondo, H., Nishimiya, Y., Horii, K., Matsushima, M., Ogasahara, K., Yutani, K., Kumagai, I.
Deposit date:2001-03-30
Release date:2001-07-18
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (2.1 Å)
Cite:Structural evidence for entropic contribution of salt bridge formation to a protein antigen-antibody interaction: the case of hen lysozyme-HyHEL-10 Fv complex.
J.Biol.Chem., 276, 2001
1IR1
  • Download 1ir1
  • View 1ir1
Molmil generated image of 1ir1
CRYSTAL STRUCTURE OF SPINACH RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE (RUBISCO) COMPLEXED WITH CO2, MG2+ AND 2-CARBOXYARABINITOL-1,5-BISPHOSPHATE
Descriptor:Large subunit of Rubisco, Small subunit of Rubisco, MAGNESIUM ION, ...
Authors:Mizohata, E., Matsumura, H., Okano, Y., Kumei, M., Takuma, H., Onodera, J., Kato, K., Shibata, N., Inoue, T., Yokota, A., Kai, Y.
Deposit date:2001-08-31
Release date:2002-03-13
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Crystal structure of activated ribulose-1,5-bisphosphate carboxylase/oxygenase from green alga Chlamydomonas reinhardtii complexed with 2-carboxyarabinitol-1,5-bisphosphate.
J.Mol.Biol., 316, 2002
1IR2
  • Download 1ir2
  • View 1ir2
Molmil generated image of 1ir2
CRYSTAL STRUCTURE OF ACTIVATED RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE (RUBISCO) FROM GREEN ALGA, CHLAMYDOMONAS REINHARDTII COMPLEXED WITH 2-CARBOXYARABINITOL-1,5-BISPHOSPHATE (2-CABP)
Descriptor:Large subunit of Rubisco, Small subunit of Rubisco, MAGNESIUM ION, ...
Authors:Mizohata, E., Matsumura, H., Okano, Y., Kumei, M., Takuma, H., Onodera, J., Kato, K., Shibata, N., Inoue, T., Yokota, A., Kai, Y.
Deposit date:2001-09-03
Release date:2002-03-20
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (1.84 Å)
Cite:Crystal structure of activated ribulose-1,5-bisphosphate carboxylase/oxygenase from green alga Chlamydomonas reinhardtii complexed with 2-carboxyarabinitol-1,5-bisphosphate.
J.Mol.Biol., 316, 2002
1IWA
  • Download 1iwa
  • View 1iwa
Molmil generated image of 1iwa
RUBISCO FROM GALDIERIA PARTITA
Descriptor:ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit, ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit, SULFATE ION
Authors:Okano, Y., Mizohata, E., Xie, Y., Matsumura, H., Sugawara, H., Inoue, T., Yokota, A., Kai, Y.
Deposit date:2002-04-30
Release date:2003-04-30
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (2.6 Å)
Cite:X-Ray Structure of Galdieria Rubisco Complexed with one sulfate ion per active site
FEBS LETT., 527, 2002
2EIZ
  • Download 2eiz
  • View 2eiz
Molmil generated image of 2eiz
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
  • Download 2eks
  • View 2eks
Molmil generated image of 2eks
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
  • Download 2yss
  • View 2yss
Molmil generated image of 2yss
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
2Z44
  • Download 2z44
  • View 2z44
Molmil generated image of 2z44
CRYSTAL STRUCTURE OF SELENOMETHIONINE-LABELED ORF134
Descriptor:ORF134
Authors:Tomimoto, Y., Ihara, K., Onizuka, T., Kanai, S., Ashida, H., Yokota, A., Tanaka, S., Miyasaka, H., Yamada, Y., Kato, R., Wakatsuki, S.
Deposit date:2007-06-12
Release date:2008-06-24
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (2.5 Å)
Cite:Crystal Structure of ORF134
To be Published
2Z45
  • Download 2z45
  • View 2z45
Molmil generated image of 2z45
CRYSTAL STRUCTURE OF ZN-BOUND ORF134
Descriptor:ORF134, ZINC ION
Authors:Tomimoto, Y., Ihara, K., Onizuka, T., Kanai, S., Ashida, H., Yokota, A., Tanaka, S., Miyasaka, H., Yamada, Y., Kato, R., Wakatsuki, S.
Deposit date:2007-06-12
Release date:2008-06-24
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (2.15 Å)
Cite:Crystal Structure of ORF134
To be Published
2Z46
  • Download 2z46
  • View 2z46
Molmil generated image of 2z46
CRYSTAL STRUCTURE OF NATIVE-ORF134
Descriptor:ORF134
Authors:Tomimoto, Y., Ihara, K., Onizuka, T., Kanai, S., Ashida, H., Yokota, A., Tanaka, S., Miyasaka, H., Yamada, Y., Kato, R., Wakatsuki, S.
Deposit date:2007-06-12
Release date:2008-06-24
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (2.97 Å)
Cite:Crystal Structure of ORF134
To be Published
4M6R
  • Download 4m6r
  • View 4m6r
Molmil generated image of 4m6r
STRUCTURAL AND BIOCHEMICAL BASIS FOR THE INHIBITION OF CELL DEATH BY APIP, A METHIONINE SALVAGE ENZYME
Descriptor:Methylthioribulose-1-phosphate dehydratase, ZINC ION
Authors:Kang, W., Hong, S.H., Lee, H.M., Kim, N.Y., Lim, Y.C., Le, L.T.M., Lim, B., Kim, H.C., Kim, T.Y., Ashida, H., Yokota, A., Hah, S.S., Chun, K.H., Jung, Y.K., Yang, J.K.
Deposit date:2013-08-10
Release date:2014-01-29
Method:X-RAY DIFFRACTION (2 Å)
Cite:Structural and biochemical basis for the inhibition of cell death by APIP, a methionine salvage enzyme.
Proc.Natl.Acad.Sci.USA, 111, 2014
5AYU
  • Download 5ayu
  • View 5ayu
Molmil generated image of 5ayu
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
1WDD
  • Download 1wdd
  • View 1wdd
Molmil generated image of 1wdd
CRYSTAL STRUCTURE OF ACTIVATED RICE RUBISCO COMPLEXED WITH 2-CARBOXYARABINITOL-1,5-BISPHOSPHATE
Descriptor:Ribulose bisphosphate carboxylase large chain, Ribulose bisphosphate carboxylase small chain C, MAGNESIUM ION, ...
Authors:Mizohata, E., Matsumura, H., Ueno, T., Ishida, H., Inoue, T., Makino, A., Mae, T., Kai, Y.
Deposit date:2004-05-13
Release date:2004-11-13
Last modified:2013-06-05
Method:X-RAY DIFFRACTION (1.35 Å)
Cite:Crystal structure of rice Rubisco and implications for activation induced by positive effectors NADPH and 6-phosphogluconate
J.Mol.Biol., 422, 2012
<123>