1PRV
 
 | | PURINE REPRESSOR DNA-BINDING DOMAIN DNA BINDING | | Descriptor: | PURINE REPRESSOR | | Authors: | Nagadoi, A, Morikawa, S, Nakamura, H, Enari, M, Kobayashi, K, Yamamoto, H, Sampei, G, Mizobuchi, K, Schumacher, M.A, Brennan, R.G, Nishimura, Y. | | Deposit date: | 1995-05-08 | | Release date: | 1996-03-08 | | Last modified: | 2024-05-01 | | Method: | SOLUTION NMR | | Cite: | Structural comparison of the free and DNA-bound forms of the purine repressor DNA-binding domain.
Structure, 3, 1995
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6Y1N
 | | Crystal structure of the phosphonate-modified A.5 antibody FAB fragment | | Descriptor: | 8-METHYL-8-AZABICYCLO[3.2.1]OCTAN-3-YL PHENYLPHOSPHONATE, FAB A.5 Heavy chain, FAB A.5 Light Chain | | Authors: | Chatziefthimiou, S, Mokrushina, Y, Smirnov, I, Gabibov, A, Wilmanns, M. | | Deposit date: | 2020-02-12 | | Release date: | 2020-09-23 | | Last modified: | 2024-01-24 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Multiscale computation delivers organophosphorus reactivity and stereoselectivity to immunoglobulin scavengers.
Proc.Natl.Acad.Sci.USA, 117, 2020
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1VA2
 | | Solution Structure of Transcription Factor Sp1 DNA Binding Domain (Zinc Finger 2) | | Descriptor: | Transcription factor Sp1, ZINC ION | | Authors: | Oka, S, Shiraishi, Y, Yoshida, T, Ohkubo, T, Sugiura, Y, Kobayashi, Y. | | Deposit date: | 2004-02-07 | | Release date: | 2005-02-08 | | Last modified: | 2023-12-27 | | Method: | SOLUTION NMR | | Cite: | NMR structure of transcription factor Sp1 DNA binding domain
Biochemistry, 43, 2004
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1BZA
 | | BETA-LACTAMASE TOHO-1 FROM ESCHERICHIA COLI TUH12191 | | Descriptor: | BETA-LACTAMASE, SULFATE ION | | Authors: | Ibuka, A, Taguchi, A, Ishiguro, M, Fushinobu, S, Ishii, Y, Kamitori, S, Okuyama, K, Yamaguchi, K, Konno, M, Matsuzawa, H. | | Deposit date: | 1998-10-28 | | Release date: | 1999-04-27 | | Last modified: | 2024-05-22 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Crystal structure of the E166A mutant of extended-spectrum beta-lactamase Toho-1 at 1.8 A resolution.
J.Mol.Biol., 285, 1999
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1KW6
 | | Crystal structure of 2,3-dihydroxybiphenyl dioxygenase (BphC) in complex with 2,3-dihydroxybiphenyl at 1.45 A resolution | | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, 2,3-Dihydroxybiphenyl dioxygenase, BIPHENYL-2,3-DIOL, ... | | Authors: | Sato, N, Uragami, Y, Nishizaki, T, Takahashi, Y, Sazaki, G, Sugimoto, K, Nonaka, T, Masai, E, Fukuda, M, Senda, T. | | Deposit date: | 2002-01-28 | | Release date: | 2003-01-28 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (1.45 Å) | | Cite: | Crystal Structures of the Reaction Intermediate and its Homologue of an Extradiol-cleaving Catecholic Dioxygenase
J.Mol.Biol., 321, 2002
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7D7U
 | | Crystal structure of Ago2 MID domain in complex with 8-Br-adenosin-5'-monophosphate | | Descriptor: | 8-BROMO-ADENOSINE-5'-MONOPHOSPHATE, Protein argonaute-2 | | Authors: | Suzuki, M, Takahashi, Y, Saito, J, Miyagi, H, Shinohara, F. | | Deposit date: | 2020-10-06 | | Release date: | 2020-11-25 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | siRNA potency enhancement via chemical modifications of nucleotide bases at the 5'-end of the siRNA guide strand.
