4TSQ
 
 | | Crystal structure of FraC with DHPC bound (crystal form III) | | Descriptor: | 1,2-dihexanoyl-sn-glycero-3-phosphocholine, CHLORIDE ION, Fragaceatoxin C, ... | | Authors: | Caaveiro, J.M.M, Tanaka, K, Tsumoto, K. | | Deposit date: | 2014-06-19 | | Release date: | 2015-03-04 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.6 Å) | | Cite: | Structural basis for self-assembly of a cytolytic pore lined by protein and lipid
Nat Commun, 6, 2015
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5E8D
 | | Crystal structure of human epiregulin in complex with the Fab fragment of murine monoclonal antibody 9E5 | | Descriptor: | CHLORIDE ION, GLYCEROL, Proepiregulin, ... | | Authors: | Kado, Y, Mizohata, E, Nagatoishi, S, Iijima, M, Shinoda, K, Miyafusa, T, Nakayama, T, Yoshizumi, T, Sugiyama, A, Kawamura, T, Lee, Y.H, Matsumura, H, Doi, H, Fujitani, H, Kodama, T, Shibasaki, Y, Tsumoto, K, Inoue, T. | | Deposit date: | 2015-10-14 | | Release date: | 2015-12-09 | | Last modified: | 2020-02-19 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Epiregulin Recognition Mechanisms by Anti-epiregulin Antibody 9E5: STRUCTURAL, FUNCTIONAL, AND MOLECULAR DYNAMICS SIMULATION ANALYSES
J.Biol.Chem., 291, 2016
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5GHW
 | | Crystal structure of broad neutralizing antibody 10E8 with long epitope bound | | Descriptor: | Endogenous retrovirus group K member 8 Env polyprotein, FAB 10E8 HEAVY CHAIN, FAB 10E8 LIGHT CHAIN, ... | | Authors: | Caaveiro, J.M.M, Rujas, E, Morante, K, Nieva, J.L, Tsumoto, K. | | Deposit date: | 2016-06-21 | | Release date: | 2016-11-23 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | Structural basis for broad neutralization of HIV-1 through the molecular recognition of 10E8 helical epitope at the membrane interface
Sci Rep, 6, 2016
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4YRD
 | | Crystal structure of CapF with inhibitor 3-isopropenyl-tropolone | | Descriptor: | 2-hydroxy-3-(prop-1-en-2-yl)cyclohepta-2,4,6-trien-1-one, Capsular polysaccharide synthesis enzyme Cap5F, ZINC ION | | Authors: | Nakano, K, Chigira, T, Miyafusa, T, Nagatoishi, S, Caaveiro, J.M.M, Tsumoto, K. | | Deposit date: | 2015-03-15 | | Release date: | 2015-10-21 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.44 Å) | | Cite: | Discovery and characterization of natural tropolones as inhibitors of the antibacterial target CapF from Staphylococcus aureus.
Sci Rep, 5, 2015
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7XL0
 | | Crystal structure of Vobarilizumab at 1.70 Angstrom | | Descriptor: | GLYCEROL, Nanobody Vobarilizumab, SULFATE ION | | Authors: | Caaveiro, J.M.M, Mori, C, Kinoshita, S, Nakakido, M, Tsumoto, K. | | Deposit date: | 2022-04-20 | | Release date: | 2022-11-09 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.7 Å) | | Cite: | Molecular basis for thermal stability and affinity in a VHH: Contribution of the framework region and its influence in the conformation of the CDR3.
Protein Sci., 31, 2022
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7XL1
 | | Crystal structure of chimeric 7D12-Vob nanobody at 1.65 Angstrom | | Descriptor: | Chimeric 7D12-Vob nanobody, MALONATE ION | | Authors: | Caaveiro, J.M.M, Kinoshita, S, Mori, C, Nakakido, M, Tsumoto, K. | | Deposit date: | 2022-04-20 | | Release date: | 2022-11-09 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.65 Å) | | Cite: | Molecular basis for thermal stability and affinity in a VHH: Contribution of the framework region and its influence in the conformation of the CDR3.
