5Z0H
 
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5Z0G
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2KFK
 | | Solution structure of Bem1p PB1 domain complexed with Cdc24p PB1 domain | | Descriptor: | Bud emergence protein 1, Cell division control protein 24 | | Authors: | Kobashigawa, Y, Yoshinaga, S, Tandai, T, Ogura, K, Inagaki, F. | | Deposit date: | 2009-02-23 | | Release date: | 2009-10-06 | | Last modified: | 2024-05-29 | | Method: | SOLUTION NMR | | Cite: | NMR structure of the heterodimer of Bem1 and Cdc24 PB1 domains from Saccharomyces cerevisiae
J.Biochem., 146, 2009
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3X44
 | | Crystal structure of O-ureido-L-serine-bound K43A mutant of O-ureido-L-serine synthase | | Descriptor: | (E)-O-(carbamoylamino)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-serine, O-ureido-L-serine synthase | | Authors: | Matoba, Y, Uda, N, Oda, K, Sugiyama, M. | | Deposit date: | 2015-03-13 | | Release date: | 2015-07-29 | | Last modified: | 2024-05-29 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | The structural and mutational analyses of O-ureido-L-serine synthase necessary for D-cycloserine biosynthesis.
Febs J., 282, 2015
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5B1I
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1I56
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6JIL
 | | Crystal structure of D-cycloserine synthetase DcsG | | Descriptor: | ADENOSINE-5'-DIPHOSPHATE, Cycloserine biosynthesis protein DcsG, L(+)-TARTARIC ACID, ... | | Authors: | Matoba, Y, Sugiyama, M. | | Deposit date: | 2019-02-22 | | Release date: | 2019-12-18 | | Last modified: | 2024-10-23 | | Method: | X-RAY DIFFRACTION (2.32 Å) | | Cite: | Cyclization mechanism catalyzed by an ATP-grasp enzyme essential for d-cycloserine biosynthesis.
Febs J., 287, 2020
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5B1H
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1KP4
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2PA2
 | | Crystal structure of human Ribosomal protein L10 core domain | | Descriptor: | 60S ribosomal protein L10, POTASSIUM ION | | Authors: | Nishimura, M, Kaminishi, T, Takemoto, C, Kawazoe, M, Yoshida, T, Tanaka, A, Sugano, S, Shirouzu, M, Ohkubo, T, Yokoyama, S, Kobayashi, Y, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2007-03-27 | | Release date: | 2008-03-11 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Crystal Structure of Human Ribosomal Protein L10 Core Domain Reveals Eukaryote-Specific Motifs in Addition to the Conserved Fold
J.Mol.Biol., 377, 2008
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3VOR
 | | Crystal Structure Analysis of the CofA | | Descriptor: | CFA/III pilin | | Authors: | Fukakusa, S, Kawahara, K, Nakamura, S, Iwasita, T, Baba, S, Nishimura, M, Kobayashi, Y, Honda, T, Iida, T, Taniguchi, T, Ohkubo, T. | | Deposit date: | 2012-02-06 | | Release date: | 2012-09-26 | | Last modified: | 2024-10-30 | | Method: | X-RAY DIFFRACTION (0.9 Å) | | Cite: | Structure of the CFA/III major pilin subunit CofA from human enterotoxigenic Escherichia coli determined at 0.90 A resolution by sulfur-SAD phasing
Acta Crystallogr.,Sect.D, 68, 2012
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9KKU
 | | Helix-loop-helix peptide (M49) in complex with VEGF-A | | Descriptor: | M49, Vascular endothelial growth factor A, long form | | Authors: | Kamo, M, Michigami, M, Inaka, K, Furubayashi, N, Kaito, S, Kobayashi, Y, Shinohara, Y, Fujii, I. | | Deposit date: | 2024-11-14 | | Release date: | 2024-12-11 | | Method: | X-RAY DIFFRACTION (1.46 Å) | | Cite: | Structural Insights into Helix-Loop-Helix Peptides for "Ligand-Targeting" Intracellular Drug Delivery via VEGF Receptor-Mediated Endocytosis.
