8JU3
 
 | | Mu phage tail fiber | | Descriptor: | Tail fiber protein S,Tail fiber protein S' | | Authors: | Yamashita, E, Takeda, S. | | Deposit date: | 2023-06-24 | | Release date: | 2024-02-28 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Determination of three-dimensional structure of bacteriophase Mu tail fiber
To Be Published
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2E74
 | | Crystal Structure of the Cytochrome b6f Complex from M.laminosus | | Descriptor: | (7R,17E)-4-HYDROXY-N,N,N,7-TETRAMETHYL-7-[(8E)-OCTADEC-8-ENOYLOXY]-10-OXO-3,5,9-TRIOXA-4-PHOSPHAHEPTACOS-17-EN-1-AMINIUM 4-OXIDE, 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL, Apocytochrome f, ... | | Authors: | Cramer, W.A, Yamashita, E, Zhang, H. | | Deposit date: | 2007-01-05 | | Release date: | 2007-06-12 | | Last modified: | 2011-07-13 | | Method: | X-RAY DIFFRACTION (3 Å) | | Cite: | Structure of the Cytochrome b(6)f Complex: Quinone Analogue Inhibitors as Ligands of Heme c(n)
J.Mol.Biol., 370, 2007
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2E76
 | | Crystal Structure of the Cytochrome b6f Complex with tridecyl-stigmatellin (TDS) from M.laminosus | | Descriptor: | (7R,17E)-4-HYDROXY-N,N,N,7-TETRAMETHYL-7-[(8E)-OCTADEC-8-ENOYLOXY]-10-OXO-3,5,9-TRIOXA-4-PHOSPHAHEPTACOS-17-EN-1-AMINIUM 4-OXIDE, 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL, 8-HYDROXY-5,7-DIMETHOXY-3-METHYL-2-TRIDECYL-4H-CHROMEN-4-ONE, ... | | Authors: | Cramer, W.A, Yamashita, E, Zhang, H. | | Deposit date: | 2007-01-05 | | Release date: | 2007-06-12 | | Last modified: | 2011-07-13 | | Method: | X-RAY DIFFRACTION (3.41 Å) | | Cite: | Structure of the Cytochrome b(6)f Complex: Quinone Analogue Inhibitors as Ligands of Heme c(n)
J.Mol.Biol., 370, 2007
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2E75
 | | Crystal Structure of the Cytochrome b6f Complex with 2-nonyl-4-hydroxyquinoline N-oxide (NQNO) from M.laminosus | | Descriptor: | (7R,17E)-4-HYDROXY-N,N,N,7-TETRAMETHYL-7-[(8E)-OCTADEC-8-ENOYLOXY]-10-OXO-3,5,9-TRIOXA-4-PHOSPHAHEPTACOS-17-EN-1-AMINIUM 4-OXIDE, 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL, 2-NONYL-4-HYDROXYQUINOLINE N-OXIDE, ... | | Authors: | Cramer, W.A, Yamashita, E, Zhang, H. | | Deposit date: | 2007-01-05 | | Release date: | 2007-06-12 | | Last modified: | 2011-07-13 | | Method: | X-RAY DIFFRACTION (3.55 Å) | | Cite: | Structure of the Cytochrome b(6)f Complex: Quinone Analogue Inhibitors as Ligands of Heme c(n)
J.Mol.Biol., 370, 2007
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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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2ZLD
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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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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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5X1B
 | | CO bound cytochrome c oxidase at 20 nsec after pump laser irradiation to release CO from O2 reduction center | | 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, A, Kubo, M, Baba, S, Yamashita, K, Hirata, K, Ueno, G, Nomura, T, Kimura, T, Shinzawa-Itoh, K, Baba, J, Hatano, K, Eto, Y, Miyamoto, A, Murakami, H, Kumasaka, T, Owada, S, Tono, K, Yabashi, M, Yamaguchi, Y, Yanagisawa, S, Sakaguchi, M, Ogura, T, Komiya, R, Yan, J, Yamashita, E, Yamamoto, M, Ago, H, Yoshikawa, S, Tsukihara, T. | | Deposit date: | 2017-01-25 | | Release date: | 2017-08-09 | | Last modified: | 2017-12-06 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | A nanosecond time-resolved XFEL analysis of structural changes associated with CO release from cytochrome c oxidase.
Sci Adv, 3, 2017
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5X19
 | | CO bound cytochrome c oxidase at 100 micro sec after pump laser irradiation to release CO from O2 reduction center | | 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, A, Kubo, M, Baba, S, Yamashita, K, Hirata, K, Ueno, G, Nomura, T, Kimura, T, Shinzawa-Itoh, K, Baba, J, Hatano, K, Eto, Y, Miyamoto, A, Murakami, H, Kumasaka, T, Owada, S, Tono, K, Yabashi, M, Yamaguchi, Y, Yanagisawa, S, Sakaguchi, M, Ogura, T, Komiya, R, Yan, J, Yamashita, E, Yamamoto, M, Ago, H, Yoshikawa, S, Tsukihara, T. | | Deposit date: | 2017-01-25 | | Release date: | 2017-08-09 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | A nanosecond time-resolved XFEL analysis of structural changes associated with CO release from cytochrome c oxidase.
