6A3K
| Crystal structure of cytochrome c' from Shewanella benthica DB6705 | Descriptor: | Cytochrome c, HEME C, PENTAETHYLENE GLYCOL | Authors: | Suka, A, Oki, H, Kato, Y, Kawahara, K, Ohkubo, T, Maruno, T, Kobayashi, Y, Fujii, S, Wakai, S, Sambongi, Y. | Deposit date: | 2018-06-15 | Release date: | 2019-06-12 | Last modified: | 2019-10-02 | Method: | X-RAY DIFFRACTION (1.71 Å) | Cite: | Stability of cytochromes c' from psychrophilic and piezophilic Shewanella species: implications for complex multiple adaptation to low temperature and high hydrostatic pressure. Extremophiles, 23, 2019
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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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1AYG
| SOLUTION STRUCTURE OF CYTOCHROME C-552, NMR, 20 STRUCTURES | Descriptor: | CYTOCHROME C-552, HEME C | Authors: | Hasegawa, J, Yoshida, T, Yamazaki, T, Sambongi, Y, Yu, Y, Igarashi, Y, Kodama, T, Yamazaki, K, Hakusui, H, Kyogoku, Y, Kobayashi, Y. | Deposit date: | 1997-11-04 | Release date: | 1998-11-25 | Last modified: | 2022-02-16 | Method: | SOLUTION NMR | Cite: | Solution structure of thermostable cytochrome c-552 from Hydrogenobacter thermophilus determined by 1H-NMR spectroscopy. Biochemistry, 37, 1998
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5Z0A
| ST0452(Y97N)-GlcNAc binding form | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, Dual sugar-1-phosphate nucleotidylyltransferase | Authors: | Honda, Y, Nakano, S, Ito, S, Dadashipour, M, Zhang, Z, Kawarabayasi, Y. | Deposit date: | 2017-12-19 | Release date: | 2018-10-31 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2.09 Å) | Cite: | Improvement of ST0452N-Acetylglucosamine-1-Phosphate Uridyltransferase Activity by the Cooperative Effect of Two Single Mutations Identified through Structure-Based Protein Engineering Appl. Environ. Microbiol., 84, 2018
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2WOQ
| Porphobilinogen Synthase (HemB) in Complex with 5-acetamido-4- oxohexanoic acid (Alaremycin 2) | Descriptor: | 3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL, 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, ALAREMYCIN 2, ... | Authors: | Heinemann, I.U, Schulz, C, Schubert, W.-D, Heinz, D.W, Wang, Y.-G, Kobayashi, Y, Awa, Y, Wachi, M, Jahn, D, Jahn, M. | Deposit date: | 2009-07-27 | Release date: | 2009-10-27 | Last modified: | 2023-12-20 | Method: | X-RAY DIFFRACTION (1.75 Å) | Cite: | Structure of the heme biosynthetic Pseudomonas aeruginosa porphobilinogen synthase in complex with the antibiotic alaremycin. Antimicrob. Agents Chemother., 54, 2010
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3ORY
| Crystal structure of Flap endonuclease 1 from hyperthermophilic archaeon Desulfurococcus amylolyticus | Descriptor: | PHOSPHATE ION, flap endonuclease 1 | Authors: | Mase, T, Kubota, K, Miyazono, K, Kawarabayashii, Y, Tanokura, M. | Deposit date: | 2010-09-08 | Release date: | 2011-02-09 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Structure of flap endonuclease 1 from the hyperthermophilic archaeon Desulfurococcus amylolyticus Acta Crystallogr.,Sect.F, 67, 2011
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1DVV
| SOLUTION STRUCTURE OF THE QUINTUPLE MUTANT OF CYTOCHROME C-551 FROM PSEUDOMONAS AERUGINOSA | Descriptor: | CYTOCHROME C551, PROTOPORPHYRIN IX CONTAINING FE | Authors: | Hasegawa, J, Uchiyama, S, Tanimoto, Y, Mizutani, M, Kobayashi, Y, Sambongi, Y, Igarashi, Y. | Deposit date: | 2000-01-22 | Release date: | 2000-11-29 | Last modified: | 2024-04-10 | Method: | SOLUTION NMR | Cite: | Selected mutations in a mesophilic cytochrome c confer the stability of a thermophilic counterpart. J.Biol.Chem., 275, 2000
