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PDB: 58 results

3HJN
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Crystal structure of thymidylate kinase in complex with dTDP and ADP from Thermotoga maritima
Descriptor: ADENOSINE-5'-DIPHOSPHATE, MAGNESIUM ION, THYMIDINE-5'-DIPHOSPHATE, ...
Authors:Yoshikawa, S, Nakagawa, N, Shirouzu, M, Yokoyama, S, Kuramitsu, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Deposit date:2009-05-22
Release date:2009-06-02
Last modified:2023-11-01
Method:X-RAY DIFFRACTION (2.1 Å)
Cite:Crystal structure of thymidylate kinase in complex with dTDP and ADP from Thermotoga maritima
To be Published
3VJO
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Crystal structure of the wild-type EGFR kinase domain in complex with AMPPNP.
Descriptor: Epidermal growth factor receptor, PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
Authors:Yoshikawa, S, Kukimoto-Niino, M, Shirouzu, M, Semba, K, Yamamoto, T, Yokoyama, S.
Deposit date:2011-10-27
Release date:2012-03-07
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (2.64 Å)
Cite:Structural basis for the altered drug sensitivities of non-small cell lung cancer-associated mutants of human epidermal growth factor receptor.
Oncogene, 32, 2013
3VJN
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Crystal structure of the mutated EGFR kinase domain (G719S/T790M) in complex with AMPPNP.
Descriptor: Epidermal growth factor receptor, PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
Authors:Yoshikawa, S, Kukimoto-Niino, M, Shirouzu, M, Semba, K, Yamamoto, T, Yokoyama, S.
Deposit date:2011-10-27
Release date:2012-03-07
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (2.34 Å)
Cite:Structural basis for the altered drug sensitivities of non-small cell lung cancer-associated mutants of human epidermal growth factor receptor.
Oncogene, 32, 2013
2EB2
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Crystal structure of mutated EGFR kinase domain (G719S)
Descriptor: Epidermal growth factor receptor
Authors:Yoshikawa, S, Kukimoto-Niino, M, Chen, L, Liu, Z.J, Wang, B.C, Shirouzu, M, Senba, K, Yamamoto, T, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Deposit date:2007-02-06
Release date:2008-02-12
Last modified:2023-10-25
Method:X-RAY DIFFRACTION (2.5 Å)
Cite:Structural basis for the altered drug sensitivities of non-small cell lung cancer-associated mutants of human epidermal growth factor receptor
Oncogene, 2012
2EB3
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Crystal structure of mutated EGFR kinase domain (L858R) in complex with AMPPNP
Descriptor: Epidermal growth factor receptor, PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
Authors:Yoshikawa, S, Kukimoto-Niino, M, Shirouzu, M, Senba, K, Yamamoto, T, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Deposit date:2007-02-06
Release date:2008-02-12
Last modified:2023-10-25
Method:X-RAY DIFFRACTION (2.84 Å)
Cite:Structural basis for the altered drug sensitivities of non-small cell lung cancer-associated mutants of human epidermal growth factor receptor
Oncogene, 2012
2DBR
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BU of 2dbr by Molmil
Crystal Structure of Glyoxylate Reductase (PH0597) from Pyrococcus horikoshii OT3, Complexed with NADP (P1)
Descriptor: Glyoxylate reductase, NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE, SULFATE ION
Authors:Yoshikawa, S, Arai, R, Kinoshita, Y, Uchikubo-Kamo, T, Akasaka, R, Terada, T, Shirouzu, M, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Deposit date:2005-12-16
Release date:2006-06-16
Last modified:2023-10-25
Method:X-RAY DIFFRACTION (2.61 Å)
Cite:Structure of archaeal glyoxylate reductase from Pyrococcus horikoshii OT3 complexed with nicotinamide adenine dinucleotide phosphate.
Acta Crystallogr.,Sect.D, 63, 2007
2DBQ
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Crystal Structure of Glyoxylate Reductase (PH0597) from Pyrococcus horikoshii OT3, Complexed with NADP (I41)
Descriptor: GLYCEROL, Glyoxylate reductase, NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE, ...
Authors:Yoshikawa, S, Arai, R, Kinoshita, Y, Uchikubo-Kamo, T, Akasaka, R, Terada, T, Shirouzu, M, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Deposit date:2005-12-16
Release date:2006-06-16
Last modified:2017-10-11
Method:X-RAY DIFFRACTION (1.7 Å)
Cite:Structure of archaeal glyoxylate reductase from Pyrococcus horikoshii OT3 complexed with nicotinamide adenine dinucleotide phosphate.