Sci Adv, 3, 2017
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5X1F
 | | CO bound cytochrome c oxidase without pump laser irradiation at 278K | | 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, A, Kubo, M, Baba, S, Yamashita, K, Hirata, K, Ueno, G, Nomura, T, Kimura, T, Shinzawa-Itoh, K, Baba, J, Hatano, K, Eto, Y, Miyamoto, A, Murakami, H, Kumasaka, T, Owada, S, Tono, K, Yabashi, M, Yamaguchi, Y, Yanagisawa, S, Sakaguchi, M, Ogura, T, Komiya, R, Yan, J, Yamashita, E, Yamamoto, M, Ago, H, Yoshikawa, S, Tsukihara, T. | | Deposit date: | 2017-01-25 | | Release date: | 2017-08-09 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | A nanosecond time-resolved XFEL analysis of structural changes associated with CO release from cytochrome c oxidase.
Sci Adv, 3, 2017
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4WY3
 | | Structure of SARS-3CL protease complex with a phenylbenzoyl (R,S)-N-decalin type inhibitor | | Descriptor: | (2S)-2-({[(3R,4aS,8aR)-2-(biphenyl-4-ylcarbonyl)decahydroisoquinolin-3-yl]methyl}amino)-3-(1H-imidazol-5-yl)propanal, 3C-like proteinase | | Authors: | Akaji, K, Teruya, K, Shimamoto, Y, Sanjho, A, Yamashita, E, Nakagawa, A. | | Deposit date: | 2014-11-15 | | Release date: | 2015-02-18 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.89 Å) | | Cite: | Fused-ring structure of decahydroisoquinolin as a novel scaffold for SARS 3CL protease inhibitors.
Bioorg.Med.Chem., 23, 2015
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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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1UKL
 | | Crystal structure of Importin-beta and SREBP-2 complex | | Descriptor: | Importin beta-1 subunit, Sterol regulatory element binding protein-2 | | Authors: | Lee, S.J, Sekimoto, T, Yamashita, E, Nagoshi, E, Nakagawa, A, Imamoto, N, Yoshimura, M, Sakai, H, Tsukihara, T, Yoneda, Y. | | Deposit date: | 2003-08-26 | | Release date: | 2003-12-09 | | Last modified: | 2023-11-15 | | Method: | X-RAY DIFFRACTION (3 Å) | | Cite: | The Structure of Importin-beta Bound to SREBP-2: Nuclear Import of a Transcription Factor
Science, 302, 2003
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4P76
 | | Cellular response to a crystal-forming protein | | Descriptor: | Photoconvertible fluorescent protein, SODIUM ION | | Authors: | Tsutsui, H, Jinno, Y, Shoda, K, Tomita, A, Matsuda, M, Yamashita, E, Katayama, H, Nakagawa, A, Miyawaki, A. | | Deposit date: | 2014-03-26 | | Release date: | 2015-04-29 | | Last modified: | 2023-11-15 | | Method: | X-RAY DIFFRACTION (2.9 Å) | | Cite: | A diffraction-quality protein crystal processed as an autophagic cargo
Mol.Cell, 58, 2015
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4PV1
 | | Cytochrome B6F structure from M. laminosus with the quinone analog inhibitor stigmatellin | | Descriptor: | (1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate, (7R,17E)-4-HYDROXY-N,N,N,7-TETRAMETHYL-7-[(8E)-OCTADEC-8-ENOYLOXY]-10-OXO-3,5,9-TRIOXA-4-PHOSPHAHEPTACOS-17-EN-1-AMINIUM 4-OXIDE, 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL, ... | | Authors: | Hasan, S.S, Yamashita, E, Cramer, W.A. | | Deposit date: | 2014-03-14 | | Release date: | 2014-08-20 | | Last modified: | 2021-03-10 | | Method: | X-RAY DIFFRACTION (3 Å) | | Cite: | Traffic within the cytochrome b6f lipoprotein complex: gating of the quinone portal.