Rna, 27, 2021
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1VA3
 | | Solution Structure of Transcription Factor Sp1 DNA Binding Domain (Zinc Finger 3) | | Descriptor: | Transcription factor Sp1, ZINC ION | | Authors: | Oka, S, Shiraishi, Y, Yoshida, T, Ohkubo, T, Sugiura, Y, Kobayashi, Y. | | Deposit date: | 2004-02-07 | | Release date: | 2005-02-08 | | Last modified: | 2023-12-27 | | Method: | SOLUTION NMR | | Cite: | NMR structure of transcription factor Sp1 DNA binding domain
Biochemistry, 43, 2004
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1VA1
 | | Solution Structure of Transcription Factor Sp1 DNA Binding Domain (Zinc Finger 1) | | Descriptor: | Transcription factor Sp1, ZINC ION | | Authors: | Oka, S, Shiraishi, Y, Yoshida, T, Ohkubo, T, Sugiura, Y, Kobayashi, Y. | | Deposit date: | 2004-02-07 | | Release date: | 2005-02-08 | | Last modified: | 2023-12-27 | | Method: | SOLUTION NMR | | Cite: | NMR structure of transcription factor Sp1 DNA binding domain
Biochemistry, 43, 2004
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1BA5
 | | DNA-BINDING DOMAIN OF HUMAN TELOMERIC PROTEIN, HTRF1, NMR, 18 STRUCTURES | | Descriptor: | HTRF1 | | Authors: | Nishikawa, T, Nagadoi, A, Yoshimura, S, Aimoto, S, Nishimura, Y. | | Deposit date: | 1998-04-22 | | Release date: | 1999-04-27 | | Last modified: | 2024-05-22 | | Method: | SOLUTION NMR | | Cite: | Solution structure of the DNA-binding domain of human telomeric protein, hTRF1.
Structure, 6, 1998
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3W08
 | | Crystal structure of aldoxime dehydratase | | Descriptor: | Aldoxime dehydratase, PROTOPORPHYRIN IX CONTAINING FE | | Authors: | Hashimoto, H, Nomura, J, Hashimoto, Y, Oinuma, K.I, Wada, K, Hishiki, A, Hara, K, Kobayashi, M. | | Deposit date: | 2012-10-24 | | Release date: | 2013-02-20 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Crystal structure of aldoxime dehydratase and its catalytic mechanism involved in carbon-nitrogen triple-bond synthesis.
Proc.Natl.Acad.Sci.USA, 110, 2013
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3WFE
 | | Reduced and cyanide-bound cytochrome c-dependent nitric oxide reductase (cNOR) from Pseudomonas aeruginosa in complex with antibody fragment | | Descriptor: | CALCIUM ION, CYANIDE ION, FE (III) ION, ... | | Authors: | Sato, N, Ishii, S, Hino, T, Sugimoto, H, Fukumori, Y, Shiro, Y, Tosha, T. | | Deposit date: | 2013-07-18 | | Release date: | 2014-05-28 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.49 Å) | | Cite: | Structures of reduced and ligand-bound nitric oxide reductase provide insights into functional differences in respiratory enzymes.
Proteins, 82, 2014
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8JLB
 | | Cryo-EM structure of the 145 bp human nucleosome containing H3.2 C110A mutant | | Descriptor: | DNA (145-MER), Histone H2A type 1-B/E, Histone H2B type 1-J, ... | | Authors: | Oishi, T, Hatazawa, S, Kujirai, T, Kato, J, Kobayashi, Y, Ogasawara, M, Akatsu, M, Takizawa, Y, Kurumizaka, H. | | Deposit date: | 2023-06-02 | | Release date: | 2023-10-04 | | Last modified: | 2023-11-08 | | Method: | ELECTRON MICROSCOPY (2.36 Å) | | Cite: | Contributions of histone tail clipping and acetylation in nucleosome transcription by RNA polymerase II.
