Author results

3VYM
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DIMERIC HYDROGENOBACTER THERMOPHILUS CYTOCHROME C552
Descriptor:Cytochrome c-552, HEME C
Authors:Hayashi, Y., Nagao, S., Osuka, H., Komori, H., Higuchi, Y., Hirota, S.
Deposit date:2012-09-28
Release date:2012-11-07
Last modified:2017-11-22
Method:X-RAY DIFFRACTION (2 Å)
Cite:Domain Swapping of the Heme and N-Terminal alpha-Helix in Hydrogenobacter thermophilus Cytochrome c(552) Dimer
Biochemistry, 51, 2012
4ZID
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DIMERIC HYDROGENOBACTER THERMOPHILUS CYTOCHROME C552 OBTAINED FROM ESCHERICHIA COLI
Descriptor:Cytochrome c-552, HEME C
Authors:Hayashi, Y., Yamanaka, M., Nagao, S., Komori, H., Higuchi, Y., Hirota, S.
Deposit date:2015-04-28
Release date:2016-02-10
Last modified:2016-02-24
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Domain swapping oligomerization of thermostable c-type cytochrome in E. coli cells
Sci Rep, 6, 2016
2E9L
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CRYSTAL STRUCTURE OF HUMAN CYTOSOLIC NEUTRAL BETA-GLYCOSYLCERAMIDASE (KLOTHO-RELATED PROTE:KLRP) COMPLEX WITH GLUCOSE AND FATTY ACIDS
Descriptor:Cytosolic beta-glucosidase, BETA-D-GLUCOSE, PALMITIC ACID, ...
Authors:Kakuta, Y., Hayashi, Y., Okino, N., Ito, M.
Deposit date:2007-01-25
Release date:2007-09-11
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (1.6 Å)
Cite:Klotho-related protein is a novel cytosolic neutral beta-glycosylceramidase.
J.Biol.Chem., 282, 2007
2E9M
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CRYSTAL STRUCTURE OF HUMAN CYTOSOLIC NEUTRAL BETA-GLYCOSYLCERAMIDASE (KLOTHO-RELATED PROTE:KLRP) COMPLEX WITH GALACTOSE AND FATTY ACIDS
Descriptor:Cytosolic beta-glucosidase, BETA-D-GALACTOSE, PALMITIC ACID, ...
Authors:Kakuta, Y., Hayashi, Y., Okino, N., Ito, M.
Deposit date:2007-01-25
Release date:2007-09-11
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Klotho-related protein is a novel cytosolic neutral beta-glycosylceramidase.
J.Biol.Chem., 282, 2007
3CVE
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CRYSTAL STRUCTURE OF THE CARBOXY TERMINUS OF HOMER1
Descriptor:Homer protein homolog 1
Authors:Hayashi, M.K., Stearns, M.H., Giannini, V., Xu, R.-M., Sala, C., Hayashi, Y.
Deposit date:2008-04-18
Release date:2009-03-31
Last modified:2017-10-25
Method:X-RAY DIFFRACTION (1.75 Å)
Cite:The postsynaptic density proteins Homer and Shank form a polymeric network structure.
Cell(Cambridge,Mass.), 137, 2009
3CVF
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CRYSTAL STRUCTURE OF THE CARBOXY TERMINUS OF HOMER3
Descriptor:Homer protein homolog 3
Authors:Hayashi, M.K., Stearns, M.H., Giannini, V., Xu, R.-M., Sala, C., Hayashi, Y.
Deposit date:2008-04-18
Release date:2009-03-31
Last modified:2017-10-25
Method:X-RAY DIFFRACTION (2.9 Å)
Cite:The postsynaptic density proteins Homer and Shank form a polymeric network structure.
Cell(Cambridge,Mass.), 137, 2009
4XFP
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CRYSTAL STRUCTURE OF HIGHLY ACTIVE MUTANT OF BACILLUS SP. TB-90 URATE OXIDASE
Descriptor:Urate oxidase, 8-AZAXANTHINE, CHLORIDE ION, ...
Authors:Hibi, T., Hayashi, Y., Kawamura, A., Itoh, T.
Deposit date:2014-12-28
Release date:2016-01-13
Method:X-RAY DIFFRACTION (1.66 Å)
Cite:Glycine Substitution of Surface Proline 287 Involves Entropic Enhancement of Bacillus sp. TB-90 Uricase Activity
To be published
2ZOX
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CRYSTAL STRUCTURE OF THE COVALENT INTERMEDIATE OF HUMAN CYTOSOLIC BETA-GLUCOSIDASE
Descriptor:Cytosolic beta-glucosidase, ALPHA-D-GLUCOSE, 4'-NITROPHENYL-ALPHA-D-GLUCOPYRANOSIDE, ...