Biochem.Biophys.Res.Commun., 741, 2024
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9JU1
 | | Helix-loop-helix peptide (VS42-LR3) in complex with VEGF-A | | Descriptor: | SULFATE ION, VS42-LR3, Vascular endothelial growth factor A, ... | | Authors: | Kamo, M, Michigami, M, Inaka, K, Furubayashi, N, Kaito, S, Kobayashi, Y, Shinohara, Y, Fujii, I. | | Deposit date: | 2024-10-07 | | Release date: | 2024-12-25 | | Method: | X-RAY DIFFRACTION (1.45 Å) | | Cite: | Structural insights into molecular-targeting helix-loop-helix peptide against vascular endothelial growth factor-A.
Biochem Biophys Res Commun, 734, 2024
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3WJ4
 | | Crystal structure of PPARgamma ligand binding domain in complex with tributyltin | | Descriptor: | Peroxisome proliferator-activated receptor gamma, tributylstannanyl | | Authors: | Harada, S, Hiromori, Y, Fukakusa, S, Kawahara, K, Nakamura, S, Noda, M, Uchiyama, S, Fukui, K, Nishikawa, J, Nagase, H, Kobayashi, Y, Ohkubo, T, Yoshida, T, Nakanishi, T. | | Deposit date: | 2013-10-04 | | Release date: | 2014-10-15 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (1.95 Å) | | Cite: | Structural basis for PPARgamma transactivation by endocrine disrupting organotin compounds
To be Published
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3WJ5
 | | Crystal structure of PPARgamma ligand binding domain in complex with triphenyltin | | Descriptor: | Peroxisome proliferator-activated receptor gamma, triphenylstannanyl | | Authors: | Harada, S, Hiromori, Y, Fukakusa, S, Kawahara, K, Nakamura, S, Noda, M, Uchiyama, S, Fukui, K, Nishikawa, J, Nagase, H, Kobayashi, Y, Ohkubo, T, Yoshida, T, Nakanishi, T. | | Deposit date: | 2013-10-04 | | Release date: | 2014-10-15 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (1.89 Å) | | Cite: | Structural basis for PPARgamma transactivation by endocrine disrupting organotin compounds
To be Published
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2E5E
 | | Solution Structure of Variable-type Domain of Human Receptor for Advanced Glycation Endproducts | | Descriptor: | Advanced glycosylation end product-specific receptor | | Authors: | Matsumoto, S, Yoshida, T, Yasumatsu, I, Yamamoto, H, Kobayashi, Y, Ohkubo, T. | | Deposit date: | 2006-12-20 | | Release date: | 2007-12-25 | | Last modified: | 2024-10-30 | | Method: | SOLUTION NMR | | Cite: | Solution Structure of Variable-type Domain of Human Receptor for Advanced Glycation Endproducts
to be published
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9L6Z
 | | Crystal structure of the L7Ae derivative protein LS12 in RNA-free state | | Descriptor: | Large ribosomal subunit protein eL8, SODIUM ION | | Authors: | Teramoto, T, Nakashima, M, Fukunaga, K, Yokobayashi, Y, Kakuta, Y. | | Deposit date: | 2024-12-25 | | Release date: | 2025-04-02 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Structural insights into lab-coevolved RNA-RBP pairs and applications of synthetic riboswitches in cell-free system.
