3AOD
| Structures of the multidrug exporter AcrB reveal a proximal multisite drug-binding pocket | Descriptor: | (4S,4AS,5AR,12AS)-4,7-BIS(DIMETHYLAMINO)-3,10,12,12A-TETRAHYDROXY-1,11-DIOXO-1,4,4A,5,5A,6,11,12A-OCTAHYDROTETRACENE-2- CARBOXAMIDE, Acriflavine resistance protein B, RIFAMPICIN | Authors: | Nakashima, R, Sakurai, K, Yamaguchi, A. | Deposit date: | 2010-09-23 | Release date: | 2011-11-30 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (3.3 Å) | Cite: | Structures of the multidrug exporter AcrB reveal a proximal multisite drug-binding pocket Nature, 480, 2011
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3AOA
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3AOB
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3AOC
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8IAU
| Crystal structure of Streptococcus pneumoniae pyruvate kinase in complex with oxalate and fructose 1,6-bisphosphate | Descriptor: | 1,6-di-O-phosphono-beta-D-fructofuranose, DI(HYDROXYETHYL)ETHER, MAGNESIUM ION, ... | Authors: | Nakashima, R, Taguchi, A. | Deposit date: | 2023-02-09 | Release date: | 2023-06-14 | Last modified: | 2023-07-19 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Functional and structural characterization of Streptococcus pneumoniae pyruvate kinase involved in fosfomycin resistance. J.Biol.Chem., 299, 2023
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8IAV
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8IAS
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8IAW
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8IAT
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8IAX
| Crystal structure of Streptococcus pneumoniae pyruvate kinase in complex with phosphoenolpyruvate and fructose 1,6-bisphosphate | Descriptor: | 1,6-di-O-phosphono-beta-D-fructofuranose, MAGNESIUM ION, PHOSPHOENOLPYRUVATE, ... | Authors: | Nakashima, R, Taguchi, A. | Deposit date: | 2023-02-09 | Release date: | 2023-06-14 | Last modified: | 2023-07-19 | Method: | X-RAY DIFFRACTION (1.8 Å) | Cite: | Functional and structural characterization of Streptococcus pneumoniae pyruvate kinase involved in fosfomycin resistance. J.Biol.Chem., 299, 2023
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7CAO
| Crystal structure of red chromoprotein from Olindias formosa | Descriptor: | Chromoprotein | Authors: | Nakashima, R, Zhai, L, Ike, Y, Matsudz, T, Nagai, T. | Deposit date: | 2020-06-09 | Release date: | 2022-04-20 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.05 Å) | Cite: | Structure-based analysis and evolution of a monomerized red-colored chromoprotein from the Olindias formosa jellyfish. Protein Sci., 31, 2022
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6IIA
| MexB in complex with LMNG | Descriptor: | Lauryl Maltose Neopentyl Glycol, Multidrug resistance protein MexB | Authors: | Nakashima, R, Sakurai, K, Nakao, K. | Deposit date: | 2018-10-04 | Release date: | 2019-03-27 | Last modified: | 2023-12-13 | Method: | X-RAY DIFFRACTION (2.91 Å) | Cite: | Crystal structures of multidrug efflux pump MexB bound with high-molecular-mass compounds. Sci Rep, 9, 2019
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6IE9
| RamR in complex with chenodeoxycholic acid | Descriptor: | CHENODEOXYCHOLIC ACID, Regulatory protein, SULFATE ION | Authors: | Nakashima, R, Sakurai, K, Yamasaki, S, Nishino, K. | Deposit date: | 2018-09-13 | Release date: | 2019-02-13 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (1.78 Å) | Cite: | Crystal structure of the multidrug resistance regulator RamR complexed with bile acids. Sci Rep, 9, 2019
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6IE8
| RamR in complex with cholic acid | Descriptor: | CHOLIC ACID, Regulatory protein, SULFATE ION | Authors: | Nakashima, R, Sakurai, K, Yamasaki, S, Nishino, K. | Deposit date: | 2018-09-13 | Release date: | 2019-02-13 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Crystal structure of the multidrug resistance regulator RamR complexed with bile acids. Sci Rep, 9, 2019
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6J1C
| Photoswitchable fluorescent protein Gamillus, N150C/T204V double mutant, off-state | Descriptor: | CHLORIDE ION, GLYCEROL, Green fluorescent protein | Authors: | Nakashima, R, Shinoda, H, Matsuda, T, Nagai, T. | Deposit date: | 2018-12-28 | Release date: | 2019-11-06 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2.09 Å) | Cite: | Acid-Tolerant Reversibly Switchable Green Fluorescent Protein for Super-resolution Imaging under Acidic Conditions. Cell Chem Biol, 26, 2019
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6J1B
| Photoswitchable fluorescent protein Gamillus, N150C/T204V double mutant, on-state | Descriptor: | CHLORIDE ION, GLYCEROL, Green fluorescent protein, ... | Authors: | Nakashima, R, Shinoda, H, Matsuda, T, Nagai, T. | Deposit date: | 2018-12-28 | Release date: | 2019-11-06 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (1.99 Å) | Cite: | Acid-Tolerant Reversibly Switchable Green Fluorescent Protein for Super-resolution Imaging under Acidic Conditions. Cell Chem Biol, 26, 2019