Authors:Noguchi, J., Hayashi, Y., Baba, Y., Okino, N., Kimura, M., Ito, M., Kakuta, Y.
Deposit date:2008-06-17
Release date:2008-09-30
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:Crystal structure of the covalent intermediate of human cytosolic beta-glucosidase
Biochem.Biophys.Res.Commun., 374, 2008
2ANL
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X-RAY CRYSTAL STRUCTURE OF THE ASPARTIC PROTEASE PLASMEPSIN 4 FROM THE MALARIAL PARASITE PLASMODIUM MALARIAE BOUND TO AN ALLOPHENYLNORSTATINE BASED INHIBITOR
Descriptor:plasmepsin IV, (4R)-3-{(2S,3S)-2-hydroxy-3-[(3-hydroxy-2-methylbenzoyl)amino]-4-phenylbutanoyl}-5,5-dimethyl-N-(2-methylbenzyl)-1,3-thiazolidine-4-carboxamide
Authors:Clemente, J.C., Govindasamy, L., Madabushi, A., Fisher, S.Z., Moose, R.E., Yowell, C.A., Hidaka, K., Kimura, T., Hayashi, Y., Kiso, Y., Agbandje-McKenna, M., Dame, J.B., Dunn, B.M., McKenna, R.
Deposit date:2005-08-11
Release date:2006-04-04
Last modified:2017-10-11
Method:X-RAY DIFFRACTION (3.3 Å)
Cite:Structure of the aspartic protease plasmepsin 4 from the malarial parasite Plasmodium malariae bound to an allophenylnorstatine-based inhibitor.
Acta Crystallogr.,Sect.D, 62, 2006
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
3VKK
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CRYSTAL STRUCTURE OF THE COVALENT INTERMEDIATE OF HUMAN CYTOSOLIC BETA-GLUCOSIDASE-MANNOSE COMPLEX
Descriptor:Cytosolic beta-glucosidase, GLYCEROL, CHLORIDE ION, ...
Authors:Noguchi, J., Hayashi, Y., Okino, N., Ito, M., Kimura, M., Kakuta, Y.
Deposit date:2011-11-17
Release date:2012-11-21
Method:X-RAY DIFFRACTION (2 Å)
Cite:Structural basis for inhibition mechanism of human cytosolic beta-glucosidase by monnoside
To be Published
4EBW
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STRUCTURE OF FOCAL ADHESION KINASE CATALYTIC DOMAIN IN COMPLEX WITH NOVEL ALLOSTERIC INHIBITOR
Descriptor:Focal adhesion kinase 1, 1-ethyl-8-(4-ethylphenyl)-5-methyl-1,5-dihydropyrazolo[4,3-c][2,1]benzothiazine 4,4-dioxide
Authors:Iwatani, M., Iwata, H., Okabe, A., Skene, R.J., Tomita, N., Hayashi, Y., Aramaki, Y., Hosfield, D.J., Hori, A., Baba, A., Miki, H.
Deposit date:2012-03-25
Release date:2012-07-25
Last modified:2013-03-27
Method:X-RAY DIFFRACTION (2.65 Å)
Cite:Discovery and characterization of novel allosteric FAK inhibitors.
Eur.J.Med.Chem., 61, 2013
3WLV
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THERMOSTABLE URATE OXIDASE FROM BACILLUS SP. TB-90
Descriptor:Urate oxidase, 8-AZAXANTHINE, SULFATE ION, ...
Authors:Hibi, T., Hayashi, Y., Itoh, T.
Deposit date:2013-11-14
Release date:2014-06-18
Method:X-RAY DIFFRACTION (1.747 Å)
Cite:Intersubunit Salt Bridges with a Sulfate Anion Control Subunit Dissociation and Thermal Stabilization of Bacillus sp. TB-90 Urate Oxidase
Biochemistry, 2014
5ZC6
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SOLUTION STRUCTURE OF H-RAST35S MUTANT PROTEIN IN COMPLEX WITH KBFM123
Descriptor:GTPase HRas, PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER, 3-oxidanyl-~{N}-[[(2~{R})-oxolan-2-yl]methyl]naphthalene-2-carboxamide, ...
Authors:Matsumoto, S., Hayashi, Y., Hiraga, T., Matsuo, K., Kataoka, T.
