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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:2023-11-08
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Domain swapping oligomerization of thermostable c-type cytochrome in E. coli cells
Sci Rep, 6, 2016
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
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, GLYCEROL, OLEIC ACID, ...
Authors:Kakuta, Y, Hayashi, Y, Okino, N, Ito, M.
Deposit date:2007-01-25
Release date:2007-09-11
Last modified:2023-10-25
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, OLEIC ACID, PALMITIC ACID, ...
Authors:Kakuta, Y, Hayashi, Y, Okino, N, Ito, M.
Deposit date:2007-01-25
Release date:2007-09-11
Last modified:2023-10-25
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Klotho-related protein is a novel cytosolic neutral beta-glycosylceramidase.
J.Biol.Chem., 282, 2007
4XFP
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Crystal Structure of Highly Active Mutant of Bacillus sp. TB-90 Urate Oxidase
Descriptor: 8-AZAXANTHINE, CHLORIDE ION, SULFATE ION, ...
Authors:Hibi, T, Hayashi, Y, Kawamura, A, Itoh, T.
Deposit date:2014-12-28
Release date:2016-01-13
Last modified:2023-11-08
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
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: (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, plasmepsin IV
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:2024-04-03
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
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:2023-11-15
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
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:2021-10-20
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
4EBW
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Structure of Focal Adhesion Kinase catalytic domain in complex with novel allosteric inhibitor
Descriptor: 1-ethyl-8-(4-ethylphenyl)-5-methyl-1,5-dihydropyrazolo[4,3-c][2,1]benzothiazine 4,4-dioxide, Focal adhesion kinase 1
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
1UIL
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BU of 1uil by Molmil
Double-stranded RNA-binding motif of Hypothetical protein BAB28848
Descriptor: Double-stranded RNA-binding motif
Authors:Nagata, T, Muto, Y, Hayashi, F, Hamana, H, Shirouzu, M, Terada, T, Kigawa, T, Inoue, M, Yabuki, T, Aoki, M, Seki, E, Matsuda, T, Hirota, H, Yoshida, M, Kobayashi, N, Tanaka, A, Osanai, T, Matsuo, Y, Hayashizaki, Y, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Deposit date:2003-07-17
Release date:2004-11-16
Last modified:2023-12-27
Method:SOLUTION NMR
Cite:Structure of Double-stranded RNA-binding motif of Hypothetical protein BAB28848
To be Published
3VKK
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Crystal Structure Of The Covalent Intermediate Of Human Cytosolic Beta-Glucosidase-mannose complex
Descriptor: CHLORIDE ION, Cytosolic beta-glucosidase, GLYCEROL, ...
Authors:Noguchi, J, Hayashi, Y, Okino, N, Ito, M, Kimura, M, Kakuta, Y.
Deposit date:2011-11-17
Release date:2012-11-21
Last modified:2020-07-29
Method:X-RAY DIFFRACTION (2 Å)
Cite:Structural basis for inhibition mechanism of human cytosolic beta-glucosidase by monnoside
To be Published
3WLV
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BU of 3wlv by Molmil
Thermostable urate oxidase from Bacillus sp. TB-90
Descriptor: 8-AZAXANTHINE, CHLORIDE ION, POTASSIUM ION, ...
Authors:Hibi, T, Hayashi, Y, Itoh, T.
Deposit date:2013-11-14
Release date:2014-06-18
Last modified:2024-05-29
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, 53, 2014
1UHW
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Solution structure of the DEP domain of mouse pleckstrin
Descriptor: Pleckstrin
Authors:Inoue, K, Yoshida, M, Hatta, R, Hayashi, F, Shirouzu, M, Terada, T, Kigawa, T, Inoue, M, Yabuki, T, Aoki, M, Seki, E, Matsuda, T, Hirota, H, Tanaka, A, Osanai, T, Matsuo, Y, Arakawa, T, Carninci, P, Kawai, J, Hayashizaki, Y, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Deposit date:2003-07-11
Release date:2004-01-11
Last modified:2023-12-27
Method:SOLUTION NMR
Cite:Solution structure of the DEP domain of mouse pleckstrin
To be Published
1UGJ
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Solution structure of a murine hypothetical protein from RIKEN cDNA 2310057J16
Descriptor: RIKEN cDNA 2310057J16 protein
Authors:Nagashima, T, Hayashi, F, Shirouzu, M, Terada, T, Kigawa, T, Inoue, M, Yabuki, T, Aoki, M, Seki, E, Matsuda, T, Hirota, H, Yoshida, M, Tanaka, A, Osanai, T, Arakawa, T, Carninci, P, Kawai, J, Hayashizaki, Y, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Deposit date:2003-06-16
Release date:2004-08-03
Last modified:2023-12-27
Method:SOLUTION NMR
Cite:Solution structure of a murine hypothetical protein from RIKEN cDNA 2310057J16
To be Published
1UH6
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Solution Structure of the murine ubiquitin-like 5 protein from RIKEN cDNA 0610031K06
Descriptor: ubiquitin-like 5
Authors:Hayashi, F, Shirouzu, M, Terada, T, Kigawa, T, Inoue, M, Yabuki, T, Aoki, M, Seki, E, Matsuda, T, Hirota, H, Yoshida, M, Tanaka, A, Osanai, T, Arakawa, T, Carninci, P, Kawai, J, Hayashizaki, Y, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Deposit date:2003-06-25
Release date:2003-12-25
Last modified:2023-12-27
Method:SOLUTION NMR
Cite:Solution Structure of the murine ubiquitin-like 5 protein from RIKEN cDNA 0610031K06
To be Published
7E18
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BU of 7e18 by Molmil
Crystal structure of SAR-CoV-2 3CL protease complex with inhibitor YH-53
Descriptor: 1,2-ETHANEDIOL, N-[(2S)-1-[[(2S)-1-(1,3-benzothiazol-2-yl)-1-oxidanylidene-3-[(3S)-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]-4-methoxy-1H-indole-2-carboxamide, Replicase polyprotein 1ab
Authors:Senda, M, Konno, S, Hayashi, Y, Senda, T.