Nucleic Acids Res., 51, 2023
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8JL9
 | | Cryo-EM structure of the human nucleosome with scFv | | Descriptor: | DNA (193-MER), Histone H2A type 1-B/E, Histone H2B type 1-J, ... | | Authors: | Oishi, T, Hatazawa, S, Kujirai, T, Kato, J, Kobayashi, Y, Ogasawara, M, Akatsu, M, Takizawa, Y, Kurumizaka, H. | | Deposit date: | 2023-06-02 | | Release date: | 2023-10-04 | | Last modified: | 2023-11-08 | | Method: | ELECTRON MICROSCOPY (2.65 Å) | | Cite: | Contributions of histone tail clipping and acetylation in nucleosome transcription by RNA polymerase II.
Nucleic Acids Res., 51, 2023
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8JLD
 | | Cryo-EM structure of the 145 bp human nucleosome containing acetylated H3 tail | | Descriptor: | DNA (145-MER), Histone H2A type 1-B/E, Histone H2B type 1-J, ... | | Authors: | Oishi, T, Hatazawa, S, Kujirai, T, Kato, J, Kobayashi, Y, Ogasawara, M, Akatsu, M, Takizawa, Y, Kurumizaka, H. | | Deposit date: | 2023-06-02 | | Release date: | 2023-10-04 | | Last modified: | 2023-11-15 | | Method: | ELECTRON MICROSCOPY (2.48 Å) | | Cite: | Contributions of histone tail clipping and acetylation in nucleosome transcription by RNA polymerase II.
Nucleic Acids Res., 51, 2023
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8JLA
 | | Cryo-EM structure of the human nucleosome lacking N-terminal region of H2A, H2B, H3, and H4 | | Descriptor: | DNA (193-MER), Histone H2A type 1-B/E, Histone H2B type 1-J, ... | | Authors: | Oishi, T, Hatazawa, S, Kujirai, T, Kato, J, Kobayashi, Y, Ogasawara, M, Akatsu, M, Takizawa, Y, Kurumizaka, H. | | Deposit date: | 2023-06-02 | | Release date: | 2023-10-04 | | Last modified: | 2023-11-08 | | Method: | ELECTRON MICROSCOPY (3.44 Å) | | Cite: | Contributions of histone tail clipping and acetylation in nucleosome transcription by RNA polymerase II.
Nucleic Acids Res., 51, 2023
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3WFC
 | | Reduced and carbonmonoxide-bound cytochrome c-dependent nitric oxide reductase (cNOR) from Pseudomonas aeruginosa in complex with antibody fragment | | Descriptor: | CALCIUM ION, CARBON MONOXIDE, FE (III) ION, ... | | Authors: | Sato, N, Ishii, S, Hino, T, Sugimoto, H, Fukumori, Y, Shiro, Y, Tosha, T. | | Deposit date: | 2013-07-18 | | Release date: | 2014-05-28 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Structures of reduced and ligand-bound nitric oxide reductase provide insights into functional differences in respiratory enzymes.
Proteins, 82, 2014
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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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2ISM
 | | Crystal structure of the putative oxidoreductase (glucose dehydrogenase) (TTHA0570) from thermus theromophilus HB8 | | Descriptor: | CALCIUM ION, CHLORIDE ION, Putative oxidoreductase | | Authors: | Jeyakanthan, J, Kanaujia, S.P, Vasuki Ranjani, C, Sekar, K, Ebihara, A, Shinkai, A, Nakagawa, N, Shimizu, N, Yamamoto, M, Kuramitsu, S, Shiro, Y, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2006-10-18 | | Release date: | 2007-11-13 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Crystal Structure of the Putative Oxidoreductase (Glucose Dehydrogenase) (TTHA0570) from Thermus Theromophilus HB8
To be Published
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3WFD
 | | Reduced and acetaldoxime-bound cytochrome c-dependent nitric oxide reductase (cNOR) from Pseudomonas aeruginosa in complex with antibody fragment | | Descriptor: | (1E)-N-hydroxyethanimine, CALCIUM ION, FE (III) ION, ... | | Authors: | Sato, N, Ishii, S, Hino, T, Sugimoto, H, Fukumori, Y, Shiro, Y, Tosha, T. | | Deposit date: | 2013-07-18 | | Release date: | 2014-05-28 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Structures of reduced and ligand-bound nitric oxide reductase provide insights into functional differences in respiratory enzymes.
