1J31
 
 | | Crystal Structure of Hypothetical Protein PH0642 from Pyrococcus horikoshii | | Descriptor: | ACETATE ION, Hypothetical protein PH0642 | | Authors: | Sakai, N, Tajika, Y, Yao, M, Watanabe, N, Tanaka, I. | | Deposit date: | 2003-01-16 | | Release date: | 2004-03-09 | | Last modified: | 2024-10-30 | | Method: | X-RAY DIFFRACTION (1.6 Å) | | Cite: | Crystal structure of hypothetical protein PH0642 from Pyrococcus horikoshii at 1.6A resolution.
Proteins, 57, 2004
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1ION
 | | THE SEPTUM SITE-DETERMINING PROTEIN MIND COMPLEXED WITH MG-ADP FROM PYROCOCCUS HORIKOSHII OT3 | | Descriptor: | ADENOSINE-5'-DIPHOSPHATE, MAGNESIUM ION, PROBABLE CELL DIVISION INHIBITOR MIND | | Authors: | Sakai, N, Yao, M, Itou, H, Watanabe, N, Yumoto, F, Tanokura, M, Tanaka, I. | | Deposit date: | 2001-03-21 | | Release date: | 2001-09-26 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | The three-dimensional structure of septum site-determining protein MinD from Pyrococcus horikoshii OT3 in complex with Mg-ADP.
Structure, 9, 2001
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3A8S
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6JUX
 | | Crystal structure of human ALK2 kinase domain with R206H mutation in complex with RK-71807 | | Descriptor: | 4-(1-ethyl-3-pyridin-3-yl-pyrazol-4-yl)-~{N}-(4-piperazin-1-ylphenyl)pyrimidin-2-amine, Activin receptor type-1, SULFATE ION | | Authors: | Sakai, N, Mishima-Tsumagari, C, Matsumoto, T, Shirouzu, M. | | Deposit date: | 2019-04-15 | | Release date: | 2020-04-15 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.75 Å) | | Cite: | Structural Basis of Activin Receptor-Like Kinase 2 (R206H) Inhibition by Bis-heteroaryl Pyrazole-Based Inhibitors for the Treatment of Fibrodysplasia Ossificans Progressiva Identified by the Integration of Ligand-Based and Structure-Based Drug Design Approaches.
Acs Omega, 5, 2020
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7WB8
 | | Crystal structure of Bovine Pancreatic Trypsin in complex with 5-Methoxytryptamine at Room Temperature | | Descriptor: | 2-(5-methoxy-1H-indol-3-yl)ethanamine, CALCIUM ION, Cationic trypsin, ... | | Authors: | Sakai, N, Okumura, H, Yamamoto, M, Kumasaka, T. | | Deposit date: | 2021-12-15 | | Release date: | 2022-06-15 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.38 Å) | | Cite: | In situ crystal data-collection and ligand-screening system at SPring-8.
Acta Crystallogr.,Sect.F, 78, 2022
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7WB6
 | | Crystal structure of Bovine Pancreatic Trypsin in complex with 4-Bromobenzamidine at Room Temperature | | Descriptor: | 4-bromanylbenzenecarboximidamide, CALCIUM ION, Cationic trypsin, ... | | Authors: | Sakai, N, Okumura, H, Yamamoto, M, Kumasaka, T. | | Deposit date: | 2021-12-15 | | Release date: | 2022-06-15 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.48 Å) | | Cite: | In situ crystal data-collection and ligand-screening system at SPring-8.
Acta Crystallogr.,Sect.F, 78, 2022
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7WB9
 | | Crystal structure of Bovine Pancreatic Trypsin in complex with 5-Chlorotryptamine at Room Temperature | | Descriptor: | 2-(5-chloranyl-1~{H}-indol-3-yl)ethanamine, CALCIUM ION, Cationic trypsin, ... | | Authors: | Sakai, N, Okumura, H, Yamamoto, M, Kumasaka, T. | | Deposit date: | 2021-12-15 | | Release date: | 2022-06-15 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.56 Å) | | Cite: | In situ crystal data-collection and ligand-screening system at SPring-8.
Acta Crystallogr.,Sect.F, 78, 2022
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7WA0
 | | Crystal structure of Bovine Pancreatic Trypsin in complex with Benzamidine at Room Temperature | | Descriptor: | BENZAMIDINE, CALCIUM ION, Cationic trypsin, ... | | Authors: | Sakai, N, Okumura, H, Yamamoto, M, Kumasaka, T. | | Deposit date: | 2021-12-11 | | Release date: | 2022-06-15 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.77 Å) | | Cite: | In situ crystal data-collection and ligand-screening system at SPring-8.