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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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7ZKC
| Catalytic domain of UDP-Glucose Glycoprotein Glucosyltransferase from Chaetomium thermophilum (apo form) | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, CALCIUM ION, UDP-glucose-glycoprotein glucosyltransferase-like protein | Authors: | Roversi, P, Zitzmann, N, Bayo, Y, Le Cornu, J.D. | Deposit date: | 2022-04-12 | Release date: | 2022-04-20 | Last modified: | 2024-01-31 | Method: | X-RAY DIFFRACTION (1.769 Å) | Cite: | A quinolin-8-ol sub-millimolar inhibitor of UGGT, the ER glycoprotein folding quality control checkpoint. Iscience, 26, 2023
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7ZLU
| Catalytic domain of UDP-Glucose Glycoprotein Glucosyltransferase from Chaetomium thermophilum in complex with UDP-2-deoxy-2-fluoro-D-glucose | Descriptor: | 1,3-PROPANDIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose, CALCIUM ION, ... | Authors: | Roversi, P, Zitzmann, N, Bayo, Y, Ibba, R. | Deposit date: | 2022-04-15 | Release date: | 2022-06-22 | Last modified: | 2024-01-31 | Method: | X-RAY DIFFRACTION (2.049 Å) | Cite: | A quinolin-8-ol sub-millimolar inhibitor of UGGT, the ER glycoprotein folding quality control checkpoint. Iscience, 26, 2023
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1IS1
| Crystal structure of ribosome recycling factor from Vibrio parahaemolyticus | Descriptor: | RIBOSOME RECYCLING FACTOR | Authors: | Nakano, H, Yamaichi, Y, Uchiyama, S, Yoshida, T, Nishina, K, Kato, H, Ohkubo, T, Honda, T, Yamagata, Y, Kobayashi, Y. | Deposit date: | 2001-11-05 | Release date: | 2003-06-17 | Last modified: | 2023-12-27 | Method: | X-RAY DIFFRACTION (2.2 Å) | Cite: | Structure and binding mode of a ribosome recycling factor (RRF) from mesophilic bacterium J.BIOL.CHEM., 278, 2003
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1WZB
| Crystal structure of the collagen triple helix model [{HYP(R)-HYP(R)-GLY}10]3 | Descriptor: | Collagen triple helix | Authors: | Kawahara, K, Nakamura, S, Nishi, Y, Uchiyama, S, Nishiuchi, Y, Nakazawa, T, Ohkubo, T, Kobayashi, Y. | Deposit date: | 2005-03-03 | Release date: | 2006-01-31 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (1.5 Å) | Cite: | Effect of hydration on the stability of the collagen-like triple-helical structure of [4(R)-hydroxyprolyl-4(R)-hydroxyprolylglycine]10 Biochemistry, 44, 2005
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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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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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1ISE
| Crystal structure of a mutant of ribosome recycling factor from Escherichia coli, Arg132Gly | Descriptor: | Ribosome Recycling Factor | Authors: | Nakano, H, Yoshida, T, Oka, S, Uchiyama, S, Nishina, K, Ohkubo, T, Kato, H, Yamagata, Y, Kobayashi, Y. | Deposit date: | 2001-11-30 | Release date: | 2003-10-07 | Last modified: | 2023-12-27 | Method: | X-RAY DIFFRACTION (2.2 Å) | Cite: | Crystal structure of a mutant of ribosome recycling factor from Escherichia coli, Arg132Gly To be Published
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2Z6W
