Author results

2E3M
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CRYSTAL STRUCTURE OF CERT START DOMAIN
Descriptor:Lipid-transfer protein CERT
Authors:Kudo, N., Kumagai, K., Wakatsuki, S., Nishijima, M., Hanada, K., Kato, R.
Deposit date:2006-11-28
Release date:2007-12-18
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:Structural basis for specific lipid recognition by CERT responsible for nonvesicular trafficking of ceramide.
Proc.Natl.Acad.Sci.Usa, 105, 2008
2E3N
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CRYSTAL STRUCTURE OF CERT START DOMAIN IN COMPLEX WITH C6-CERAMIDE (P212121)
Descriptor:Lipid-transfer protein CERT, N-((E,2S,3R)-1,3-DIHYDROXYOCTADEC-4-EN-2-YL)HEXANAMIDE
Authors:Kudo, N., Kumagai, K., Wakatsuki, S., Nishijima, M., Hanada, K., Kato, R.
Deposit date:2006-11-28
Release date:2007-12-18
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (1.4 Å)
Cite:Structural basis for specific lipid recognition by CERT responsible for nonvesicular trafficking of ceramide.
Proc.Natl.Acad.Sci.Usa, 105, 2008
2E3O
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CRYSTAL STRUCTURE OF CERT START DOMAIN IN COMPLEX WITH C16-CERAMIDE (P212121)
Descriptor:Lipid-transfer protein CERT, N-((E,2S,3R)-1,3-DIHYDROXYOCTADEC-4-EN-2-YL)PALMITAMIDE, DIMETHYL SULFOXIDE
Authors:Kudo, N., Kumagai, K., Wakatsuki, S., Nishijima, M., Hanada, K., Kato, R.
Deposit date:2006-11-28
Release date:2007-12-18
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (1.55 Å)
Cite:Structural basis for specific lipid recognition by CERT responsible for nonvesicular trafficking of ceramide.
Proc.Natl.Acad.Sci.Usa, 105, 2008
2E3P
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CRYSTAL STRUCTURE OF CERT START DOMAIN IN COMPLEX WITH C16-CEARMIDE (P1)
Descriptor:Lipid-transfer protein CERT, N-((E,2S,3R)-1,3-DIHYDROXYOCTADEC-4-EN-2-YL)PALMITAMIDE
Authors:Kudo, N., Kumagai, K., Wakatsuki, S., Nishijima, M., Hanada, K., Kato, R.
Deposit date:2006-11-28
Release date:2007-12-18
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (1.4 Å)
Cite:Structural basis for specific lipid recognition by CERT responsible for nonvesicular trafficking of ceramide.
Proc.Natl.Acad.Sci.Usa, 105, 2008
2E3Q
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CRYSTAL STRUCTURE OF CERT START DOMAIN IN COMPLEX WITH C18-CERAMIDE (P212121)
Descriptor:Lipid-transfer protein CERT, N-((E,2S,3R)-1,3-DIHYDROXYOCTADEC-4-EN-2-YL)STEARAMIDE, DIMETHYL SULFOXIDE
Authors:Kudo, N., Kumagai, K., Wakatsuki, S., Nishijima, M., Hanada, K., Kato, R.
Deposit date:2006-11-28
Release date:2007-12-18
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (2.08 Å)
Cite:Structural basis for specific lipid recognition by CERT responsible for nonvesicular trafficking of ceramide.
Proc.Natl.Acad.Sci.Usa, 105, 2008
2E3R
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CRYSTAL STRUCTURE OF CERT START DOMAIN IN COMPLEX WITH C18-CERAMIDE (P1)
Descriptor:Lipid-transfer protein CERT, N-((E,2S,3R)-1,3-DIHYDROXYOCTADEC-4-EN-2-YL)STEARAMIDE
Authors:Kudo, N., Kumagai, K., Wakatsuki, S., Nishijima, M., Hanada, K., Kato, R.
Deposit date:2006-11-28
Release date:2007-12-18
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (1.65 Å)
Cite:Structural basis for specific lipid recognition by CERT responsible for nonvesicular trafficking of ceramide.
Proc.Natl.Acad.Sci.Usa, 105, 2008
2E3S
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CRYSTAL STRUCTURE OF CERT START DOMAIN CO-CRYSTALLIZED WITH C24-CERAMIDE (P21)
Descriptor:Lipid-transfer protein CERT
Authors:Kudo, N., Kumagai, K., Wakatsuki, S., Nishijima, M., Hanada, K., Kato, R.