Acta Crystallogr.,Sect.F, 78, 2022
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7WBA
 | | Crystal structure of Bovine Pancreatic Trypsin in complex with Tryptamine at Room Temperature | | Descriptor: | 2-(1H-INDOL-3-YL)ETHANAMINE, CALCIUM ION, Cationic trypsin, ... | | Authors: | Sakai, N, Okumura, H, Yamamoto, M, Kumasaka, T. | | Deposit date: | 2021-12-15 | | Release date: | 2022-06-15 | | Last modified: | 2024-10-16 | | Method: | X-RAY DIFFRACTION (1.45 Å) | | Cite: | In situ crystal data-collection and ligand-screening system at SPring-8.
Acta Crystallogr.,Sect.F, 78, 2022
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7WA2
 | | Crystal structure of Bovine Pancreatic Trypsin in complex with 4-Methoxybenzamidine at Room Temperature | | Descriptor: | 4-methoxybenzenecarboximidamide, CALCIUM ION, Cationic trypsin, ... | | Authors: | Sakai, N, Okumura, H, Yamamoto, M, Kumasaka, T. | | Deposit date: | 2021-12-11 | | Release date: | 2022-06-15 | | Last modified: | 2024-10-23 | | Method: | X-RAY DIFFRACTION (1.52 Å) | | Cite: | In situ crystal data-collection and ligand-screening system at SPring-8.
Acta Crystallogr.,Sect.F, 78, 2022
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7WB7
 | | Crystal structure of Bovine Pancreatic Trypsin in complex with Serotonin at Room Temperature | | Descriptor: | CALCIUM ION, Cationic trypsin, DIMETHYL SULFOXIDE, ... | | Authors: | Sakai, N, Okumura, H, Yamamoto, M, Kumasaka, T. | | Deposit date: | 2021-12-15 | | Release date: | 2022-06-15 | | Last modified: | 2024-10-16 | | Method: | X-RAY DIFFRACTION (1.45 Å) | | Cite: | In situ crystal data-collection and ligand-screening system at SPring-8.
Acta Crystallogr.,Sect.F, 78, 2022
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3WCK
 | | Crystal structure of monomeric photosensitizing fluorescent protein, Supernova | | Descriptor: | Monomeric photosenitizing fluorescent protein supernova | | Authors: | Sakai, N, Matsuda, T, Takemoto, K, Nagai, T. | | Deposit date: | 2013-05-27 | | Release date: | 2013-10-02 | | Last modified: | 2023-11-15 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | SuperNova, a monomeric photosensitizing fluorescent protein for chromophore-assisted light inactivation
Sci Rep, 3, 2013
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7C3G
 | | Crystal structure of human ALK2 kinase domain with R206H mutation in complex with a bicyclic pyrazole inhibitor RK-73134 | | Descriptor: | 1,2-ETHANEDIOL, Activin receptor type-1, SULFATE ION, ... | | Authors: | Sakai, N, Mishima-Tsumagari, C, Matsumoto, T, Shirouzu, M. | | Deposit date: | 2020-05-12 | | Release date: | 2021-03-03 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.802 Å) | | Cite: | Novel bicyclic pyrazoles as potent ALK2 (R206H) inhibitors for the treatment of fibrodysplasia ossificans progressiva.
Bioorg.Med.Chem.Lett., 38, 2021
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6ACR
 | | Crystal structure of human ALK2 kinase domain with R206H mutation in complex with RK-59638 | | Descriptor: | Activin receptor type-1, N-(4-methoxyphenyl)-4-[3-(pyridin-3-yl)-1H-pyrazol-4-yl]pyrimidin-2-amine, SULFATE ION | | Authors: | Sakai, N, Mishima-Tsumagari, C, Matsumoto, T, Shirouzu, M. | | Deposit date: | 2018-07-27 | | Release date: | 2019-03-20 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.01 Å) | | Cite: | Bis-Heteroaryl Pyrazoles: Identification of Orally Bioavailable Inhibitors of Activin Receptor-Like Kinase-2 (R206H).
Chem. Pharm. Bull., 67, 2019
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5NGN
 | | Lybatide 2, a cystine-rich peptide from Lycium barbarum | | Descriptor: | ACETONITRILE, GLYCEROL, TETRAETHYLENE GLYCOL, ... | | Authors: | Lei, J, Tan, W.L, Sakai, N, Hilgenfeld, R. | | Deposit date: | 2017-03-18 | | Release date: | 2017-07-26 | | Last modified: | 2024-10-16 | | Method: | X-RAY DIFFRACTION (1.48 Å) | | Cite: | Lybatides from Lycium barbarum Contain An Unusual Cystine-stapled Helical Peptide Scaffold.