Deposit date:2018-02-15
Release date:2018-09-12
Last modified:2018-09-26
Method:SOLUTION NMR
Cite:Molecular Basis for Allosteric Inhibition of GTP-Bound H-Ras Protein by a Small-Molecule Compound Carrying a Naphthalene Ring
Biochemistry, 57, 2018
1K5O
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CPI-17(35-120) DELETION MUTANT
Descriptor:CPI-17
Authors:Ohki, S., Eto, M., Kariya, E., Hayano, T., Hayashi, Y., Yazawa, M., Brautigan, D., Kainosho, M.
Deposit date:2001-10-11
Release date:2002-10-11
Last modified:2011-07-13
Method:SOLUTION NMR
Cite:Solution NMR Structure of the Myosin Phosphatase Inhibitor Protein CPI-17 Shows Phosphorylation-induced Conformational Changes Responsible for Activation
J.Mol.Biol., 314, 2001
5Y7F
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CRYSTAL STRUCTURE OF CATALYTIC DOMAIN OF UGGT (UDP-BOUND FORM) FROM THERMOMYCES DUPONTII
Descriptor:UGGT, URIDINE-5'-DIPHOSPHATE, 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, ...
Authors:Satoh, T., Song, C., Zhu, T., Toshimori, T., Murata, K., Hayashi, Y., Kamikubo, H., Uchihashi, T., Kato, K.
Deposit date:2017-08-17
Release date:2017-09-27
Last modified:2017-11-01
Method:X-RAY DIFFRACTION (1.35 Å)
Cite:Visualisation of a flexible modular structure of the ER folding-sensor enzyme UGGT.
Sci Rep, 7, 2017
5Y7O
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CRYSTAL STRUCTURE OF FOLDING SENSOR REGION OF UGGT FROM THERMOMYCES DUPONTII
Descriptor:UGGT
Authors:Satoh, T., Song, C., Zhu, T., Toshimori, T., Murata, K., Hayashi, Y., Kamikubo, H., Uchihashi, T., Kato, K.
Deposit date:2017-08-17
Release date:2017-09-27
Last modified:2017-11-01
Method:X-RAY DIFFRACTION (3.1 Å)
Cite:Visualisation of a flexible modular structure of the ER folding-sensor enzyme UGGT.
Sci Rep, 7, 2017
3WJT
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CRYSTAL STRUCTURE OF THE L68D VARIANT OF MLOLB
Descriptor:Outer-membrane lipoprotein LolB, SULFATE ION, CHLORIDE ION
Authors:Takeda, K., Tokuda, H., Miki, K.
Deposit date:2013-10-16
Release date:2014-03-05
Last modified:2014-04-30
Method:X-RAY DIFFRACTION (1.55 Å)
Cite:Roles of the Protruding Loop of Factor B Essential for the Localization of Lipoproteins (LolB) in the Anchoring of Bacterial Triacylated Proteins to the Outer Membran
J.Biol.Chem., 289, 2014
3WJU
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CRYSTAL STRUCTURE OF THE L68D VARIANT OF MLOLB FROM ESCHERICHIA COLI
Descriptor:Outer-membrane lipoprotein LolB, SULFATE ION
Authors:Takeda, K., Tokuda, H., Miki, K.
Deposit date:2013-10-16
Release date:2014-03-05
Last modified:2014-04-30
Method:X-RAY DIFFRACTION (2.5 Å)
Cite:Roles of the Protruding Loop of Factor B Essential for the Localization of Lipoproteins (LolB) in the Anchoring of Bacterial Triacylated Proteins to the Outer Membran
J.Biol.Chem., 289, 2014
3WJV
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CRYSTAL STRUCTURE OF THE L68E VARIANT OF MLOLB
Descriptor:Outer-membrane lipoprotein LolB, SULFATE ION
Authors:Takeda, K., Tokuda, H., Miki, K.
