5B19
 
 | | Picrophilus torridus aspartate racemase | | Descriptor: | Aspartate racemase, L(+)-TARTARIC ACID | | Authors: | Aihara, T, Ito, T, Yamanaka, Y, Noguchi, K, Odaka, M, Sekine, M, Homma, H, Yohda, M. | | Deposit date: | 2015-11-30 | | Release date: | 2016-06-22 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.851 Å) | | Cite: | Structural and functional characterization of aspartate racemase from the acidothermophilic archaeon Picrophilus torridus
Extremophiles, 20, 2016
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1FXI
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1V55
 | | Bovine heart cytochrome c oxidase at the fully reduced state | | 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: | Tsukihara, T, Shimokata, K, Katayama, Y, Shimada, H, Muramoto, K, Aoyama, H, Mochizuki, M, Shinzawa-Itoh, K, Yamashita, E, Yao, M, Ishimura, Y, Yoshikawa, S. | | Deposit date: | 2003-11-21 | | Release date: | 2003-12-23 | | Last modified: | 2023-12-20 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | The low-spin heme of cytochrome c oxidase as the driving element of the proton-pumping process.
Proc.Natl.Acad.Sci.Usa, 100, 2003
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1V54
 | | Bovine heart cytochrome c oxidase at the fully oxidized state | | 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: | Tsukihara, T, Shimokata, K, Katayama, Y, Shimada, H, Muramoto, K, Aoyama, H, Mochizuki, M, Shinzawa-Itoh, K, Yamashita, E, Yao, M, Ishimura, Y, Yoshikawa, S. | | Deposit date: | 2003-11-21 | | Release date: | 2003-12-23 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | The low-spin heme of cytochrome c oxidase as the driving element of the proton-pumping process.
Proc.Natl.Acad.Sci.Usa, 100, 2003
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2OCC
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1TNV
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1FRR
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7CP5
 | | Bovine heart cytochrome c oxidase in a catalytic intermediate of E at 1.76 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: | Tsukihara, T, Shimada, A. | | Deposit date: | 2020-08-06 | | Release date: | 2021-07-21 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.76 Å) | | Cite: | Critical roles of the Cu B site in efficient proton pumping as revealed by crystal structures of mammalian cytochrome c oxidase catalytic intermediates.
J.Biol.Chem., 297, 2021
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7D5W
 | | Bovine heart cytochrome c oxidase in a catalytic intermediate of O at 1.84 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: | Tsukihara, T, Shimada, A. | | Deposit date: | 2020-09-28 | | Release date: | 2021-07-21 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.84 Å) | | Cite: | Critical roles of the Cu B site in efficient proton pumping as revealed by crystal structures of mammalian cytochrome c oxidase catalytic intermediates.
J.Biol.Chem., 297, 2021
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7D5X
 | | Bovine heart cytochrome c oxidase in a catalytic intermediate, IO10, at 1.74 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: | Tsukihara, T, Shimada, A. | | Deposit date: | 2020-09-28 | | Release date: | 2021-07-21 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.74 Å) | | Cite: | Critical roles of the Cu B site in efficient proton pumping as revealed by crystal structures of mammalian cytochrome c oxidase catalytic intermediates.
J.Biol.Chem., 297, 2021
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1V6C
 | | Crystal Structure of Psychrophilic Subtilisin-like Protease Apa1 from Antarctic Psychrotroph Pseudoalteromonas sp. AS-11 | | Descriptor: | CALCIUM ION, SULFATE ION, alkaline serine protease, ... | | Authors: | Dong, D, Ihara, T, Motoshima, H, Watanabe, K. | | Deposit date: | 2003-11-28 | | Release date: | 2004-12-28 | | Last modified: | 2024-10-23 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Crystal Structure of Psychrophilic Subtilisin-like Protease Apa1 from Antarctic Psychrotroph Pseudoalteromonas sp. AS-11
To be Published
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5IY5
 | | Electron transfer complex of cytochrome c and cytochrome c oxidase at 2.0 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: | Shimada, S, Baba, J, Aoe, S, Shimada, A, Yamashita, E, Tsukihara, T. | | Deposit date: | 2016-03-24 | | Release date: | 2017-01-11 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Complex structure of cytochrome c-cytochrome c oxidase reveals a novel protein-protein interaction mode
EMBO J., 36, 2017
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1K9A
 | | Crystal structure analysis of full-length carboxyl-terminal Src kinase at 2.5 A resolution | | Descriptor: | Carboxyl-terminal Src kinase | | Authors: | Ogawa, A, Takayama, Y, Nagata, A, Chong, K.T, Takeuchi, S, Sakai, H, Nakagawa, A, Nada, S, Okada, M, Tsukihara, T. | | Deposit date: | 2001-10-28 | | Release date: | 2002-03-20 | | Last modified: | 2011-07-13 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Structure of the carboxyl-terminal Src kinase, Csk.