| Crystal structure of human cyclophilin D in complex with cyclosporin A | Descriptor: | CITRIC ACID, CYCLOSPORIN A, PEPTIDYL-PROLYL CIS-TRANS ISOMERASE | Authors: | Kajitani, K, Fujihashi, M, Kobayashi, Y, Shimizu, S, Tsujimoto, Y, Miki, K. | Deposit date: | 2007-08-09 | Release date: | 2008-04-29 | Last modified: | 2023-11-15 | Method: | X-RAY DIFFRACTION (0.96 Å) | Cite: | Crystal Structure of Human Cyclophilin D in Complex with its Inhibitor, Cyclosporin a at 0.96-A Resolution. Proteins, 70, 2008
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2Z2T
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3AHA
| Crystal structure of the complex between gp41 fragments N36 and C34 mutant N126K/E137Q | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, CHLORIDE ION, Transmembrane protein gp41 | Authors: | Izumi, K, Nakamura, S, Nakano, H, Shimura, K, Sakagami, Y, Oishi, S, Uchiyama, S, Ohkubo, T, Kobayashi, Y, Fujii, N, Matsuoka, M, Kodama, E.N. | Deposit date: | 2010-04-22 | Release date: | 2010-05-19 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (1.7 Å) | Cite: | Characterization of HIV-1 resistance to a fusion inhibitor, N36, derived from the gp41 amino terminal heptad repeat. Antiviral Res., 2010
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1IY5
| Solution structure of wild type OMSVP3 | Descriptor: | OMSVP3 | Authors: | Hemmi, H, Kumazaki, T, Yamazaki, T, Kojima, S, Yoshida, T, Kyogoku, Y, Katsu, M, Yokosawa, H, Miura, K, Kobayashi, Y. | Deposit date: | 2002-07-23 | Release date: | 2003-03-11 | Last modified: | 2023-12-27 | Method: | SOLUTION NMR | Cite: | Inhibitory Specificity Change of Ovomucoid Third Domain of the Silver Pheasant upon Introduction of an Engineered Cys14-Cys39 Bond BIOCHEMISTRY, 42, 2003
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1IY6
| Solution structure of OMSVP3 variant, P14C/N39C | Descriptor: | OMSVP3 | Authors: | Hemmi, H, Kumazaki, T, Yamazaki, T, Kojima, S, Yoshida, T, Kyogoku, Y, Katsu, M, Yokosawa, H, Miura, K, Kobayashi, Y. | Deposit date: | 2002-07-23 | Release date: | 2003-03-11 | Last modified: | 2023-12-27 | Method: | SOLUTION NMR | Cite: | Inhibitory Specificity Change of Ovomucoid Third Domain of the Silver Pheasant upon Introduction of an Engineered Cys14-Cys39 Bond BIOCHEMISTRY, 42, 2003
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1IW4
| Solution structure of ascidian trypsin inhibitor | Descriptor: | trypsin inhibitor | Authors: | Hemmi, H, Yoshida, T, Kumazaki, T, Nemoto, N, Hasegawa, J, Nishioka, F, Kyogoku, Y, Yokosawa, H, Kobayashi, Y. | Deposit date: | 2002-04-19 | Release date: | 2002-08-28 | Last modified: | 2023-06-14 | Method: | SOLUTION NMR | Cite: | Solution structure of ascidian trypsin inhibitor determined by nuclear magnetic resonance spectroscopy. Biochemistry, 41, 2002
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1WPK
| Methylated Form of N-terminal Transcriptional Regulator Domain of Escherichia Coli Ada Protein | Descriptor: | ADA regulatory protein, ZINC ION | Authors: | Takinowaki, H, Matsuda, Y, Yoshida, T, Kobayashi, Y, Ohkubo, T. | Deposit date: | 2004-09-07 | Release date: | 2005-09-13 | Last modified: | 2022-03-02 | Method: | SOLUTION NMR | Cite: | The solution structure of the methylated form of the N-terminal 16-kDa domain of Escherichia coli Ada protein Protein Sci., 15, 2006
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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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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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