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2Z9Z
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BU of 2z9z by Molmil
Crystal structure of CERT START domain(N504A mutant), in complex with C10-diacylglycerol
Descriptor: (2S)-3-hydroxypropane-1,2-diyl didecanoate, Lipid-transfer protein CERT
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:2023-11-01
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
2Z9Y
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BU of 2z9y by Molmil
Crystal structure of CERT START domain in complex with C10-diacylglycerol
Descriptor: (2S)-3-hydroxypropane-1,2-diyl didecanoate, Lipid-transfer protein CERT
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:2023-11-01
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
3H3S
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BU of 3h3s by Molmil
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:2024-03-20
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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BU of 3h3t by Molmil
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:2023-11-01
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
3H3Q
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BU of 3h3q by Molmil
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:2023-11-01
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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BU of 3h3r by Molmil
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:2023-11-01
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
5Y0Z
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BU of 5y0z by Molmil
Human SIRT2 in complex with a specific inhibitor, NPD11033
Descriptor: (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, NAD-dependent protein deacetylase sirtuin-2, ZINC ION
Authors:Kudo, N, Ito, A, Yoshida, M.
Deposit date:2017-07-19
Release date:2018-07-25
Last modified:2023-11-22
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
2E3Q
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BU of 2e3q by Molmil
Crystal structure of CERT START domain in complex with C18-ceramide (P212121)
Descriptor: DIMETHYL SULFOXIDE, 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:2024-03-13
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
2E3P
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BU of 2e3p by Molmil
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:2024-03-13
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
2E3M
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BU of 2e3m by Molmil
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:2024-03-13
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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BU of 2e3n by Molmil
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:2024-03-13
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
2E3R
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BU of 2e3r by Molmil
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:2024-03-13
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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BU of 2e3s by Molmil
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:2024-03-13
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
2E3O
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BU of 2e3o by Molmil
Crystal structure of CERT START domain in complex with C16-ceramide (P212121)
Descriptor: DIMETHYL SULFOXIDE, 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:2024-03-13
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
3VTG
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BU of 3vtg by Molmil
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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BU of 3vvh by Molmil
X-ray structure of the human mitogen-activated protein kinase kinase 1 (MEK1) in complex with an inhibitor and MgATP
Descriptor: ADENOSINE-5'-TRIPHOSPHATE, Dual specificity mitogen-activated protein kinase kinase 1, MAGNESIUM ION, ...
Authors:Kudo, N, Kato, R, Wakatsuki, S.
Deposit date:2012-07-24
Release date:2013-08-28
Last modified:2023-11-08
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
7BOT
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BU of 7bot by Molmil
Human SIRT2 in complex with myristoyl thiourea inhibitor, No.23
Descriptor: N-dodecylmethanethioamide, NAD-dependent protein deacetylase sirtuin-2, ZINC ION, ...
Authors:Kudo, N, Olsen, C.A, Minoru, Y.
Deposit date:2020-03-19
Release date:2021-03-24
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (1.7 Å)
Cite:Mechanism-based inhibitors of SIRT2: structure-activity relationship, X-ray structures, target engagement, regulation of alpha-tubulin acetylation and inhibition of breast cancer cell migration.
Rsc Chem Biol, 2, 2021
7BOS
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BU of 7bos by Molmil
Human SIRT2 in complex with myristoyl thiourea inhibitor, No.13
Descriptor: Myristoyl thiourea inhibitor, No.13, N-dodecylmethanethioamide, ...
Authors:Kudo, N, Olsen, C.A, Minoru, Y.
Deposit date:2020-03-19
Release date:2021-03-24
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (1.7 Å)
Cite:Mechanism-based inhibitors of SIRT2: structure-activity relationship, X-ray structures, target engagement, regulation of alpha-tubulin acetylation and inhibition of breast cancer cell migration.
Rsc Chem Biol, 2, 2021
5Y4H
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BU of 5y4h by Molmil
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
Last modified:2023-11-22
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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BU of 4y6l by Molmil
Human SIRT2 in complex with myristoylated peptide (H3K9myr)
Descriptor: NAD-dependent protein deacetylase sirtuin-2, ZINC ION, peptide THR-ALA-ARG-MYK-SER-THR-GLY
Authors:Kudo, N, Ito, A, Yoshida, M.
Deposit date:2015-02-13
Release date:2016-01-06
Last modified:2023-11-08
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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BU of 4y6q by Molmil
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
Last modified:2023-11-08
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
4Y6O
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BU of 4y6o by Molmil
Human SIRT2 in complex with myristoylated peptide (TNF-alphaK20myr)
Descriptor: NAD-dependent protein deacetylase sirtuin-2, ZINC ION, peptide LEU-PRO-LYS-MYK-THR-GLY-GLY
Authors:Kudo, N, Ito, A, Yoshida, M.
Deposit date:2015-02-13
Release date:2016-01-06
Last modified:2023-11-08
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
3AAD
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BU of 3aad by Molmil
Structure of the histone chaperone CIA/ASF1-double bromodomain complex linking histone modifications and site-specific histone eviction
Descriptor: Histone chaperone ASF1A, SULFATE ION, Transcription initiation factor TFIID subunit 1
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
1V3Y
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BU of 1v3y by Molmil
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:2023-12-27
Method:X-RAY DIFFRACTION (1.81 Å)
Cite:The crystal structure of peptide deformylase from Thermus thermophilus HB8
to be published
1EQK
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BU of 1eqk by Molmil
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:2022-02-16
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

 

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