Sci Rep, 7, 2017
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8J9F
 | | Structure of STG-hydrolyzing beta-glucosidase 1 (PSTG1) | | Descriptor: | Beta-glucosidase, GLYCEROL | | Authors: | Yanai, T, Imaizumi, R, Takahashi, Y, Katsumura, E, Yamamoto, M, Nakayama, T, Yamashita, S, Takeshita, K, Sakai, N, Matsuura, H. | | Deposit date: | 2023-05-03 | | Release date: | 2024-04-10 | | Last modified: | 2024-07-17 | | Method: | X-RAY DIFFRACTION (2.85 Å) | | Cite: | Structural insights into a bacterial beta-glucosidase capable of degrading sesaminol triglucoside to produce sesaminol: toward the understanding of the aglycone recognition mechanism by the C-terminal lid domain.
J.Biochem., 174, 2023
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8X36
 | | Neryl diphosphate synthase from Solanum lycopersicum complexed with DMSAPP, IPP, and magnesium ion (form B) | | Descriptor: | 3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE, DIMETHYLALLYL S-THIOLODIPHOSPHATE, MAGNESIUM ION, ... | | Authors: | Imaizumi, R, Matsuura, H, Yanai, T, Takeshita, K, Misawa, S, Yamaguchi, H, Sakai, N, Miyagi-Inoue, Y, Suenaga-Hiromori, M, Kataoka, K, Nakayama, T, Yamamoto, M, Takahashi, S, Yamashita, S. | | Deposit date: | 2023-11-12 | | Release date: | 2024-02-07 | | Last modified: | 2024-10-09 | | Method: | X-RAY DIFFRACTION (2.28 Å) | | Cite: | Structural-Functional Correlations between Unique N-terminal Region and C-terminal Conserved Motif in Short-chain cis-Prenyltransferase from Tomato.
Chembiochem, 25, 2024
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8X35
 | | Neryl diphosphate synthase from Solanum lycopersicum complexed with DMSAPP, IPP, and magnesium ion (form A) | | Descriptor: | 1,2-ETHANEDIOL, 3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE, DI(HYDROXYETHYL)ETHER, ... | | Authors: | Imaizumi, R, Matsuura, H, Yanai, T, Takeshita, K, Misawa, S, Yamaguchi, H, Sakai, N, Miyagi-Inoue, Y, Suenaga-Hiromori, M, Kataoka, K, Nakayama, T, Yamamoto, M, Takahashi, S, Yamashita, S. | | Deposit date: | 2023-11-12 | | Release date: | 2024-02-07 | | Last modified: | 2024-10-23 | | Method: | X-RAY DIFFRACTION (1.92 Å) | | Cite: | Structural-Functional Correlations between Unique N-terminal Region and C-terminal Conserved Motif in Short-chain cis-Prenyltransferase from Tomato.
Chembiochem, 25, 2024
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8X37
 | | Neryl diphosphate synthase from Solanum lycopersicum complexed with DMSAPP | | Descriptor: | DIMETHYLALLYL S-THIOLODIPHOSPHATE, MAGNESIUM ION, Neryl-diphosphate synthase 1 | | Authors: | Imaizumi, R, Matsuura, H, Yanai, T, Takeshita, K, Misawa, S, Yamaguchi, H, Sakai, N, Miyagi-Inoue, Y, Suenaga-Hiromori, M, Kataoka, K, Nakayama, T, Yamamoto, M, Takahashi, S, Yamashita, S. | | Deposit date: | 2023-11-12 | | Release date: | 2024-02-07 | | Last modified: | 2024-04-24 | | Method: | X-RAY DIFFRACTION (1.98 Å) | | Cite: | Structural-Functional Correlations between Unique N-terminal Region and C-terminal Conserved Motif in Short-chain cis-Prenyltransferase from Tomato.
Chembiochem, 25, 2024
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8GQ1
 | | HyHEL10 Fab complexed with hen egg lysozyme carrying arginine cluster in framework region of light chain. | | Descriptor: | Heavy Chain of HyHel10 Antibody Fragment (Fab), Light Chain of HyHel10 Antibody Fragment (Fab), Lysozyme C, ... | | Authors: | Matsuura, H, Hirata, K, Sakai, N, Nakakido, M, Tsumoto, K. | | Deposit date: | 2022-08-28 | | Release date: | 2023-08-30 | | Last modified: | 2024-10-16 | | Method: | X-RAY DIFFRACTION (3.13 Å) | | Cite: | Arginine cluster introduction on framework region in anti-lysozyme antibody improved association rate constant by changing conformational diversity of CDR loops.