Deposit date:2006-11-28
Release date:2007-12-18
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (1.94 Å)
Cite:Structural basis for specific lipid recognition by CERT responsible for nonvesicular trafficking of ceramide.
Proc.Natl.Acad.Sci.Usa, 105, 2008
2Z9Y
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CRYSTAL STRUCTURE OF CERT START DOMAIN IN COMPLEX WITH C10-DIACYLGLYCEROL
Descriptor:Lipid-transfer protein CERT, (2S)-3-hydroxypropane-1,2-diyl didecanoate
Authors:Kudo, N., Kumagai, K., Wakatsuki, S., Nishijima, M., Hanada, K., Kato, R.
Deposit date:2007-09-26
Release date:2008-02-12
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Structural basis for specific lipid recognition by CERT responsible for nonvesicular trafficking of ceramide.
Proc.Natl.Acad.Sci.Usa, 105, 2008
2Z9Z
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CRYSTAL STRUCTURE OF CERT START DOMAIN(N504A MUTANT), IN COMPLEX WITH C10-DIACYLGLYCEROL
Descriptor:Lipid-transfer protein CERT, (2S)-3-hydroxypropane-1,2-diyl didecanoate
Authors:Kudo, N., Kumagai, K., Wakatsuki, S., Nishijima, M., Hanada, K., Kato, R.
Deposit date:2007-09-26
Release date:2008-02-12
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (1.74 Å)
Cite:Structural basis for specific lipid recognition by CERT responsible for nonvesicular trafficking of ceramide.
Proc.Natl.Acad.Sci.Usa, 105, 2008
3H3Q
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CRYSTAL STRUCTURE OF THE CERT START DOMAIN IN COMPLEX WITH HPA-13
Descriptor:Goodpasture antigen binding protein, N-[(1R,3R)-3-hydroxy-1-(hydroxymethyl)-3-phenylpropyl]tridecanamide
Authors:Kudo, N., Wakatsuki, S., Kato, R.
Deposit date:2009-04-17
Release date:2010-03-02
Last modified:2017-11-01
Method:X-RAY DIFFRACTION (2 Å)
Cite:Crystal structures of the CERT START domain with inhibitors provide insights into the mechanism of ceramide transfer.
J.Mol.Biol., 396, 2010
3H3R
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CRYSTAL STRUCTURE OF THE CERT START DOMAIN IN COMPLEX WITH HPA-14
Descriptor:Goodpasture antigen binding protein, N-[(1R,3R)-3-hydroxy-1-(hydroxymethyl)-3-phenylpropyl]tetradecanamide
Authors:Kudo, N., Wakatsuki, S., Kato, R.
Deposit date:2009-04-17
Release date:2010-03-02
Last modified:2017-11-01
Method:X-RAY DIFFRACTION (1.85 Å)
Cite:Crystal structures of the CERT START domain with inhibitors provide insights into the mechanism of ceramide transfer.
J.Mol.Biol., 396, 2010
3H3S
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CRYSTAL STRUCTURE OF THE CERT START DOMAIN IN COMPLEX WITH HPA-15
Descriptor:Goodpasture antigen binding protein, N-[(1R,3R)-3-hydroxy-1-(hydroxymethyl)-3-phenylpropyl]pentadecanamide
Authors:Kudo, N., Wakatsuki, S., Kato, R.
Deposit date:2009-04-17
Release date:2010-03-02
Last modified:2017-11-01
Method:X-RAY DIFFRACTION (1.66 Å)
Cite:Crystal structures of the CERT START domain with inhibitors provide insights into the mechanism of ceramide transfer.
J.Mol.Biol., 396, 2010
3H3T
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CRYSTAL STRUCTURE OF THE CERT START DOMAIN IN COMPLEX WITH HPA-16
Descriptor:Goodpasture antigen binding protein, N-[(1R,3R)-3-hydroxy-1-(hydroxymethyl)-3-phenylpropyl]hexadecanamide
Authors:Kudo, N., Wakatsuki, S., Kato, R.
Deposit date:2009-04-17
Release date:2010-03-02
Last modified:2017-11-01
Method:X-RAY DIFFRACTION (2.4 Å)
Cite:Crystal structures of the CERT START domain with inhibitors provide insights into the mechanism of ceramide transfer.