Deposit date:2021-02-01
Release date:2021-06-23
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (1.65 Å)
Cite:3CL Protease Inhibitors with an Electrophilic Arylketone Moiety as Anti-SARS-CoV-2 Agents.
J.Med.Chem., 65, 2022
7E19
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Crystal structure of SAR-CoV-2 3CL protease complex with inhibitor SH-5
Descriptor: (phenylmethyl) N-[(2S)-1-[[(2S)-1-[[(2S)-1-(1,3-benzothiazol-2-yl)-1-oxidanylidene-3-[(3S)-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]amino]-3-methyl-1-oxidanylidene-butan-2-yl]carbamate, 3C-like proteinase
Authors:Senda, M, Konno, S, Hayashi, Y, Senda, T.
Deposit date:2021-02-01
Release date:2021-06-23
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.15 Å)
Cite:3CL Protease Inhibitors with an Electrophilic Arylketone Moiety as Anti-SARS-CoV-2 Agents.
J.Med.Chem., 65, 2022
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:2024-05-29
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
5ZC6
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BU of 5zc6 by Molmil
Solution structure of H-RasT35S mutant protein in complex with KBFM123
Descriptor: 3-oxidanyl-~{N}-[[(2~{R})-oxolan-2-yl]methyl]naphthalene-2-carboxamide, GTPase HRas, MAGNESIUM ION, ...
Authors:Matsumoto, S, Hayashi, Y, Hiraga, T, Matsuo, K, Kataoka, T.
Deposit date:2018-02-15
Release date:2018-09-12
Last modified:2024-05-01
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
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
5Y7F
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Crystal structure of catalytic domain of UGGT (UDP-bound form) from Thermomyces dupontii
Descriptor: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, CALCIUM ION, 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:2023-11-22
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
2ZOX
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Crystal Structure of the Covalent Intermediate of Human Cytosolic beta-Glucosidase
Descriptor: 4-nitrophenyl alpha-D-glucopyranoside, Cytosolic beta-glucosidase, GLYCEROL, ...
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:2023-11-01
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
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
2ROK
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BU of 2rok by Molmil
Solution structure of the cap-binding domain of PARN complexed with the cap analog
Descriptor: 7N-METHYL-8-HYDROGUANOSINE-5'-MONOPHOSPHATE, GUANOSINE-5'-DIPHOSPHATE, poly(A)-specific ribonuclease
Authors:Nagata, T, Suzuki, S, Endo, R, Shirouzu, M, Terada, T, Inoue, M, Kigawa, T, Guntert, P, Hayashizaki, Y, Muto, Y, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Deposit date:2008-03-28
Release date:2009-02-10
Last modified:2024-05-29
Method:SOLUTION NMR
Cite:The RRM domain of poly(A)-specific ribonuclease has a noncanonical binding site for mRNA cap analog recognition.
Nucleic Acids Res., 36, 2008
2RNE
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Solution structure of the second RNA recognition motif (RRM) of TIA-1
Descriptor: Tia1 protein
Authors:Takahashi, M, Kuwasako, K, Abe, C, Tsuda, K, Inoue, M, Terada, T, Shirouzu, M, Kobayashi, N, Kigawa, T, Taguchi, S, Guntert, P, Hayashizaki, Y, Tanaka, A, Muto, Y, Yokoyama, S.
Deposit date:2007-12-19
Release date:2008-11-04
Last modified:2024-05-29
Method:SOLUTION NMR
Cite:Solution structure of the second RNA recognition motif (RRM) domain of murine T cell intracellular antigen-1 (TIA-1) and its RNA recognition mode
Biochemistry, 47, 2008

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