Protein Sci., 32, 2023
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8JRD
 | | Chalcone synthase from Glycine max (L.) Merr (soybean) complexed with naringenin and coenzyme A | | Descriptor: | 1,2-ETHANEDIOL, COENZYME A, DI(HYDROXYETHYL)ETHER, ... | | Authors: | Waki, T, Imaizumi, R, Nakata, S, Yanai, T, Takeshita, K, Sakai, N, Kataoka, K, Yamamoto, M, Nakayama, T, Yamashita, S. | | Deposit date: | 2023-06-16 | | Release date: | 2024-06-19 | | Last modified: | 2024-07-17 | | Method: | X-RAY DIFFRACTION (1.83 Å) | | Cite: | Structural insights into catalytic promiscuity of chalcone synthase from Glycine max (L.) Merr.: Coenzyme A-induced alteration of product specificity.
Biochem.Biophys.Res.Commun., 718, 2024
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8KGA
 | | SlNDPS1-AtcPT4 Chimera | | Descriptor: | 1,2-ETHANEDIOL, DI(HYDROXYETHYL)ETHER, Dimethylallylcistransferase CPT1, ... | | Authors: | Suenaga-Hiromori, M, Ishii, T, Imaizumi, R, Takeshita, K, Yanai, T, Matsuura, H, Sakai, N, Yamaguchi, H, Yanbe, F, Waki, T, Tozawa, Y, Miyagi-Inoue, Y, Yamamoto, M, Kataoka, K, Nakayama, T, Yamashita, S, Takahashi, S. | | Deposit date: | 2023-08-18 | | Release date: | 2024-08-21 | | Method: | X-RAY DIFFRACTION (2.182 Å) | | Cite: | Biosynthesising various rubber-like polymers by reconstituting prenyltransferases on Hevea rubber particles: molecular and structural bases of the versatile system
To Be Published
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8KGB
 | | SlNDPS1-AtcPT4 Chimera complexed with GSPP, Mg2+, and IPP | | Descriptor: | 3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE, Dimethylallylcistransferase CPT1, chloroplastic,Dehydrodolichyl diphosphate synthase 2, ... | | Authors: | Suenaga-Hiromori, M, Ishii, T, Imaizumi, R, Takeshita, K, Yanai, T, Matsuura, H, Sakai, N, Yamaguchi, H, Yanbe, F, Waki, T, Tozawa, Y, Miyagi-Inoue, Y, Yamamoto, M, Kataoka, K, Nakayama, T, Yamashita, S, Takahashi, S. | | Deposit date: | 2023-08-18 | | Release date: | 2024-08-21 | | Last modified: | 2024-10-30 | | Method: | X-RAY DIFFRACTION (2.32 Å) | | Cite: | A versatile system for enzymatic synthesis of natural and unnatural polyisoprenoids on rubber particles
To Be Published
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8H4M
 | | Crystal Structure of GTP-bound Irgb6_T95D mutant | | Descriptor: | GUANOSINE-5'-TRIPHOSPHATE, T-cell-specific guanine nucleotide triphosphate-binding protein 2 | | Authors: | Saijo-Hamano, Y, Okuma, H, Sakai, N, Kato, T, Imasaki, T, Nitta, R. | | Deposit date: | 2022-10-10 | | Release date: | 2023-10-18 | | Method: | X-RAY DIFFRACTION (1.68 Å) | | Cite: | Structural basis of Irgb6 inactivation by Toxoplasma gondii through the phosphorylation of switch I
To Be Published
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8H4O
 | | Crystal Structure of nucleotide-free Irgb6_T95D mutant | | Descriptor: | T-cell-specific guanine nucleotide triphosphate-binding protein 2 | | Authors: | Saijo-Hamano, Y, Okuma, H, Sakai, N, Kato, T, Imasaki, T, Nitta, R. | | Deposit date: | 2022-10-11 | | Release date: | 2023-10-18 | | Last modified: | 2024-07-03 | | Method: | X-RAY DIFFRACTION (2.05 Å) | | Cite: | Structural basis of Irgb6 inactivation by Toxoplasma gondii through the phosphorylation of switch I.
Genes Cells, 29, 2024
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