J.Mol.Biol., 396, 2010
3VTG
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HIGH CHORIOLYTIC ENZYME 1 (HCE-1), A HATCHING ENZYME ZINC-PROTEASE FROM ORYZIAS LATIPES (MEDAKA FISH)
Descriptor:High choriolytic enzyme 1, ZINC ION
Authors:Kudo, N., Yasumasu, S., Iuchi, I., Tanokura, M.
Deposit date:2012-05-30
Release date:2013-06-05
Last modified:2017-11-22
Method:X-RAY DIFFRACTION (1.34 Å)
Cite:Crystal Structure of High choriolytic enzyme 1 (HCE-1), a hatching enzyme from Oryzias latipes (Medaka fish)
To be Published
3VVH
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X-RAY STRUCTURE OF THE HUMAN MITOGEN-ACTIVATED PROTEIN KINASE KINASE 1 (MEK1) IN COMPLEX WITH AN INHIBITOR AND MGATP
Descriptor:Dual specificity mitogen-activated protein kinase kinase 1, MAGNESIUM ION, ADENOSINE-5'-TRIPHOSPHATE, ...
Authors:Kudo, N., Kato, R., Wakatsuki, S.
Deposit date:2012-07-24
Release date:2013-08-28
Method:X-RAY DIFFRACTION (2 Å)
Cite:X-ray structure of the human mitogen-activated protein kinase kinase 1 (MEK1) in complex with an inhibitor and MgATP
To be Published
5Y0Z
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HUMAN SIRT2 IN COMPLEX WITH A SPECIFIC INHIBITOR, NPD11033
Descriptor:NAD-dependent protein deacetylase sirtuin-2, ZINC ION, (1~{R},9~{S})-11-[(2~{R})-3-[2,4-bis(2-methylbutan-2-yl)phenoxy]-2-oxidanyl-propyl]-7,11-diazatricyclo[7.3.1.0^{2,7}]trideca-2,4-dien-6-one
Authors:Kudo, N., Ito, A., Yoshida, M.
Deposit date:2017-07-19
Release date:2018-07-25
Method:X-RAY DIFFRACTION (2 Å)
Cite:Identification of a novel small molecule that inhibits deacetylase but not defatty-acylase reaction catalysed by SIRT2.
Philos. Trans. R. Soc. Lond., B, Biol. Sci., 373, 2018
5Y4H
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HUMAN SIRT3 IN COMPLEX WITH HALISTANOL SULFATE
Descriptor:NAD-dependent protein deacetylase sirtuin-3, mitochondrial, THr-Arg-Ser-GLY-ALY-VAL-MET-ARG-ARG-LEU-ARG-ARG, ...
Authors:Kudo, N., Ito, A., Yoshida, M.
Deposit date:2017-08-03
Release date:2018-05-16
Method:X-RAY DIFFRACTION (2.6 Å)
Cite:Halistanol sulfates I and J, new SIRT1-3 inhibitory steroid sulfates from a marine sponge of the genus Halichondria
J. Antibiot., 71, 2018
4Y6L
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HUMAN SIRT2 IN COMPLEX WITH MYRISTOYLATED PEPTIDE (H3K9MYR)
Descriptor:NAD-dependent protein deacetylase sirtuin-2, peptide THR-ALA-ARG-MYK-SER-THR-GLY, ZINC ION
Authors:Kudo, N., Ito, A., Yoshida, M.
Deposit date:2015-02-13
Release date:2016-01-06
Method:X-RAY DIFFRACTION (1.6 Å)
Cite:Kinetic and Structural Basis for Acyl-Group Selectivity and NAD(+) Dependence in Sirtuin-Catalyzed Deacylation.
Biochemistry, 54, 2015
4Y6O
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HUMAN SIRT2 IN COMPLEX WITH MYRISTOYLATED PEPTIDE (TNF-ALPHAK20MYR)
Descriptor:NAD-dependent protein deacetylase sirtuin-2, peptide LEU-PRO-LYS-MYK-THR-GLY-GLY, ZINC ION
Authors:Kudo, N., Ito, A., Yoshida, M.
Deposit date:2015-02-13
Release date:2016-01-06
Method:X-RAY DIFFRACTION (1.6 Å)
Cite:Kinetic and Structural Basis for Acyl-Group Selectivity and NAD(+) Dependence in Sirtuin-Catalyzed Deacylation.
