1BQT
| THREE-DIMENSIONAL STRUCTURE OF HUMAN INSULIN-LIKE GROWTH FACTOR-I (IGF-I) DETERMINED BY 1H-NMR AND DISTANCE GEOMETRY, 6 STRUCTURES | Descriptor: | INSULIN-LIKE GROWTH FACTOR-I | Authors: | Sato, A, Nishimura, S, Ohkubo, T, Kyogoku, Y, Koyama, S, Kobayashi, M, Yasuda, T, Kobayashi, Y. | Deposit date: | 1998-08-18 | Release date: | 1999-05-18 | Last modified: | 2022-02-16 | Method: | SOLUTION NMR | Cite: | Three-dimensional structure of human insulin-like growth factor-I (IGF-I) determined by 1H-NMR and distance geometry. Int.J.Pept.Protein Res., 41, 1993
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1BQF
| GROWTH-BLOCKING PEPTIDE (GBP) FROM PSEUDALETIA SEPARATA | Descriptor: | PROTEIN (GROWTH-BLOCKING PEPTIDE) | Authors: | Aizawa, T, Fujitani, N, Hayakawa, Y, Ohnishi, A, Ohkubo, T, Kwano, K, Hikichi, K, Nitta, K. | Deposit date: | 1998-08-09 | Release date: | 1998-12-09 | Last modified: | 2023-12-27 | Method: | SOLUTION NMR | Cite: | Solution structure of an insect growth factor, growth-blocking peptide. J.Biol.Chem., 274, 1999
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1O5P
| Solution Structure of holo-Neocarzinostatin | Descriptor: | NEOCARZINOSTATIN-CHROMOPHORE, Neocarzinostatin | Authors: | Takashima, H, Ishino, T, Yoshida, T, Hasuda, K, Ohkubo, T, Kobayashi, Y. | Deposit date: | 2003-10-04 | Release date: | 2003-10-14 | Last modified: | 2023-12-27 | Method: | SOLUTION NMR | Cite: | Solution NMR Structure Investigation for Releasing Mechanism of Neocarzinostatin Chromophore from the Holoprotein J.Biol.Chem., 280, 2005
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7EAD
| Crystal structure of beta-sheet cytochrome c prime from Thermus thermophilus. | Descriptor: | Cytochrome_P460 domain-containing protein, HEME C | Authors: | Yoshimi, T, Fujii, S, Oki, H, Igawa, T, Adams, R.H, Ueda, K, Kawahara, K, Ohkubo, T, Hough, A.M, Sambongi, Y. | Deposit date: | 2021-03-07 | Release date: | 2022-03-09 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (1.74 Å) | Cite: | Crystal structure of thermally stable homodimeric cytochrome c'-beta from Thermus thermophilus. Acta Crystallogr.,Sect.F, 78, 2022
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5H03
| Crystal structure of an ADP-ribosylating toxin BECa from C. perfringens | Descriptor: | Binary enterotoxin of Clostridium perfringens component a | Authors: | Kawahara, K, Yonogi, S, Munetomo, R, Oki, H, Yoshida, T, Ohkubo, T, Kumeda, Y, Matsuda, S, Kodama, T, Iida, T, Nakamura, S. | Deposit date: | 2016-10-03 | Release date: | 2016-11-02 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.89 Å) | Cite: | Crystal structure of the ADP-ribosylating component of BEC, the binary enterotoxin of Clostridium perfringens. Biochem.Biophys.Res.Commun., 480, 2016
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5H04
| Crystal structure of an ADP-ribosylating toxin BECa of a novel binary enterotoxin of C. perfringens with NADH | Descriptor: | 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE, Binary enterotoxin of Clostridium perfringens component a | Authors: | Kawahara, K, Yonogi, S, Munetomo, R, Oki, H, Yoshida, T, Ohkubo, T, Kumeda, Y, Matsuda, S, Kodama, T, Iida, T, Nakamura, S. | Deposit date: | 2016-10-03 | Release date: | 2016-11-02 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.825 Å) | Cite: | Crystal structure of the ADP-ribosylating component of BEC, the binary enterotoxin of Clostridium perfringens. Biochem.Biophys.Res.Commun., 480, 2016