J.Biol.Chem., 277, 2002
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1CYC
 | | THE CRYSTAL STRUCTURE OF BONITO (KATSUO) FERROCYTOCHROME C AT 2.3 ANGSTROMS RESOLUTION. II. STRUCTURE AND FUNCTION | | Descriptor: | FERROCYTOCHROME C, HEME C | | Authors: | Tanaka, N, Yamane, T, Tsukihara, T, Ashida, T, Kakudo, M. | | Deposit date: | 1976-08-01 | | Release date: | 1976-10-06 | | Last modified: | 2021-03-03 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | The crystal structure of bonito (katsuo) ferrocytochrome c at 2.3 A resolution. II. Structure and function.
J.Biochem.(Tokyo), 77, 1975
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4HL8
 | | Re-refinement of the vault ribonucleoprotein particle | | Descriptor: | Major vault protein | | Authors: | Casanas, A, Querol-Audi, J, Guerra, P, Pous, J, Tanaka, H, Tsukihara, T, Verdaguer, V, Fita, I. | | Deposit date: | 2012-10-16 | | Release date: | 2013-06-05 | | Last modified: | 2024-02-28 | | Method: | X-RAY DIFFRACTION (3.5 Å) | | Cite: | New features of vault architecture and dynamics revealed by novel refinement using the deformable elastic network approach.
Acta Crystallogr.,Sect.D, 69, 2013
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4V60
 | | The structure of rat liver vault at 3.5 angstrom resolution | | Descriptor: | Major vault protein | | Authors: | Kato, K, Zhou, Y, Tanaka, H, Yao, M, Yamashita, E, Yoshimura, M, Tsukihara, T. | | Deposit date: | 2008-10-24 | | Release date: | 2014-07-09 | | Last modified: | 2024-04-03 | | Method: | X-RAY DIFFRACTION (3.5 Å) | | Cite: | The structure of rat liver vault at 3.5 angstrom resolution
Science, 323, 2009
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1QH9
 | | ENZYME-PRODUCT COMPLEX OF L-2-HALOACID DEHALOGENASE | | Descriptor: | 2-HALOACID DEHALOGENASE, LACTIC ACID | | Authors: | Li, Y.-F, Hata, Y, Fujii, T, Kurihara, T, Esaki, N. | | Deposit date: | 1999-05-12 | | Release date: | 2000-05-24 | | Last modified: | 2023-11-15 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | The Structure of L-2-Haloacid Dehalogenase Complexed with a Reaction Product Reveals the Mechanism of Intermediate Hydrolysis in Dehalogenase
To be Published
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4FXC
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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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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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1ZRM
 | | CRYSTAL STRUCTURE OF THE REACTION INTERMEDIATE OF L-2-HALOACID DEHALOGENASE WITH 2-CHLORO-N-BUTYRATE | | Descriptor: | L-2-HALOACID DEHALOGENASE, butanoic acid | | Authors: | Li, Y.-F, Hata, Y, Fujii, T, Hisano, T, Nishihara, M, Kurihara, T, Esaki, N. | | Deposit date: | 1998-03-03 | | Release date: | 1999-03-23 | | Last modified: | 2023-08-09 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Crystal structures of reaction intermediates of L-2-haloacid dehalogenase and implications for the reaction mechanism.
J.Biol.Chem., 273, 1998
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1ZRN
 | | INTERMEDIATE STRUCTURE OF L-2-HALOACID DEHALOGENASE WITH MONOCHLOROACETATE | | Descriptor: | ACETIC ACID, L-2-HALOACID DEHALOGENASE | | Authors: | Li, Y.-F, Hata, Y, Fujii, T, Hisano, T, Nishihara, M, Kurihara, T, Esaki, N. | | Deposit date: | 1998-03-03 | | Release date: | 1999-03-23 | | Last modified: | 2023-08-09 | | Method: | X-RAY DIFFRACTION (1.83 Å) | | Cite: | Crystal structures of reaction intermediates of L-2-haloacid dehalogenase and implications for the reaction mechanism.
J.Biol.Chem., 273, 1998
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2D1N
 | | Collagenase-3 (MMP-13) complexed to a hydroxamic acid inhibitor | | Descriptor: | CALCIUM ION, Collagenase 3, SM-25453, ... | | Authors: | Kohno, T, Hochigai, H, Yamashita, E, Tsukihara, T, Kanaoka, M. | | Deposit date: | 2005-08-29 | | Release date: | 2006-06-27 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2.37 Å) | | Cite: | Crystal structures of the catalytic domain of human stromelysin-1 (MMP-3) and collagenase-3 (MMP-13) with a hydroxamic acid inhibitor SM-25453
Biochem.Biophys.Res.Commun., 344, 2006
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2ZZQ
 | | Crystal structure analysis of the HEV capsid protein, PORF2 | | Descriptor: | Protein ORF3, Capsid protein | | Authors: | Miyazaki, N, Xing, L, Wang, C.-Y, Li, T.-C, Takeda, N, Higashiura, A, Nakagawa, A, Tsukihara, T, Miyamura, T, Cheng, R.H. | | Deposit date: | 2009-02-23 | | Release date: | 2010-03-09 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (3.81 Å) | | Cite: | Role of protein domain-modularity in designating capsid assembly and antigenicity
To be Published
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3ABM
 | | Bovine heart cytochrome c oxidase at the fully oxidized state (200-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 (1.95 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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