Biochemistry, 54, 2015
4Y6Q
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HUMAN SIRT2 IN COMPLEX WITH 2-O-MYRISTOYL-ADP-RIBOSE
Descriptor:NAD-dependent protein deacetylase sirtuin-2, ZINC ION, [(2S,3R,4R,5R)-5-[[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxymethyl]-2,4-bis(oxidanyl)oxolan-3-yl] tetradecanoate
Authors:Kudo, N., Ito, A., Yoshida, M.
Deposit date:2015-02-13
Release date:2016-01-06
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:Kinetic and Structural Basis for Acyl-Group Selectivity and NAD(+) Dependence in Sirtuin-Catalyzed Deacylation.
Biochemistry, 54, 2015
3AAD
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STRUCTURE OF THE HISTONE CHAPERONE CIA/ASF1-DOUBLE BROMODOMAIN COMPLEX LINKING HISTONE MODIFICATIONS AND SITE-SPECIFIC HISTONE EVICTION
Descriptor:Transcription initiation factor TFIID subunit 1, Histone chaperone ASF1A, SULFATE ION
Authors:Akai, Y., Adachi, N., Hayashi, Y., Eitoku, M., Sano, N., Natsume, R., Kudo, N., Tanokura, M., Senda, T., Horikoshi, M.
Deposit date:2009-11-16
Release date:2010-04-28
Last modified:2017-10-11
Method:X-RAY DIFFRACTION (3.3 Å)
Cite:Structure of the histone chaperone CIA/ASF1-double bromodomain complex linking histone modifications and site-specific histone eviction
Proc.Natl.Acad.Sci.USA, 107, 2010
1EQK
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SOLUTION STRUCTURE OF ORYZACYSTATIN-I, A CYSTEINE PROTEINASE INHIBITOR OF THE RICE, ORYZA SATIVA L. JAPONICA
Descriptor:ORYZACYSTATIN-I
Authors:Nagata, K., Kudo, N., Abe, K., Arai, S., Tanokura, M.
Deposit date:2000-04-05
Release date:2001-01-10
Last modified:2011-07-13
Method:SOLUTION NMR
Cite:Three-dimensional solution structure of oryzacystatin-I, a cysteine proteinase inhibitor of the rice, Oryza sativa L. japonica.
Biochemistry, 39, 2000
1V3Y
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THE CRYSTAL STRUCTURE OF PEPTIDE DEFORMYLASE FROM THERMUS THERMOPHILUS HB8
Descriptor:Peptide deformylase
Authors:Kamo, M., Kudo, N., Lee, W.C., Ito, K., Motoshim, H., Tanokura, M., RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Deposit date:2003-11-07
Release date:2004-12-28
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (1.81 Å)
Cite:The crystal structure of peptide deformylase from Thermus thermophilus HB8
to be published
2D36
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THE CRYSTAL STRUCTURE OF FLAVIN REDUCTASE HPAC
Descriptor:hypothetical NADH-dependent FMN oxidoreductase, FLAVIN MONONUCLEOTIDE
Authors:Okai, M., Kudo, N., Lee, W.C., Kamo, M., Nagata, K., Tanokura, M.
Deposit date:2005-09-26
Release date:2006-05-30
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (2.3 Å)
Cite:Crystal structures of the short-chain flavin reductase HpaC from Sulfolobus tokodaii strain 7 in its three states: NAD(P)(+)(-)free, NAD(+)(-)bound, and NADP(+)(-)bound
Biochemistry, 45, 2006
2D37
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THE CRYSTAL STRUCTURE OF FLAVIN REDUCTASE HPAC COMPLEXED WITH NAD+
Descriptor:hypothetical NADH-dependent FMN oxidoreductase, FLAVIN MONONUCLEOTIDE, NICOTINAMIDE-ADENINE-DINUCLEOTIDE
Authors:Okai, M., Kudo, N., Lee, W.C., Kamo, M., Nagata, K., Tanokura, M.
Deposit date:2005-09-26
Release date:2006-05-30
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (1.7 Å)
Cite:Crystal structures of the short-chain flavin reductase HpaC from Sulfolobus tokodaii strain 7 in its three states: NAD(P)(+)(-)free, NAD(+)(-)bound, and NADP(+)(-)bound
Biochemistry, 45, 2006
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