Acta Crystallogr.,Sect.D, 63, 2007
2DBZ
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Crystal Structure of Glyoxylate Reductase (PH0597) from Pyrococcus horikoshii OT3, Complexed with NADP (P61)
Descriptor: Glyoxylate reductase, NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE, SULFATE ION
Authors:Yoshikawa, S, Arai, R, Kinoshita, Y, Uchikubo-Kamo, T, Akasaka, R, Terada, T, Shirouzu, M, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Deposit date:2005-12-16
Release date:2006-06-16
Last modified:2023-10-25
Method:X-RAY DIFFRACTION (2.45 Å)
Cite:Structure of archaeal glyoxylate reductase from Pyrococcus horikoshii OT3 complexed with nicotinamide adenine dinucleotide phosphate.
Acta Crystallogr.,Sect.D, 63, 2007
2ZV2
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Crystal structure of human calcium/calmodulin-dependent protein kinase kinase 2, beta, CaMKK2 kinase domain in complex with STO-609
Descriptor: 7-oxo-7H-benzimidazo[2,1-a]benz[de]isoquinoline-3-carboxylic acid, Calcium/calmodulin-dependent protein kinase kinase 2
Authors:Yoshikawa, S, Kukimoto-niino, M, Shirouzu, M, Suzuki, A, Lee, S, Minokoshi, Y, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Deposit date:2008-10-31
Release date:2009-11-03
Last modified:2023-11-01
Method:X-RAY DIFFRACTION (2.4 Å)
Cite:Crystal structure of the Ca2+/calmodulin-dependent protein kinase kinase in complex with the inhibitor STO-609
J.Biol.Chem., 286, 2011
2CYX
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Structure of human ubiquitin-conjugating enzyme E2 G2 (UBE2G2/UBC7)
Descriptor: Ubiquitin-conjugating enzyme E2 G2
Authors:Yoshikawa, S, Arai, R, Murayama, K, Imai, Y, Takahashi, R, Shirouzu, M, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Deposit date:2005-07-08
Release date:2006-04-25
Last modified:2023-10-25
Method:X-RAY DIFFRACTION (2.56 Å)
Cite:Structure of human ubiquitin-conjugating enzyme E2 G2 (UBE2G2/UBC7)
Acta Crystallogr.,Sect.F, 62, 2006
2CZG
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BU of 2czg by Molmil
Crystal structure of Probable phosphoribosylglycinamide formyl transferase (PH0318) from Pyrococcus horikoshii OT3
Descriptor: GLYCEROL, SULFATE ION, phosphoribosylglycinamide formyl transferase
Authors:Yoshikawa, S, Arai, R, Kamo-Uchikubo, T, Shirouzu, M, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Deposit date:2005-07-13
Release date:2006-01-13
Last modified:2023-10-25
Method:X-RAY DIFFRACTION (2.35 Å)
Cite:Crystal structure of Probable phosphoribosylglycinamide formyl transferase (PH0318) from Pyrococcus horikoshii OT3
To be Published
2DBS
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BU of 2dbs by Molmil
Crystal structure of a hypothetical protein TTHC002 from Thermus thermophilus HB8
Descriptor: hypothetical protein TTHC002
Authors:Yoshikawa, S, Arai, R, Kamo-Uchikubo, T, Fusatomi, E, Akasaka, R, Bessho, Y, Murayama, K, Terada, T, Shirouzu, M, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Deposit date:2005-12-16
Release date:2006-06-16
Last modified:2024-10-30
Method:X-RAY DIFFRACTION (2.1 Å)
Cite:Crystal structure of a hypothetical protein TTHC002 from Thermus thermophilus HB8
To be Published
2DWC
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Crystal structure of Probable phosphoribosylglycinamide formyl transferase from Pyrococcus horikoshii OT3 complexed with ADP
Descriptor: 433aa long hypothetical phosphoribosylglycinamide formyl transferase, ADENOSINE-5'-DIPHOSPHATE, SULFATE ION
Authors:Yoshikawa, S, Arai, R, Kamo-Uchikubo, T, Shirouzu, M, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Deposit date:2006-08-10
Release date:2007-02-10
Last modified:2023-10-25
Method:X-RAY DIFFRACTION (1.7 Å)
Cite:Crystal structure of Probable phosphoribosylglycinamide formyl transferase from Pyrococcus horikoshii OT3 complexed with ADP
To be Published
2ZKY
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BU of 2zky by Molmil
Crystal structure of human Cu-Zn superoxide dismutase mutant G93A
Descriptor: Superoxide dismutase [Cu-Zn], ZINC ION
Authors:Yoshikawa, S, Kukimoto-Niino, M, Ito, K, Shirouzu, M, Urushitani, M, Takahashi, R, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Deposit date:2008-03-31
Release date:2009-03-24
Last modified:2023-11-01
Method:X-RAY DIFFRACTION (2.4 Å)
Cite:Crystal structure of human Cu-Zn superoxide dismutase mutant G93A