Nucleic Acids Res., 53, 2025
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1WKI
 | | solution structure of ribosomal protein L16 from thermus thermophilus HB8 | | Descriptor: | LSU ribosomal protein L16P | | Authors: | Nishimura, M, Yoshida, T, Shirouzu, M, Terada, T, Kuramitsu, S, Yokoyama, S, Ohkubo, T, Kobayashi, Y, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2004-05-31 | | Release date: | 2004-12-14 | | Last modified: | 2024-05-01 | | Method: | SOLUTION NMR | | Cite: | Solution Structure of Ribosomal Protein L16 from Thermus thermophilus HB8
J.Mol.Biol., 344, 2004
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1Y69
 | | RRF domain I in complex with the 50S ribosomal subunit from Deinococcus radiodurans | | Descriptor: | 23S ribosomal RNA, 50S ribosomal protein L16, 50S ribosomal protein L27, ... | | Authors: | Wilson, D.N, Schluenzen, F, Harms, J.M, Yoshida, T, Ohkubo, T, Albrecht, R, Buerger, J, Kobayashi, Y, Fucini, P. | | Deposit date: | 2004-12-04 | | Release date: | 2005-03-01 | | Last modified: | 2023-08-23 | | Method: | X-RAY DIFFRACTION (3.33 Å) | | Cite: | X-ray crystallography on ribosome recycling: mechanism of binding and action of RRF on the 50S ribosomal subunit
EMBO J., 24, 2005
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1V6R
 | | Solution Structure of Endothelin-1 with its C-terminal Folding | | Descriptor: | Endothelin-1 | | Authors: | Takashima, H, Mimura, N, Ohkubo, T, Yoshida, T, Tamaoki, H, Kobayashi, Y. | | Deposit date: | 2003-12-03 | | Release date: | 2004-03-16 | | Last modified: | 2024-10-30 | | Method: | SOLUTION NMR | | Cite: | Distributed Computing and NMR Constraint-Based High-Resolution Structure
Determination: Applied for Bioactive Peptide Endothelin-1 To Determine C-Terminal
Folding
J.Am.Chem.Soc., 126, 2004
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3AQB
 | | M. luteus B-P 26 heterodimeric hexaprenyl diphosphate synthase in complex with magnesium | | Descriptor: | CHLORIDE ION, Component A of hexaprenyl diphosphate synthase, Component B of hexaprenyl diphosphate synthase, ... | | Authors: | Sasaki, D, Fujihashi, M, Okuyama, N, Kobayashi, Y, Noike, M, Koyama, T, Miki, K. | | Deposit date: | 2010-10-28 | | Release date: | 2010-11-10 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | Crystal structure of heterodimeric hexaprenyl diphosphate synthase from Micrococcus luteus B-P 26 reveals that the small subunit is directly involved in the product chain length regulation.
J.Biol.Chem., 286, 2011
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2A4W
 | | Crystal Structure Of Mitomycin C-Binding Protein Complexed with Copper(II)-Bleomycin A2 | | Descriptor: | BLEOMYCIN A2, COPPER (II) ION, Mitomycin-Binding Protein | | Authors: | Danshiitsoodol, N, de Pinho, C.A, Matoba, Y, Kumagai, T, Sugiyama, M. | | Deposit date: | 2005-06-30 | | Release date: | 2006-07-18 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (1.5 Å) | | Cite: | The Mitomycin C (MMC)-binding Protein from MMC-producing Microorganisms Protects from the Lethal Effect of Bleomycin: Crystallographic Analysis to Elucidate the Binding Mode of the Antibiotic to the Protein
J.Mol.Biol., 360, 2006
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2E5D
 | | Crystal structure of Human NMPRTase complexed with nicotinamide | | Descriptor: | NICOTINAMIDE, Nicotinamide phosphoribosyltransferase | | Authors: | Takahashi, R, Nakamura, S, Kobayashi, Y, Ohkubo, T. | | Deposit date: | 2006-12-20 | | Release date: | 2007-12-25 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Structure and reaction mechanism of human nicotinamide phosphoribosyltransferase
J.Biochem., 147, 2010
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3AQC
 | | M. luteus B-P 26 heterodimeric hexaprenyl diphosphate synthase in complex with magnesium and FPP analogue | | Descriptor: | (2E,6E)-7,11-dimethyldodeca-2,6,10-trien-1-yl trihydrogen diphosphate, CHLORIDE ION, Component A of hexaprenyl diphosphate synthase, ... | | Authors: | Sasaki, D, Fujihashi, M, Okuyama, N, Kobayashi, Y, Noike, M, Koyama, T, Miki, K. | | Deposit date: | 2010-10-28 | | Release date: | 2010-11-10 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (2.61 Å) | | Cite: | Crystal structure of heterodimeric hexaprenyl diphosphate synthase from Micrococcus luteus B-P 26 reveals that the small subunit is directly involved in the product chain length regulation.
J.Biol.Chem., 286, 2011
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2E5C
 | | Crystal structure of Human NMPRTase complexed with 5'-phosphoribosyl-1'-pyrophosphate | | Descriptor: | 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose, Nicotinamide phosphoribosyltransferase | | Authors: | Takahashi, R, Nakamura, S, Kobayashi, Y, Ohkubo, T. | | Deposit date: | 2006-12-20 | | Release date: | 2007-12-25 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Structure and reaction mechanism of human nicotinamide phosphoribosyltransferase
J.Biochem., 147, 2010
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