5AZS
 
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5B1A
 | | Bovine heart cytochrome c oxidase in the fully oxidized state at 1.5 angstrom resolution | | Descriptor: | (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE, (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE, (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE, ... | | Authors: | Yano, N, Muramoto, K, Shimada, A, Takemura, S, Baba, J, Fujisawa, H, Mochizuki, M, Shinzawa-Itoh, K, Yamashita, E, Tsukihara, T, Yoshikawa, S. | | Deposit date: | 2015-12-01 | | Release date: | 2016-09-14 | | Last modified: | 2020-02-26 | | Method: | X-RAY DIFFRACTION (1.5 Å) | | Cite: | The Mg2+-containing Water Cluster of Mammalian Cytochrome c Oxidase Collects Four Pumping Proton Equivalents in Each Catalytic Cycle.
J.Biol.Chem., 291, 2016
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5C5N
 | | Structure of SARS-3CL protease complex with a phenyl-beta-alanyl (R,S)-N-decalin type inhibitor | | Descriptor: | (2S)-3-(1H-imidazol-5-yl)-2-({[(3R,4aS,8aR)-2-(N-phenyl-beta-alanyl)decahydroisoquinolin-3-yl]methyl}amino)propanal, 3C-like proteinase | | Authors: | Akaji, K, Teruya, K, Shimamoto, Y, Sanjho, A, Yamashita, E, Nakagawa, A. | | Deposit date: | 2015-06-21 | | Release date: | 2016-06-22 | | Last modified: | 2020-01-29 | | Method: | X-RAY DIFFRACTION (1.69 Å) | | Cite: | Fused-ring structure of N-decalin as a novel scaffold for SARS 3CL protease inhibitors
to be published
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5C5O
 | | Structure of SARS-3CL protease complex with a phenyl-beta-alanyl (S,R)-N-decalin type inhibitor | | Descriptor: | (2S)-3-(1H-imidazol-5-yl)-2-({[(3S,4aR,8aS)-2-(N-phenyl-beta-alanyl)decahydroisoquinolin-3-yl]methyl}amino)propanal, 3C-like proteinase | | Authors: | Akaji, K, Teruya, K, Shimamoto, Y, Sanjho, A, Yamashita, E, Nakagawa, A. | | Deposit date: | 2015-06-21 | | Release date: | 2016-06-22 | | Last modified: | 2020-01-29 | | Method: | X-RAY DIFFRACTION (1.5 Å) | | Cite: | Fused-ring structure of N-decalin as a novel scaffold for SARS 3CL protease inhibitors
to be published
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5AZO
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5B1B
 | | Bovine heart cytochrome c oxidase in the fully reduced state at 1.6 angstrom resolution | | Descriptor: | (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE, (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE, (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE, ... | | Authors: | Yano, N, Muramoto, K, Shimada, A, Takemura, S, Baba, J, Fujisawa, H, Mochizuki, M, Shinzawa-Itoh, K, Yamashita, E, Tsukihara, T, Yoshikawa, S. | | Deposit date: | 2015-12-01 | | Release date: | 2016-09-14 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.6 Å) | | Cite: | The Mg2+-containing Water Cluster of Mammalian Cytochrome c Oxidase Collects Four Pumping Proton Equivalents in Each Catalytic Cycle.
J.Biol.Chem., 291, 2016
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6IOL
 | | Cryo-EM structure of multidrug efflux pump MexAB-OprM (60 degree state) | | Descriptor: | Multidrug resistance protein MexA, Multidrug resistance protein MexB, Outer membrane protein OprM | | Authors: | Tsutsumi, K, Yonehara, R, Nakagawa, A, Yamashita, E. | | Deposit date: | 2018-10-30 | | Release date: | 2019-04-03 | | Last modified: | 2024-03-27 | | Method: | ELECTRON MICROSCOPY (3.76 Å) | | Cite: | Structures of the wild-type MexAB-OprM tripartite pump reveal its complex formation and drug efflux mechanism.
Nat Commun, 10, 2019
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6IOK
 | | Cryo-EM structure of multidrug efflux pump MexAB-OprM (0 degree state) | | Descriptor: | Multidrug resistance protein MexA, Multidrug resistance protein MexB, Outer membrane protein OprM | | Authors: | Tsutsumi, K, Yonehara, R, Nakagawa, A, Yamashita, E. | | Deposit date: | 2018-10-30 | | Release date: | 2019-04-03 | | Last modified: | 2019-04-17 | | Method: | ELECTRON MICROSCOPY (3.64 Å) | | Cite: | Structures of the wild-type MexAB-OprM tripartite pump reveal its complex formation and drug efflux mechanism.