To be Published
2ZKX
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Crystal structure of human Cu-Zn superoxide dismutase mutant G85R in space group I212121
Descriptor: COPPER (I) ION, Superoxide dismutase [Cu-Zn], ZINC ION
Authors:Yoshikawa, S, Kukimoto-Niino, M, Ito, K, Chen, L, Fu, Z.Q, Chrzas, J, Wang, B.C, Shirouzu, M, Urushitani, M, Takahashi, R, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Deposit date:2008-03-31
Release date:2009-03-24
Last modified:2023-11-01
Method:X-RAY DIFFRACTION (2.72 Å)
Cite:Crystal structure of human Cu-Zn superoxide dismutase mutant G85R in space group I212121
To be Published
2ZKW
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Crystal structure of human Cu-Zn superoxide dismutase mutant G85R in space group P21
Descriptor: COPPER (I) ION, Superoxide dismutase [Cu-Zn], ZINC ION
Authors:Yoshikawa, S, Kukimoto-Niino, M, Ito, K, Chen, L, Fu, Z.Q, Chrzas, J, Wang, B.C, Shirouzu, M, Urushitani, M, Takahashi, R, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Deposit date:2008-03-31
Release date:2009-03-24
Last modified:2023-11-01
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:Crystal structure of human Cu-Zn superoxide dismutase mutant G85R in space group P21
To be Published
5X1B
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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
5X19
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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
2RU3
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BU of 2ru3 by Molmil
Solution structure of c.elegans SUP-12 RRM in complex with RNA
Descriptor: Protein SUP-12, isoform a, RNA (5'-R(*GP*UP*GP*UP*GP*C)-3')
Authors:Takahashi, M, Kuwasako, K, Unzai, S, Tsuda, K, Yoshikawa, S, He, F, Kobayashi, N, Guntert, P, Shirouzu, M, Ito, T, Tanaka, A, Yokoyama, S, Hagiwara, M, Kuroyanagi, H, Muto, Y.
Deposit date:2013-11-12
Release date:2014-08-13
Last modified:2024-05-15
Method:SOLUTION NMR
Cite:RBFOX and SUP-12 sandwich a G base to cooperatively regulate tissue-specific splicing
Nat.Struct.Mol.Biol., 21, 2014
1OCC
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BU of 1occ by Molmil
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
1V55
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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
1V54
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BU of 1v54 by Molmil
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
2MGZ
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BU of 2mgz by Molmil
Solution structure of RBFOX family ASD-1 RRM and SUP-12 RRM in ternary complex with RNA
Descriptor: Protein ASD-1, isoform a, Protein SUP-12, ...
Authors:Takahashi, M, Kuwasako, K, Unzai, S, Tsuda, K, Yoshikawa, S, He, F, Kobayashi, N, Guntert, P, Shirouzu, M, Ito, T, Tanaka, A, Yokoyama, S, Hagiwara, M, Kuroyanagi, H, Muto, Y.
Deposit date:2013-11-12
Release date:2014-08-13
Last modified:2024-05-01
Method:SOLUTION NMR
Cite:RBFOX and SUP-12 sandwich a G base to cooperatively regulate tissue-specific splicing
Nat.Struct.Mol.Biol., 21, 2014
7XMA
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BU of 7xma by Molmil
Crystal structure of Bovine heart cytochrome c oxidase, apo structure with DMSO
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:Nishida, Y, Shinzawa-Itoh, K, Mizuno, N, Kumasaka, T, Yoshikawa, S, Tsukihara, T, Takashima, S, Shintani, Y.
Deposit date:2022-04-25
Release date:2022-12-21
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:Identifying antibiotics based on structural differences in the conserved allostery from mitochondrial heme-copper oxidases.
Nat Commun, 13, 2022
7XMB
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Crystal structure of Bovine heart cytochrome c oxidase, the structure complexed with an allosteric inhibitor T113
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:Nishida, Y, Shinzawa-Itoh, K, Mizuno, N, Kumasaka, T, Yoshikawa, S, Tsukihara, T, Shintani, Y, Takashima, S.
Deposit date:2022-04-25
Release date:2022-12-21
Last modified:2024-10-23
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:Identifying antibiotics based on structural differences in the conserved allostery from mitochondrial heme-copper oxidases.
Nat Commun, 13, 2022

 

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