Deposit date:2013-10-16
Release date:2014-03-05
Last modified:2014-04-30
Method:X-RAY DIFFRACTION (2.4 Å)
Cite:Roles of the Protruding Loop of Factor B Essential for the Localization of Lipoproteins (LolB) in the Anchoring of Bacterial Triacylated Proteins to the Outer Membran
J.Biol.Chem., 289, 2014
4RBO
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CRYSTAL STRUCTURE OF A NANOG HOMEOBOX (NANOG) FROM HOMO SAPIENS AT 3.30 A RESOLUTION
Descriptor:Putative homeobox protein NANOGP8, 5'-D(*GP*GP*CP*CP*CP*AP*TP*TP*CP*AP*AP*G)-3', 5'-D(*CP*TP*TP*GP*AP*AP*TP*GP*GP*GP*CP*C)-3'
Authors:Joint Center for Structural Genomics (JCSG), Partnership for Stem Cell Biology (STEMCELL)
Deposit date:2014-09-12
Release date:2014-10-01
Last modified:2017-11-22
Method:X-RAY DIFFRACTION (3.3 Å)
Cite:Structure-based discovery of NANOG variant with enhanced properties to promote self-renewal and reprogramming of pluripotent stem cells.
Proc.Natl.Acad.Sci.USA, 112, 2015
1LAA
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X-RAY STRUCTURE OF GLU 53 HUMAN LYSOZYME
Descriptor:HUMAN LYSOZYME
Authors:Harata, K., Muraki, M., Jigami, Y.
Deposit date:1992-06-24
Release date:1993-01-15
Last modified:2017-11-29
Method:X-RAY DIFFRACTION (1.77 Å)
Cite:X-ray structure of Glu 53 human lysozyme.
Protein Sci., 1, 1992
3VJK
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CRYSTAL STRUCTURE OF HUMAN DEPIPTIDYL PEPTIDASE IV (DPP-4) IN COMPLEX WITH MP-513
Descriptor:Dipeptidyl peptidase 4, {(2S,4S)-4-[4-(3-methyl-1-phenyl-1H-pyrazol-5-yl)piperazin-1-yl]pyrrolidin-2-yl}(1,3-thiazolidin-3-yl)methanone, N-ACETYL-D-GLUCOSAMINE
Authors:Akahoshi, F., Kishida, H., Miyaguchi, I., Yoshida, T., Ishii, S.
Deposit date:2011-10-24
Release date:2012-10-24
Last modified:2016-08-24
Method:X-RAY DIFFRACTION (2.49 Å)
Cite:Discovery and preclinical profile of teneligliptin (3-[(2S,4S)-4-[4-(3-methyl-1-phenyl-1H-pyrazol-5-yl)piperazin-1-yl]pyrrolidin-2-ylcarbonyl]thiazolidine): A highly potent, selective, long-lasting and orally active dipeptidyl peptidase IV inhibitor for the treatment of type 2 diabetes
Bioorg.Med.Chem., 20, 2012
3VJL
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CRYSTAL STRUCTURE OF HUMAN DEPIPTIDYL PEPTIDASE IV (DPP-4) IN COMPLEX WITH A PROLYLTHIAZOLIDINE INHIBITOR #2
Descriptor:Dipeptidyl peptidase 4, [(2S,4S)-4-{4-[1-phenyl-3-(trifluoromethyl)-1H-pyrazol-5-yl]piperidin-1-yl}pyrrolidin-2-yl](1,3-thiazolidin-3-yl)methanone, N-ACETYL-D-GLUCOSAMINE
Authors:Akahoshi, F., Kishida, H., Miyaguchi, I., Yoshida, T., Ishii, S.
Deposit date:2011-10-24
Release date:2012-10-24
Method:X-RAY DIFFRACTION (2.393 Å)
Cite:Discovery and preclinical profile of teneligliptin (3-[(2S,4S)-4-[4-(3-methyl-1-phenyl-1H-pyrazol-5-yl)piperazin-1-yl]pyrrolidin-2-ylcarbonyl]thiazolidine): A highly potent, selective, long-lasting and orally active dipeptidyl peptidase IV inhibitor for the treatment of type 2 diabetes
Bioorg.Med.Chem., 20, 2012
4I4E
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STRUCTURE OF FOCAL ADHESION KINASE CATALYTIC DOMAIN IN COMPLEX WITH HINGE BINDING PYRAZOLOBENZOTHIAZINE COMPOUND.
Descriptor:Focal adhesion kinase 1, [4-(2-hydroxyethyl)piperidin-1-yl][4-(5-methyl-4,4-dioxido-1,5-dihydropyrazolo[4,3-c][2,1]benzothiazin-8-yl)phenyl]methanone
Authors:Skene, R.J., Hosfield, D.J.
Deposit date:2012-11-27
Release date:2013-03-06
Last modified:2013-04-24
Method:X-RAY DIFFRACTION (1.55 Å)
Cite:Structure-based discovery of cellular-active allosteric inhibitors of FAK.
Bioorg.Med.Chem.Lett., 23, 2013
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