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4U4P
| Crystal structure of the human condensin SMC hinge domain heterodimer with short coiled coils | Descriptor: | Structural maintenance of chromosomes protein 2, Structural maintenance of chromosomes protein 4 | Authors: | Uchiyama, S, Kawahara, K, Hosokawa, Y, Fukakusa, S, Oki, H, Nakamura, S, Noda, M, Takino, R, Miyahara, Y, Maruno, T, Kobayashi, Y, Ohkubo, T, Fukui, K. | Deposit date: | 2014-07-24 | Release date: | 2015-08-26 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.89 Å) | Cite: | Structural basis for dimer information and DNA recognition of human SMC proteins to be published
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5AX6
| The crystal structure of CofB, the minor pilin subunit of CFA/III from human enterotoxigenic Escherichia coli. | Descriptor: | ACETATE ION, CofB | Authors: | Kawahara, K, Oki, K, Fukaksua, F, Maruno, T, Kobayashi, Y, Daisuke, M, Taniguchi, T, Honda, T, Iida, T, Nakamura, S, Ohkubo, T. | Deposit date: | 2015-07-16 | Release date: | 2016-03-09 | Last modified: | 2020-02-26 | Method: | X-RAY DIFFRACTION (1.88 Å) | Cite: | Homo-trimeric Structure of the Type IVb Minor Pilin CofB Suggests Mechanism of CFA/III Pilus Assembly in Human Enterotoxigenic Escherichia coli J.Mol.Biol., 428, 2016
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1GE9
| SOLUTION STRUCTURE OF THE RIBOSOME RECYCLING FACTOR | Descriptor: | RIBOSOME RECYCLING FACTOR | Authors: | Yoshida, T, Uchiyama, S, Nakano, H, Kashimori, H, Kijima, H, Ohshima, T, Saihara, Y, Ishino, T, Shimahara, T, Yoshida, T, Yokose, K, Ohkubo, T, Kaji, A, Kobayashi, Y. | Deposit date: | 2000-10-19 | Release date: | 2001-05-16 | Last modified: | 2023-12-27 | Method: | SOLUTION NMR | Cite: | Solution structure of the ribosome recycling factor from Aquifex aeolicus. Biochemistry, 40, 2001
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8H28
| Crystal structure of the K87V mutant of cytochrome c' from Shewanella benthica DB6705 | Descriptor: | Class II cytochrome c, HEME C | Authors: | Fujii, S, Sakaguchi, R, Oki, H, Kawahara, K, Ohkubo, T, Fujiyoshi, S, Sambongi, Y. | Deposit date: | 2022-10-05 | Release date: | 2023-10-11 | Last modified: | 2024-04-24 | Method: | X-RAY DIFFRACTION (2.06 Å) | Cite: | Contribution of a surface salt bridge to the protein stability of deep-sea Shewanella benthica cytochrome c'. J.Struct.Biol., 215, 2023
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3B2C
| Crystal structure of the collagen triple helix model [{PRO-HYP(R)-GLY}4-{HYP(S)-Pro-GLY}2-{PRO-HYP(R)-GLY}4]3 | Descriptor: | Collagen-like peptide | Authors: | Motooka, D, Kawahara, K, Nakamura, S, Doi, M, Nishi, Y, Nishiuchi, Y, Nakazawa, T, Yoshida, T, Ohkubo, T, Kobayashi, Y, Kang, Y.K, Uchiyama, S. | Deposit date: | 2011-07-26 | Release date: | 2012-04-04 | Method: | X-RAY DIFFRACTION (1.36 Å) | Cite: | The triple helical structure and stability of collagen model peptide with 4(S)-hydroxyprolyl-pro-gly units Biopolymers, 98, 2011
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2ZXY
| Crystal Structure of Cytochrome c555 from Aquifex aeolicus | Descriptor: | Cytochrome c552, HEME C | Authors: | Obuchi, M, Kawahara, K, Motooka, D, Nakamura, S, Yamanaka, M, Takeda, T, Uchiyama, S, Kobayashi, Y, Ohkubo, T, Sambongi, Y. | Deposit date: | 2009-01-09 | Release date: | 2009-08-04 | Last modified: | 2024-03-13 | Method: | X-RAY DIFFRACTION (1.15 Å) | Cite: | Hyperstability and crystal structure of cytochrome c(555) from hyperthermophilic Aquifex aeolicus Acta Crystallogr.,Sect.D, 65, 2009