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6J1A
| Photoswitchable fluorescent protein Gamillus, off-state | Descriptor: | CHLORIDE ION, GLYCEROL, Green fluorescent protein, ... | Authors: | Nakashima, R, Sakurai, K, shinoda, H, Matsuda, T, Nagai, T. | Deposit date: | 2018-12-28 | Release date: | 2019-11-06 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (1.96 Å) | Cite: | Acid-Tolerant Reversibly Switchable Green Fluorescent Protein for Super-resolution Imaging under Acidic Conditions. Cell Chem Biol, 26, 2019
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6JXF
| Photoswitchable fluorescent protein Gamillus, off-state (pH7.0) | Descriptor: | CHLORIDE ION, GLYCEROL, Green fluorescent protein, ... | Authors: | Nakashima, R, Sakurai, K, shinoda, H, Matsuda, T, Nagai, T. | Deposit date: | 2019-04-23 | Release date: | 2019-11-06 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (1.8 Å) | Cite: | Acid-Tolerant Reversibly Switchable Green Fluorescent Protein for Super-resolution Imaging under Acidic Conditions. Cell Chem Biol, 26, 2019
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3W9I
| Structural basis for the inhibition of bacterial multidrug exporters | Descriptor: | DODECYL-BETA-D-MALTOSIDE, Multidrug resistance protein MexB | Authors: | Sakurai, K, Nakashima, R, Hayashi, K, Yamaguchi, A. | Deposit date: | 2013-04-04 | Release date: | 2013-07-03 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.71 Å) | Cite: | Structural basis for the inhibition of bacterial multidrug exporters Nature, 500, 2013
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3W9J
| Structural basis for the inhibition of bacterial multidrug exporters | Descriptor: | DODECYL-BETA-D-MALTOSIDE, Multidrug resistance protein MexB, [{2-[({[(3R)-1-{8-[(4-tert-butyl-1,3-thiazol-2-yl)carbamoyl]-4-oxo-3-[(E)-2-(1H-tetrazol-5-yl)ethenyl]-4H-pyrido[1,2-a]pyrimidin-2-yl}piperidin-3-yl]oxy}carbonyl)amino]ethyl}(dimethyl)ammonio]acetate | Authors: | Sakurai, K, Nakashima, R, Hayashi, K, Yamaguchi, A. | Deposit date: | 2013-04-04 | Release date: | 2013-07-03 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (3.15 Å) | Cite: | Structural basis for the inhibition of bacterial multidrug exporters Nature, 500, 2013
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3W9H
| Structural basis for the inhibition of bacterial multidrug exporters | Descriptor: | Acriflavine resistance protein B, [{2-[({[(3R)-1-{8-[(4-tert-butyl-1,3-thiazol-2-yl)carbamoyl]-4-oxo-3-[(E)-2-(1H-tetrazol-5-yl)ethenyl]-4H-pyrido[1,2-a]pyrimidin-2-yl}piperidin-3-yl]oxy}carbonyl)amino]ethyl}(dimethyl)ammonio]acetate | Authors: | Sakurai, K, Nagata, C, Nakashima, R, Yamaguchi, A. | Deposit date: | 2013-04-04 | Release date: | 2013-07-03 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (3.05 Å) | Cite: | Structural basis for the inhibition of bacterial multidrug exporters Nature, 500, 2013
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5Y01
| Acid-tolerant monomeric GFP, Gamillus, non-fluorescence (OFF) state | Descriptor: | Green fluorescent protein, PHOSPHATE ION | Authors: | Nakashima, R, Sakurai, K, Shinoda, H, Matsuda, T, Nagai, T. | Deposit date: | 2017-07-14 | Release date: | 2018-01-17 | Last modified: | 2023-11-15 | Method: | X-RAY DIFFRACTION (2.65 Å) | Cite: | Acid-Tolerant Monomeric GFP from Olindias formosa. Cell Chem Biol, 25, 2018
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5Y00
| Acid-tolerant monomeric GFP, Gamillus, fluorescence (ON) state | Descriptor: | CHLORIDE ION, GLYCEROL, Green fluorescent protein, ... | Authors: | Nakashima, R, Sakurai, K, Shinoda, H, Matsuda, T, Nagai, T. | Deposit date: | 2017-07-14 | Release date: | 2018-01-17 | Last modified: | 2023-11-15 | Method: | X-RAY DIFFRACTION (1.6 Å) | Cite: | Acid-Tolerant Monomeric GFP from Olindias formosa. Cell Chem Biol, 25, 2018
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1OCC
| STRUCTURE OF BOVINE HEART CYTOCHROME C OXIDASE AT THE FULLY OXIDIZED STATE | Descriptor: | COPPER (II) ION, CYTOCHROME C OXIDASE, HEME-A, ... | Authors: | Tsukihara, T, Aoyama, H, Yamashita, E, Tomizaki, T, Yamaguchi, H, Shinzawa-Itoh, K, Nakashima, R, Yaono, R, Yoshikawa, S. | Deposit date: | 1996-04-18 | Release date: | 1996-12-07 | Last modified: | 2018-03-21 | Method: | X-RAY DIFFRACTION (2.8 Å) | Cite: | The whole structure of the 13-subunit oxidized cytochrome c oxidase at 2.8 A. Science, 272, 1996
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2DRD
| Crystal structure of a multidrug transporter reveal a functionally rotating mechanism | Descriptor: | (4S,4AS,5AR,12AS)-4,7-BIS(DIMETHYLAMINO)-3,10,12,12A-TETRAHYDROXY-1,11-DIOXO-1,4,4A,5,5A,6,11,12A-OCTAHYDROTETRACENE-2- CARBOXAMIDE, ACRB | Authors: | Murakami, S, Nakashima, R, Yamashita, E, Matsumoto, T. | Deposit date: | 2006-06-08 | Release date: | 2006-08-22 | Last modified: | 2024-03-13 | Method: | X-RAY DIFFRACTION (3.1 Å) | Cite: | Crystal structures of a multidrug transporter reveal a functionally rotating mechanism Nature, 443, 2006
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