Protein Sci., 31, 2022
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4WY7
 | | Crystal structure of recombinant 4E10 expressed in Escherichia coli with epitope bound | | Descriptor: | Envelope glycoprotein gp160, Fab 4E10 Heavy chain, Fab 4E10Light chain, ... | | Authors: | Rujas, E, Morante, K, Tsumoto, K, Nieva, J.L, Caaveiro, J.M.M. | | Deposit date: | 2014-11-16 | | Release date: | 2015-03-25 | | Last modified: | 2024-01-10 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | The Atomic Structure of the HIV-1 gp41 Transmembrane Domain and Its Connection to the Immunogenic Membrane-proximal External Region.
J.Biol.Chem., 290, 2015
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7XLI
 | | Crystal structure of IsdB linker-NEAT2 bound to a nanobody (VHH) | | Descriptor: | CALCIUM ION, CHLORIDE ION, Iron-regulated surface determinant protein B, ... | | Authors: | Caaveiro, J.M.M, Valenciano-Bellido, S, Tsumoto, K. | | Deposit date: | 2022-04-21 | | Release date: | 2023-05-31 | | Last modified: | 2024-03-06 | | Method: | X-RAY DIFFRACTION (1.7 Å) | | Cite: | Targeting hemoglobin receptors IsdH and IsdB of Staphylococcus aureus with a single VHH antibody inhibits bacterial growth.
J.Biol.Chem., 299, 2023
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7XLD
 | | Crystal structure of IsdH linker-NEAT3 bound to a nanobody (VHH) | | Descriptor: | Iron-regulated surface determinant protein H, MAGNESIUM ION, Nanobody VHH6, ... | | Authors: | Caaveiro, J.M.M, Valenciano-Bellido, S, Tsumoto, K. | | Deposit date: | 2022-04-21 | | Release date: | 2023-05-31 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.65 Å) | | Cite: | Targeting hemoglobin receptors IsdH and IsdB of Staphylococcus aureus with a single VHH antibody inhibits bacterial growth.
J.Biol.Chem., 299, 2023
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1WSC
 | | Crystal structure of ST0229, function unknown protein from Sulfolobus tokodaii | | Descriptor: | Hypothetical protein ST0229 | | Authors: | Murayama, T, Tanaka, Y, Sasaki, T, Yasutake, Y, Yao, M, Tsumoto, K, Tanaka, I, Kumagai, I. | | Deposit date: | 2004-11-05 | | Release date: | 2005-11-08 | | Last modified: | 2011-07-13 | | Method: | X-RAY DIFFRACTION (2.45 Å) | | Cite: | Crystal structure of ST0229, function unknown protein from Sulfolobus tokodaii
To be Published
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1WOZ
 | | Crystal structure of uncharacterized protein ST1454 from Sulfolobus tokodaii | | Descriptor: | (20S)-2,5,8,11,14,17-HEXAMETHYL-3,6,9,12,15,18-HEXAOXAHENICOSANE-1,20-DIOL, 177aa long conserved hypothetical protein (ST1454) | | Authors: | Sasaki, T, Tanaka, Y, Yasutake, Y, Yao, M, Tanaka, I, Tsumoto, K, Kumagai, I. | | Deposit date: | 2004-08-27 | | Release date: | 2005-10-04 | | Last modified: | 2011-07-13 | | Method: | X-RAY DIFFRACTION (1.94 Å) | | Cite: | Crystal structure of the uncharacterized protein ST1454 from Sulfolobus tokodaii.
To be Published
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1WVT
 | | Crystal structure of uncharacterized protein ST2180 from Sulfolobus tokodaii | | Descriptor: | hypothetical protein ST2180 | | Authors: | Sasaki, T, Tanaka, Y, Yasutake, Y, Tsumoto, K, Tanaka, I, Kumagai, I. | | Deposit date: | 2004-12-27 | | Release date: | 2006-01-03 | | Last modified: | 2023-11-15 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Molecular properties of two proteins homologous to PduO-type ATP:cob(I)alamin adenosyltransferase from Sulfolobus tokodaii
Proteins, 68, 2007
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6AFB
 | | DJ-1 C106S incubated with isatin | | Descriptor: | CHLORIDE ION, DIMETHYL SULFOXIDE, ISATIN, ... | | Authors: | Caaveiro, J.M.M, Tashiro, S, Tsumoto, K. | | Deposit date: | 2018-08-08 | | Release date: | 2018-08-29 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.6 Å) | | Cite: | Discovery and Optimization of Inhibitors of the Parkinson's Disease Associated Protein DJ-1.
