1C53
 
 | | S-CLASS CYTOCHROMES C HAVE A VARIETY OF FOLDING PATTERNS: STRUCTURE OF CYTOCHROME C-553 FROM DESULFOVIBRIO VULGARIS DETERMINED BY THE MULTI-WAVELENGTH ANOMALOUS DISPERSION METHOD | | Descriptor: | CYTOCHROME C553, PROTOPORPHYRIN IX CONTAINING FE | | Authors: | Nakagawa, A, Higuchi, Y, Yasuoka, N, Katsube, Y, Yaga, T. | | Deposit date: | 1991-08-26 | | Release date: | 1993-10-31 | | Last modified: | 2024-02-07 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | S-class cytochromes c have a variety of folding patterns: structure of cytochrome c-553 from Desulfovibrio vulgaris determined by the multi-wavelength anomalous dispersion method.
J.Biochem.(Tokyo), 108, 1990
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1BK7
 | | RIBONUCLEASE MC1 FROM THE SEEDS OF BITTER GOURD | | Descriptor: | PROTEIN (RIBONUCLEASE MC1) | | Authors: | Nakagawa, A, Tanaka, I. | | Deposit date: | 1998-07-15 | | Release date: | 1999-07-23 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (1.75 Å) | | Cite: | Crystal structure of a ribonuclease from the seeds of bitter gourd (Momordica charantia) at 1.75 A resolution.
Biochim.Biophys.Acta, 1433, 1999
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1RL2
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1UF2
 | | The Atomic Structure of Rice dwarf Virus (RDV) | | Descriptor: | Core protein P3, Outer capsid protein P8, Structural protein P7 | | Authors: | Nakagawa, A, Miyazaki, N, Taka, J, Naitow, H, Ogawa, A, Fujimoto, Z, Mizuno, H, Higashi, T, Watanabe, Y, Omura, T, Cheng, R.H, Tsukihara, T. | | Deposit date: | 2003-05-23 | | Release date: | 2003-10-14 | | Last modified: | 2024-04-03 | | Method: | X-RAY DIFFRACTION (3.5 Å) | | Cite: | The atomic structure of rice dwarf virus reveals the self-assembly mechanism of component proteins.
Structure, 11, 2003
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4NI0
 | | Quaternary R3 CO-liganded hemoglobin structure in complex with a thiol containing compound | | Descriptor: | 5-[(2S)-2,3-dihydro-1,4-benzodioxin-2-yl]-2,4-dihydro-3H-1,2,4-triazole-3-thione, CARBON MONOXIDE, Hemoglobin subunit alpha, ... | | Authors: | Safo, M.K, Meadows, J, Ko, T.-P, Nakagawa, A, Zapol, W. | | Deposit date: | 2013-11-05 | | Release date: | 2014-08-20 | | Last modified: | 2023-09-20 | | Method: | X-RAY DIFFRACTION (2.15 Å) | | Cite: | Identification of a Small Molecule that Increases Hemoglobin Oxygen Affinity and Reduces SS Erythrocyte Sickling.
Acs Chem.Biol., 9, 2014
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4NI1
 | | Quaternary R CO-liganded hemoglobin structure in complex with a thiol containing compound | | Descriptor: | 5-[(2R)-2,3-dihydro-1,4-benzodioxin-2-yl]-2,4-dihydro-3H-1,2,4-triazole-3-thione, CARBON MONOXIDE, Hemoglobin subunit alpha, ... | | Authors: | Safo, M.K, Meadows, J, Ko, T.-P, Nakagawa, A, Zapol, W. | | Deposit date: | 2013-11-05 | | Release date: | 2014-09-17 | | Last modified: | 2023-09-20 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Identification of a Small Molecule that Increases Hemoglobin Oxygen Affinity and Reduces SS Erythrocyte Sickling.
Acs Chem.Biol., 9, 2014
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1HUS
 | | RIBOSOMAL PROTEIN S7 | | Descriptor: | RIBOSOMAL PROTEIN S7 | | Authors: | Hosaka, H, Nakagawa, A, Tanaka, I. | | Deposit date: | 1997-08-08 | | Release date: | 1998-01-28 | | Last modified: | 2024-10-16 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Ribosomal protein S7: a new RNA-binding motif with structural similarities to a DNA architectural factor.