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5B3I
| Homo-dimeric structure of cytochrome c' from Thermophilic Hydrogenophilus thermoluteolus | Descriptor: | Cytochrome c prime, HEME C | Authors: | Fujii, S, Oki, H, Kawahara, K, Yamane, D, Yamanaka, M, Maruno, T, Kobayashi, Y, Masanari, M, Wakai, S, Nishihara, H, Ohkubo, T, Sambongi, Y. | Deposit date: | 2016-02-29 | Release date: | 2017-03-01 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.89 Å) | Cite: | Structural and functional insights into thermally stable cytochrome c' from a thermophile Protein Sci., 26, 2017
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5B6Q
| Crystal structure of monomeric cytochrome c5 from Shewanella violacea | Descriptor: | HEME C, IMIDAZOLE, Soluble cytochrome cA | Authors: | Masanari, M, Fujii, S, Kawahara, K, Oki, H, Tsujino, H, Maruno, T, Kobayashi, Y, Ohkubo, T, Nishiyama, M, Harada, Y, Wakai, S, Sambongi, Y. | Deposit date: | 2016-06-01 | Release date: | 2016-10-19 | Last modified: | 2019-10-02 | Method: | X-RAY DIFFRACTION (1.78 Å) | Cite: | Comparative study on stabilization mechanism of monomeric cytochrome c5 from deep-sea piezophilic Shewanella violacea Biosci.Biotechnol.Biochem., 2016
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2KTD
| Solution structure of mouse lipocalin-type prostaglandin D synthase / substrate analog (U-46619) complex | Descriptor: | (5Z)-7-{(1R,4S,5S,6R)-6-[(1E,3S)-3-hydroxyoct-1-en-1-yl]-2-oxabicyclo[2.2.1]hept-5-yl}hept-5-enoic acid, Prostaglandin-H2 D-isomerase | Authors: | Shimamoto, S, Maruo, H, Yoshida, T, Kato, N, Ohkubo, T. | Deposit date: | 2010-01-27 | Release date: | 2011-02-02 | Last modified: | 2011-07-13 | Method: | SOLUTION NMR | Cite: | Solution Structure of Lipocalin-type Prostaglandin D synthase / Substrate analog complex reveals Open-Closed Conformational Change required for Substrate Recognition To be Published
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5YQ0
| Crystal structure of secreted protein CofJ from ETEC. | Descriptor: | CALCIUM ION, CofJ | Authors: | Oki, H, Kawahara, K, Maruno, T, Imai, T, Muroga, Y, Fukakusa, S, Iwashita, T, Kobayashi, Y, Matsuda, S, Kodama, T, Iida, T, Yoshida, T, Ohkubo, T, Nakamura, S. | Deposit date: | 2017-11-04 | Release date: | 2018-06-27 | Last modified: | 2018-07-25 | Method: | X-RAY DIFFRACTION (1.76 Å) | Cite: | Interplay of a secreted protein with type IVb pilus for efficient enterotoxigenicEscherichia colicolonization Proc. Natl. Acad. Sci. U.S.A., 115, 2018
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5YPZ
| Crystal structure of minor pilin CofB from CFA/III complexed with N-terminal peptide fragment of CofJ | Descriptor: | CofB, CofJ | Authors: | Oki, H, Kawahara, K, Maruno, T, Imai, T, Muroga, Y, Fukakusa, S, Iwashita, T, Kobayashi, Y, Matsuda, S, Kodama, T, Iida, T, Yoshida, T, Ohkubo, T, Nakamura, S. | Deposit date: | 2017-11-04 | Release date: | 2018-06-27 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (3.521 Å) | Cite: | Interplay of a secreted protein with type IVb pilus for efficient enterotoxigenicEscherichia colicolonization. Proc. Natl. Acad. Sci. U.S.A., 115, 2018
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1DHH