Nat Commun, 10, 2019
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7COY
 | | Structure of the far-red light utilizing photosystem I of Acaryochloris marina | | Descriptor: | 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE, 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE, CHLOROPHYLL D, ... | | Authors: | Kawakami, K, Yonekura, K, Hamaguchi, T, Kashino, Y, Shinzawa-Itoh, K, Inoue-Kashino, N, Itoh, S, Ifuku, K, Yamashita, E. | | Deposit date: | 2020-08-05 | | Release date: | 2021-03-31 | | Last modified: | 2021-05-05 | | Method: | ELECTRON MICROSCOPY (2.5 Å) | | Cite: | Structure of the far-red light utilizing photosystem I of Acaryochloris marina.
Nat Commun, 12, 2021
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2ZFG
 | | Structure of OMPF PORIN | | Descriptor: | (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE, MAGNESIUM ION, Outer membrane protein F | | Authors: | Cramer, W.A, Zakharov, S.D, Yamashita, E. | | Deposit date: | 2008-01-04 | | Release date: | 2008-07-29 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (1.59 Å) | | Cite: | Crystal structures of the OmpF porin: function in a colicin translocon.
Embo J., 27, 2008
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3A6P
 | | Crystal structure of Exportin-5:RanGTP:pre-miRNA complex | | Descriptor: | 13-mer peptide, Exportin-5, GTP-binding nuclear protein Ran, ... | | Authors: | Okada, C, Yamashita, E, Lee, S.J, Shibata, S, Katahira, J, Nakagawa, A, Yoneda, Y, Tsukihara, T. | | Deposit date: | 2009-09-07 | | Release date: | 2009-12-08 | | Last modified: | 2012-04-25 | | Method: | X-RAY DIFFRACTION (2.92 Å) | | Cite: | A high-resolution structure of the pre-microRNA nuclear export machinery
Science, 326, 2009
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3AG1
 | | Bovine Heart Cytochrome c Oxidase in the Carbon Monoxide-bound Fully Reduced State at 280 K | | Descriptor: | (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE, (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE, (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE, ... | | Authors: | Muramoto, K, Ohta, K, Shinzawa-Itoh, K, Kanda, K, Taniguchi, M, Nabekura, H, Yamashita, E, Tsukihara, T, Yoshikawa, S. | | Deposit date: | 2010-03-19 | | Release date: | 2010-04-28 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Bovine cytochrome c oxidase structures enable O2 reduction with minimization of reactive oxygens and provide a proton-pumping gate
Proc.Natl.Acad.Sci.USA, 107, 2010
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2ZLD
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2ZW3
 | | Structure of the connexin-26 gap junction channel at 3.5 angstrom resolution | | Descriptor: | Gap junction beta-2 protein | | Authors: | Maeda, S, Nakagawa, S, Suga, M, Yamashita, E, Oshima, A, Fujiyoshi, Y, Tsukihara, T. | | Deposit date: | 2008-12-01 | | Release date: | 2009-04-07 | | Last modified: | 2011-07-13 | | Method: | X-RAY DIFFRACTION (3.5 Å) | | Cite: | Structure of the connexin 26 gap junction channel at 3.5 A resolution
Nature, 458, 2009
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3AG2
 | | Bovine Heart Cytochrome c Oxidase in the Carbon Monoxide-bound Fully Reduced State at 100 K | | Descriptor: | (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE, (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE, (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE, ... | | Authors: | Muramoto, K, Ohta, K, Shinzawa-Itoh, K, Kanda, K, Taniguchi, M, Nabekura, H, Yamashita, E, Tsukihara, T, Yoshikawa, S. | | Deposit date: | 2010-03-19 | | Release date: | 2010-04-28 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.802 Å) | | Cite: | Bovine cytochrome c oxidase structures enable O2 reduction with minimization of reactive oxygens and provide a proton-pumping gate
Proc.Natl.Acad.Sci.USA, 107, 2010
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3AWE
 | | Crystal structure of Pten-like domain of Ci-VSP (248-576) | | Descriptor: | ACETIC ACID, SODIUM ION, SULFATE ION, ... | | Authors: | Matsuda, M, Sakata, S, Takeshita, K, Suzuki, M, Yamashita, E, Okamura, Y, Nakagawa, A. | | Deposit date: | 2011-03-19 | | Release date: | 2011-05-04 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2.77 Å) | | Cite: | Crystal structure of the cytoplasmic phosphatase and tensin homolog (PTEN)-like region of Ciona intestinalis voltage-sensing phosphatase provides insight into substrate specificity and redox regulation of the phosphoinositide phosphatase activity
J.Biol.Chem., 286, 2011
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3ASO
 | | Bovine heart cytochrome C oxidase in the fully oxidized state measured at 0.9 angstrom wavelength | | Descriptor: | (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE, (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE, (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE, ... | | Authors: | Suga, M, Yano, N, Muramoto, K, Shinzawa-Itoh, K, Maeda, T, Yamashita, E, Tsukihara, T, Yoshikawa, S. | | Deposit date: | 2010-12-17 | | Release date: | 2011-08-03 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Distinguishing between Cl- and O2(2-) as the bridging element between Fe3+ and Cu2+ in resting-oxidized cytochrome c oxidase
Acta Crystallogr.,Sect.D, 67, 2011
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3AV4
 | | Crystal structure of mouse DNA methyltransferase 1 | | Descriptor: | DNA (cytosine-5)-methyltransferase 1, ZINC ION | | Authors: | Takeshita, K, Suetake, I, Yamashita, E, Suga, M, Narita, H, Nakagawa, A, Tajima, S. | | Deposit date: | 2011-02-22 | | Release date: | 2011-05-04 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (2.75 Å) | | Cite: | Structural insight into maintenance methylation by mouse DNA methyltransferase 1 (Dnmt1).