Structure, 5, 1997
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1QSI
 | | MAGNESIUM(II)-AND ZINC(II)-PROTOPORPHYRIN IX'S STABILIZE THE LOWEST OXYGEN AFFINITY STATE OF HUMAN HEMOGLOBIN EVEN MORE STRONGLY THAN DEOXYHEME | | Descriptor: | CARBON MONOXIDE, PROTEIN (HEMOGLOBIN ALPHA CHAIN), PROTEIN (HEMOGLOBIN BETA CHAIN), ... | | Authors: | Miyazaki, G, Morimoto, H, Yun, K.-M, Park, S.-Y, Nakagawa, A, Minagawa, H, Shibayama, N. | | Deposit date: | 1999-06-22 | | Release date: | 1999-07-02 | | Last modified: | 2024-02-14 | | Method: | X-RAY DIFFRACTION (1.7 Å) | | Cite: | Magnesium(II) and zinc(II)-protoporphyrin IX's stabilize the lowest oxygen affinity state of human hemoglobin even more strongly than deoxyheme.
J.Mol.Biol., 292, 1999
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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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5WY1
 | | Crystal structure of mouse DNA methyltransferase 1 (T1505A mutant) | | Descriptor: | DNA (cytosine-5)-methyltransferase 1, ZINC ION | | Authors: | Kanada, K, Takeshita, K, Suetake, I, Tajima, S, Nakagawa, A. | | Deposit date: | 2017-01-10 | | Release date: | 2017-05-24 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (3.27 Å) | | Cite: | Conserved threonine 1505 in the catalytic domain stabilizes mouse DNA methyltransferase 1
J. Biochem., 162, 2017
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3KLR
 | | Bovine H-protein at 0.88 angstrom resolution | | Descriptor: | GLYCEROL, Glycine cleavage system H protein, SULFATE ION | | Authors: | Higashiura, A, Kurakane, T, Matsuda, M, Suzuki, M, Inaka, K, Sato, M, Tanaka, H, Fujiwara, K, Nakagawa, A. | | Deposit date: | 2009-11-09 | | Release date: | 2010-06-09 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (0.88 Å) | | Cite: | High-resolution X-ray crystal structure of bovine H-protein at 0.88 A resolution
Acta Crystallogr.,Sect.D, 66, 2010
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1QSH
 | | MAGNESIUM(II)-AND ZINC(II)-PROTOPORPHYRIN IX'S STABILIZE THE LOWEST OXYGEN AFFINITY STATE OF HUMAN HEMOGLOBIN EVEN MORE STRONGLY THAN DEOXYHEME | | Descriptor: | PROTEIN (HEMOGLOBIN ALPHA CHAIN), PROTEIN (HEMOGLOBIN BETA CHAIN), PROTOPORPHYRIN IX CONTAINING FE, ... | | Authors: | Miyazaki, G, Morimoto, H, Yun, K.-M, Park, S.-Y, Nakagawa, A, Minagawa, H, Shibayama, N. | | Deposit date: | 1999-06-22 | | Release date: | 1999-07-02 | | Last modified: | 2024-02-14 | | Method: | X-RAY DIFFRACTION (1.7 Å) | | Cite: | Magnesium(II) and zinc(II)-protoporphyrin IX's stabilize the lowest oxygen affinity state of human hemoglobin even more strongly than deoxyheme.
J.Mol.Biol., 292, 1999
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1DPT
 | | D-DOPACHROME TAUTOMERASE | | Descriptor: | D-DOPACHROME TAUTOMERASE | | Authors: | Sugimoto, H, Taniguchi, M, Nakagawa, A, Tanaka, I. | | Deposit date: | 1998-05-11 | | Release date: | 1999-03-30 | | Last modified: | 2024-04-03 | | Method: | X-RAY DIFFRACTION (1.54 Å) | | Cite: | Crystal structure of human D-dopachrome tautomerase, a homologue of macrophage migration inhibitory factor, at 1.54 A resolution.