Proteins, 82, 2014
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8JOF
 | | solution-structure of Ras Binding Domain (RBD) in C-RAF | | Descriptor: | RAF proto-oncogene serine/threonine-protein kinase | | Authors: | Makino, Y, Matsumoto, S, Yoshikawa, Y, Kawamura, T, Kumasaka, T, Shima, F. | | Deposit date: | 2023-06-07 | | Release date: | 2024-06-12 | | Method: | SOLUTION NMR | | Cite: | Small-molecule RAS/RAF-binding Inhibitors Allosterically Disrupt RAF Conformation and Exert Efficacy Against Broad-spectrum RAS-driven Cancers
To Be Published
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8JOG
 | | solution structure of Ras Binding Domein (RBD) in C-RAF with negative allosteric modulator. | | Descriptor: | RAF proto-oncogene serine/threonine-protein kinase | | Authors: | Makino, Y, Matsumoto, S, Yoshikawa, Y, Kawamura, T, Kumasaka, T, Shima, F. | | Deposit date: | 2023-06-07 | | Release date: | 2024-06-12 | | Method: | SOLUTION NMR | | Cite: | Small-molecule RAS/RAF-binding Inhibitors Allosterically Disrupt RAF Conformation and Exert Efficacy Against Broad-spectrum RAS-driven Cancers
To Be Published
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6C9H
 | | non-phosphorylated AMP-activated protein kinase bound to pharmacological activator R734 | | Descriptor: | 5'-AMP-activated protein kinase catalytic subunit alpha-1, 5'-AMP-activated protein kinase subunit beta-1, 5'-AMP-activated protein kinase subunit gamma-1, ... | | Authors: | Yan, Y, Zhou, X.E, Novick, S, Shaw, S.J, Li, Y, Hitoshi, Y, Brunzelle, J.S, Griffin, P.R, Xu, H.E, Melcher, K. | | Deposit date: | 2018-01-26 | | Release date: | 2018-11-28 | | Last modified: | 2023-10-04 | | Method: | X-RAY DIFFRACTION (2.65 Å) | | Cite: | Structures of AMP-activated protein kinase bound to novel pharmacological activators in phosphorylated, non-phosphorylated, and nucleotide-free states.
J. Biol. Chem., 294, 2019
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1JFB
 | | X-ray structure of nitric oxide reductase (cytochrome P450nor) in the ferric resting state at atomic resolution | | Descriptor: | GLYCEROL, PROTOPORPHYRIN IX CONTAINING FE, nitric-oxide reductase cytochrome P450 55A1 | | Authors: | Shimizu, H, Adachi, S, Park, S.Y, Shiro, Y, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2001-06-20 | | Release date: | 2001-12-20 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (1 Å) | | Cite: | X-ray structure of nitric oxide reductase (cytochrome P450nor) at atomic resolution.
Acta Crystallogr.,Sect.D, 58, 2002
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8JVG
 | | Crystal structure of dephospho-coenzyme A kinase | | Descriptor: | GTP-dependent dephospho-CoA kinase | | Authors: | Kita, A, Ishida, Y, Shimosaka, T, Michimori, Y, Makarova, K, Koonin, E, Atomi, H, Miki, K. | | Deposit date: | 2023-06-28 | | Release date: | 2024-06-19 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Crystal structure of GTP-dependent dephospho-coenzyme A kinase from the hyperthermophilic archaeon, Thermococcus kodakarensis.
Proteins, 92, 2024
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8JVC
 | | Crystal structure of dephospho-coenzyme A kinase | | Descriptor: | GTP-dependent dephospho-CoA kinase | | Authors: | Kita, A, Ishida, Y, Shimosaka, T, Michimori, Y, Makarova, K, Koonin, E, Atomi, H, Miki, K. | | Deposit date: | 2023-06-28 | | Release date: | 2024-06-19 | | Method: | X-RAY DIFFRACTION (2.15 Å) | | Cite: | Crystal structure of GTP-dependent dephospho-coenzyme A kinase from the hyperthermophilic archaeon, Thermococcus kodakarensis.
Proteins, 92, 2024
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