Proc.Natl.Acad.Sci.USA, 108, 2011
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3ASN
 | | Bovine heart cytochrome C oxidase in the fully oxidized state measured at 1.7470 angstrom wavelength | | Descriptor: | (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE, (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE, (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE, ... | | Authors: | Suga, M, Yano, N, Muramoto, K, Shinzawa-Itoh, K, Maeda, T, Yamashita, E, Tsukihara, T, Yoshikawa, S. | | Deposit date: | 2010-12-17 | | Release date: | 2011-08-03 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (3 Å) | | Cite: | Distinguishing between Cl- and O2(2-) as the bridging element between Fe3+ and Cu2+ in resting-oxidized cytochrome c oxidase
Acta Crystallogr.,Sect.D, 67, 2011
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3AQJ
 | | Crystal Structure of a C-terminal domain of the bacteriophage P2 tail spike protein, gpV | | Descriptor: | Baseplate assembly protein V, CALCIUM ION, CHLORIDE ION, ... | | Authors: | Takeda, S, Yamashita, E, Nakagawa, A. | | Deposit date: | 2010-11-06 | | Release date: | 2011-08-10 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (1.27 Å) | | Cite: | The host-binding domain of the P2 phage tail spike reveals a trimeric iron-binding structure
Acta Crystallogr.,Sect.F, 67, 2011
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3AV6
 | | Crystal structure of mouse DNA methyltransferase 1 with AdoMet | | Descriptor: | DNA (cytosine-5)-methyltransferase 1, S-ADENOSYLMETHIONINE, ZINC ION | | Authors: | Takeshita, K, Suetake, I, Yamashita, E, Suga, M, Narita, H, Nakagawa, A, Tajima, S. | | Deposit date: | 2011-02-22 | | Release date: | 2011-05-04 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (3.09 Å) | | Cite: | Structural insight into maintenance methylation by mouse DNA methyltransferase 1 (Dnmt1).
Proc.Natl.Acad.Sci.USA, 108, 2011
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3AV5
 | | Crystal structure of mouse DNA methyltransferase 1 with AdoHcy | | Descriptor: | DNA (cytosine-5)-methyltransferase 1, S-ADENOSYL-L-HOMOCYSTEINE, ZINC ION | | Authors: | Takeshita, K, Suetake, I, Yamashita, E, Suga, M, Narita, H, Nakagawa, A, Tajima, S. | | Deposit date: | 2011-02-22 | | Release date: | 2011-05-04 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (3.25 Å) | | Cite: | Structural insight into maintenance methylation by mouse DNA methyltransferase 1 (Dnmt1).
Proc.Natl.Acad.Sci.USA, 108, 2011
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2Z51
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3AG3
 | | Bovine Heart Cytochrome c Oxidase in the Nitric Oxide-bound Fully Reduced State at 100 K | | Descriptor: | (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE, (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE, (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE, ... | | Authors: | Muramoto, K, Ohta, K, Shinzawa-Itoh, K, Kanda, K, Taniguchi, M, Nabekura, H, Yamashita, E, Tsukihara, T, Yoshikawa, S. | | Deposit date: | 2010-03-19 | | Release date: | 2010-04-28 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Bovine cytochrome c oxidase structures enable O2 reduction with minimization of reactive oxygens and provide a proton-pumping gate
Proc.Natl.Acad.Sci.USA, 107, 2010
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3ABL
 | | Bovine heart cytochrome c oxidase at the fully oxidized state (15-s X-ray exposure dataset) | | Descriptor: | (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE, (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE, (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE, ... | | Authors: | Aoyama, H, Muramoto, K, Shinzawa-Itoh, K, Yamashita, E, Tsukihara, T, Ogura, T, Yoshikawa, S. | | Deposit date: | 2009-12-16 | | Release date: | 2010-01-19 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | A peroxide bridge between Fe and Cu ions in the O2 reduction site of fully oxidized cytochrome c oxidase could suppress the proton pump
Proc.Natl.Acad.Sci.USA, 106, 2009
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