Biochemistry, 38, 1999
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6LYC
 | | Crystal structure of the NOD SIRPa complex with D4-2 | | Descriptor: | ACETIC ACID, D4-2, SIRPa of the NOD mouse strain | | Authors: | Murata, Y, Matsuda, M, Nakagawa, A, Matozaki, T. | | Deposit date: | 2020-02-14 | | Release date: | 2020-07-01 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.36 Å) | | Cite: | Macrocyclic Peptide-Mediated Blockade of the CD47-SIRP alpha Interaction as a Potential Cancer Immunotherapy.
Cell Chem Biol, 27, 2020
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5H5L
 | | Structure of prostaglandin synthase D of Nilaparvata lugens | | Descriptor: | 1,2-ETHANEDIOL, DI(HYDROXYETHYL)ETHER, GLUTATHIONE, ... | | Authors: | Yamamoto, K, Higashiura, A, Suzuki, S, Nakagawa, A. | | Deposit date: | 2016-11-07 | | Release date: | 2017-09-20 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.999 Å) | | Cite: | Molecular structure of a prostaglandin D synthase requiring glutathione from the brown planthopper, Nilaparvata lugens
Biochem. Biophys. Res. Commun., 492, 2017
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2ROM
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2RSY
 | | Solution structure of the SH2 domain of Csk in complex with a phosphopeptide from Cbp | | Descriptor: | Phosphoprotein associated with glycosphingolipid-enriched microdomains 1, Tyrosine-protein kinase CSK | | Authors: | Tanaka, H, Akagi, K, Oneyama, C, Tanaka, M, Sasaki, Y, Kanou, T, Lee, Y, Yokogawa, D, Debenecker, M, Nakagawa, A, Okada, M, Ikegami, T. | | Deposit date: | 2012-09-10 | | Release date: | 2013-04-10 | | Last modified: | 2024-10-16 | | Method: | SOLUTION NMR | | Cite: | Identification of a new interaction mode between the Src homology 2 domain of C-terminal Src kinase (Csk) and Csk-binding protein/phosphoprotein associated with glycosphingolipid microdomains.
J.Biol.Chem., 288, 2013
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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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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: | 2024-10-30 | | 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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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: | 2024-10-23 | | 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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4TRW
 | | Structure of BACE1 complex with a syn-HEA-type inhibitor | | Descriptor: | Beta-secretase 1, L-alpha-glutamyl-L-isoleucyl-N-[(2R,3S)-1-{[(1S)-1-carboxybutyl]amino}-2-hydroxy-5-methylhexan-3-yl]-3-thiophen-2-yl-L-alaninamide | | Authors: | Akaji, K, Teruya, K, Akiyama, T, Sanjho, A, Yamashita, E, Nakagawa, A. | | Deposit date: | 2014-06-18 | | Release date: | 2015-07-01 | | Last modified: | 2024-10-30 | | Method: | X-RAY DIFFRACTION (2.85 Å) | | Cite: | Evaluation of transition-state mimics in a superior BACE1 cleavage sequence as peptide-mimetic BACE1 inhibitors
Bioorg.Med.Chem., 23, 2015
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4TRZ
 | | Structure of BACE1 complex with 2-thiophenyl HEA-type inhibitor | | Descriptor: | 2-thiophenyl HEA-type inhibitor, Beta-secretase 1 | | Authors: | Akaji, K, Teruya, K, Akiyama, T, Sanjho, A, Yamashita, E, Nakagawa, A. | | Deposit date: | 2014-06-18 | | Release date: | 2015-07-01 | | Last modified: | 2023-11-15 | | Method: | X-RAY DIFFRACTION (3.25 Å) | | Cite: | Evaluation of transition-state mimics in a superior BACE1 cleavage sequence as peptide-mimetic BACE1 inhibitors
Bioorg.Med.Chem., 23, 2015
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1FIM
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4TWW
 | | Structure of SARS-3CL protease complex with a Bromobenzoyl (S,R)-N-decalin type inhibitor | | Descriptor: | (2S)-2-({[(3S,4aR,8aS)-2-(4-bromobenzoyl)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: | 2014-07-02 | | Release date: | 2015-02-18 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (2.42 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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4TWY
 | | Structure of SARS-3CL protease complex with a phenylbenzoyl (S,R)-N-decalin type inhibitor | | Descriptor: | (2S)-2-({[(3S,4aR,8aS)-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: | 2014-07-02 | | Release date: | 2015-02-18 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.6 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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