| NMR SOLUTION STRUCTURE OF THE DNA DUPLEX CONTAINING DNA/RNA HYBRID REGION, D(GG)R(AGAU)D(GAC)/D(GTCATCTCC) | Descriptor: | DNA (5'-D(*GP*TP*CP*AP*TP*CP*TP*CP*C)-3'), DNA/RNA (5'-D(*GP*G)-R(P*AP*GP*AP*U)-D(P*GP*AP*C)-3') | Authors: | Nishizaki, T, Iwai, S, Ohkubo, T, Kojima, C, Nakamura, H, Kyogoku, Y, Ohtsuka, E. | Deposit date: | 1995-10-18 | Release date: | 1996-04-03 | Last modified: | 2022-02-16 | Method: | SOLUTION NMR | Cite: | Solution Strucutres of DNA duplexes containing a DNA x RNA hybrid region, d(GG)r(AGAU)d(GAC) x d(GTCATCTCC) and d(GGAGA)r(UGAC) x d(GTCATCTCC). Biochemistry, 35, 1996
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1DRN
| NMR SOLUTION STRUCTURE OF THE DNA DUPLEX CONTAINING DNA/RNA HYBRID REGION, D(GGAGA)R(UGAC)/D(GTCATCTCC) | Descriptor: | DNA (5'-D(*GP*TP*CP*AP*TP*CP*TP*CP*C)-3'), DNA/RNA (5'-D(*GP*GP*AP*GP*A)-R(P*UP*GP*AP*C)-3') | Authors: | Nishizaki, T, Iwai, S, Ohkubo, T, Kojima, C, Nakamura, H, Kyogoku, Y, Ohtsuka, E. | Deposit date: | 1995-11-15 | Release date: | 1996-04-03 | Last modified: | 2022-02-16 | Method: | SOLUTION NMR | Cite: | Solution Strucutres of DNA duplexes containing a DNA x RNA hybrid region, d(GG)r(AGAU)d(GAC) x d(GTCATCTCC) and d(GGAGA)r(UGAC) x d(GTCATCTCC). Biochemistry, 35, 1996
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6KXX
| Human PPAR alpha ligand binding domain in complex with a synthetic agonist (compound A) | Descriptor: | 1-(4-chlorophenyl)-6-methyl-3-propan-2-yl-pyrazolo[3,4-b]pyridine-4-carboxylic acid, PGC1alpha, Peroxisome proliferator-activated receptor alpha | Authors: | Yoshida, T, Tachibana, K, Oki, H, Doi, M, Fukuda, S, Yuzuriha, T, Tabata, R, Ishimoto, K, Kawahara, K, Ohkubo, T, Miyachi, H, Doi, T. | Deposit date: | 2019-09-14 | Release date: | 2020-05-20 | Last modified: | 2024-03-27 | Method: | X-RAY DIFFRACTION (1.95 Å) | Cite: | Structural Basis for PPAR alpha Activation by 1H-pyrazolo-[3,4-b]pyridine Derivatives. Sci Rep, 10, 2020
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6KXY
| Human PPAR alpha ligand binding domain in complex with a synthetic agonist (compound B) | Descriptor: | 6-ethyl-1-(4-fluorophenyl)-3-pentan-3-yl-pyrazolo[3,4-b]pyridine-4-carboxylic acid, PGC1alpha, Peroxisome proliferator-activated receptor alpha | Authors: | Yoshida, T, Tachibana, K, Oki, H, Doi, M, Fukuda, S, Yuzuriha, T, Tabata, R, Ishimoto, K, Kawahara, K, Ohkubo, T, Miyachi, H, Doi, T. | Deposit date: | 2019-09-14 | Release date: | 2020-05-20 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Structural Basis for PPAR alpha Activation by 1H-pyrazolo-[3,4-b]pyridine Derivatives. Sci Rep, 10, 2020
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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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6LOS
| Crystal structure of mouse PEDF in complex with heterotrimeric collagen model peptide. | Descriptor: | Collagen model peptide, type I, alpha 1, ... | Authors: | Kawahara, K, Maruno, T, Oki, H, Yoshida, T, Ohkubo, T, Koide, T, Kobayashi, Y. | Deposit date: | 2020-01-07 | Release date: | 2020-09-02 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.476 Å) | Cite: | Spatiotemporal regulation of PEDF signaling by type I collagen remodeling. Proc.Natl.Acad.Sci.USA, 117, 2020
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2LAA
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2LAB
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