Biophys.J., 107, 2014
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2HI7
 | | Crystal structure of DsbA-DsbB-ubiquinone complex | | Descriptor: | Disulfide bond formation protein B, Thiol:disulfide interchange protein dsbA, UBIQUINONE-1, ... | | Authors: | Inaba, K, Murakami, S, Suzuki, M, Nakagawa, A, Yamashita, E, Okada, K, Ito, K. | | Deposit date: | 2006-06-29 | | Release date: | 2006-12-05 | | Last modified: | 2021-11-10 | | Method: | X-RAY DIFFRACTION (3.7 Å) | | Cite: | Crystal Structure of the DsbB-DsbA Complex Reveals a Mechanism of Disulfide Bond Generation
Cell(Cambridge,Mass.), 127, 2006
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1IOO
 | | CRYSTAL STRUCTURE OF NICOTIANA ALATA GEMETOPHYTIC SELF-INCOMPATIBILITY ASSOCIATED SF11-RNASE | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[beta-D-xylopyranose-(1-2)][alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, SF11-RNASE, beta-D-xylopyranose-(1-2)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | | Authors: | Ida, K, Sato, M, Sakiyama, F, Norioka, S, Yamamoto, M, Kumasaka, T, Yamashita, E. | | Deposit date: | 2001-03-26 | | Release date: | 2002-05-08 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (1.55 Å) | | Cite: | The 1.55 A resolution structure of Nicotiana alata S(F11)-RNase associated with gametophytic self-incompatibility.
J.Mol.Biol., 314, 2001
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2GUF
 | | In meso crystal structure of the cobalamin transporter, BtuB | | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, FORMIC ACID, Vitamin B12 transporter btuB, ... | | Authors: | Caffrey, M, Cherezov, V, Yamashita, E, Cramer, W.A. | | Deposit date: | 2006-04-29 | | Release date: | 2006-12-05 | | Last modified: | 2024-02-14 | | Method: | X-RAY DIFFRACTION (1.95 Å) | | Cite: | In Meso Structure of the Cobalamin Transporter, BtuB, at 1.95 A Resolution.
J.Mol.Biol., 364, 2006
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1DDZ
 | | X-RAY STRUCTURE OF A BETA-CARBONIC ANHYDRASE FROM THE RED ALGA, PORPHYRIDIUM PURPUREUM R-1 | | Descriptor: | CARBONIC ANHYDRASE, ZINC ION | | Authors: | Mitsuhashi, S, Mizushima, T, Yamashita, E, Miyachi, S, Tsukihara, T. | | Deposit date: | 1999-11-12 | | Release date: | 2000-03-08 | | Last modified: | 2024-02-07 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | X-ray structure of beta-carbonic anhydrase from the red alga, Porphyridium purpureum, reveals a novel catalytic site for CO(2) hydration.
J.Biol.Chem., 275, 2000
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1ERZ
 | | CRYSTAL STRUCTURE OF N-CARBAMYL-D-AMINO ACID AMIDOHYDROLASE WITH A NOVEL CATALYTIC FRAMEWORK COMMON TO AMIDOHYDROLASES | | Descriptor: | N-CARBAMYL-D-AMINO ACID AMIDOHYDROLASE | | Authors: | Nakai, T, Hasegawa, T, Yamashita, E, Yamamoto, M, Kumasaka, T, Ueki, T, Nanba, H, Ikenaka, Y, Takahashi, S, Sato, M, Tsukihara, T. | | Deposit date: | 2000-04-06 | | Release date: | 2001-04-06 | | Last modified: | 2024-02-07 | | Method: | X-RAY DIFFRACTION (1.7 Å) | | Cite: | Crystal structure of N-carbamyl-D-amino acid amidohydrolase with a novel catalytic framework common to amidohydrolases.
Structure Fold.Des., 8, 2000
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1O5W
 | | The structure basis of specific recognitions for substrates and inhibitors of rat monoamine oxidase A | | Descriptor: | Amine oxidase [flavin-containing] A, FLAVIN-ADENINE DINUCLEOTIDE, N-[3-(2,4-DICHLOROPHENOXY)PROPYL]-N-METHYL-N-PROP-2-YNYLAMINE | | Authors: | Ma, J, Yoshimura, M, Yamashita, E, Nakagawa, A, Ito, A, Tsukihara, T. | | Deposit date: | 2003-10-06 | | Release date: | 2004-04-20 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (3.2 Å) | | Cite: | Structure of rat monoamine oxidase a and its specific recognitions for substrates and inhibitors.
J.Mol.Biol., 338, 2004
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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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1WSV
 | | Crystal Structure of Human T-protein of Glycine Cleavage System | | Descriptor: | Aminomethyltransferase, N-[4-({[(6S)-2-AMINO-4-HYDROXY-5-METHYL-5,6,7,8-TETRAHYDROPTERIDIN-6-YL]METHYL}AMINO)BENZOYL]-L-GLUTAMIC ACID, SULFATE ION | | Authors: | Okamura-Ikeda, K, Hosaka, H, Yoshimura, M, Yamashita, E, Toma, S, Nakagawa, A, Fujiwara, K, Motokawa, Y, Taniguchi, H. | | Deposit date: | 2004-11-11 | | Release date: | 2005-08-16 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2.6 Å) | | Cite: | Crystal Structure of Human T-protein of Glycine Cleavage System at 2.0A Resolution and its Implication for Understanding Non-ketotic Hyperglycinemia
J.Mol.Biol., 351, 2005
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