ACS Chem. Biol., 13, 2018
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6AFL
 | | DJ-1 with compound 15 | | Descriptor: | 5-fluoranyl-1-(2-phenylethyl)indole-2,3-dione, CHLORIDE ION, Protein/nucleic acid deglycase DJ-1 | | Authors: | Caaveiro, J.M.M, Tashiro, S, Tsumoto, K. | | Deposit date: | 2018-08-08 | | Release date: | 2018-08-29 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.6 Å) | | Cite: | Discovery and Optimization of Inhibitors of the Parkinson's Disease Associated Protein DJ-1.
ACS Chem. Biol., 13, 2018
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6AFD
 | | DJ-1 with compound 6 | | Descriptor: | 7-methyl-1~{H}-indole-2,3-dione, CHLORIDE ION, Protein/nucleic acid deglycase DJ-1 | | Authors: | Caaveiro, J.M.M, Tashiro, S, Tsumoto, K. | | Deposit date: | 2018-08-08 | | Release date: | 2018-08-29 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.48 Å) | | Cite: | Discovery and Optimization of Inhibitors of the Parkinson's Disease Associated Protein DJ-1.
ACS Chem. Biol., 13, 2018
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6AFC
 | | DJ-1 with compound 4 | | Descriptor: | 5-fluoranyl-1~{H}-indole-2,3-dione, CHLORIDE ION, Protein/nucleic acid deglycase DJ-1 | | Authors: | Caaveiro, J.M.M, Tashiro, S, Tsumoto, K. | | Deposit date: | 2018-08-08 | | Release date: | 2018-08-29 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.45 Å) | | Cite: | Discovery and Optimization of Inhibitors of the Parkinson's Disease Associated Protein DJ-1.
ACS Chem. Biol., 13, 2018
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6AF7
 | | DJ-1 C106S unbound | | Descriptor: | CHLORIDE ION, PENTAETHYLENE GLYCOL, Protein/nucleic acid deglycase DJ-1 | | Authors: | Caaveiro, J.M.M, Tashiro, S, Tsumoto, K. | | Deposit date: | 2018-08-08 | | Release date: | 2018-08-29 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.3 Å) | | Cite: | Discovery and Optimization of Inhibitors of the Parkinson's Disease Associated Protein DJ-1.
ACS Chem. Biol., 13, 2018
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6AFI
 | | DJ-1 with compound 11 | | Descriptor: | 1-ethylindole-2,3-dione, CHLORIDE ION, Protein/nucleic acid deglycase DJ-1 | | Authors: | Caaveiro, J.M.M, Tashiro, S, Tsumoto, K. | | Deposit date: | 2018-08-08 | | Release date: | 2018-08-29 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.65 Å) | | Cite: | Discovery and Optimization of Inhibitors of the Parkinson's Disease Associated Protein DJ-1.
ACS Chem. Biol., 13, 2018
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6AF5
 | | DJ-1 after backsoaking | | Descriptor: | CHLORIDE ION, ISATIN, Protein/nucleic acid deglycase DJ-1 | | Authors: | Caaveiro, J.M.M, Tashiro, S, Tsumoto, K. | | Deposit date: | 2018-08-08 | | Release date: | 2018-08-29 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.65 Å) | | Cite: | Discovery and Optimization of Inhibitors of the Parkinson's Disease Associated Protein DJ-1.
ACS Chem. Biol., 13, 2018
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6AFG
 | | DJ-1 with compound 9 | | Descriptor: | 1-methylindole-2,3-dione, Protein/nucleic acid deglycase DJ-1 | | Authors: | Caaveiro, J.M.M, Tashiro, S, Tsumoto, K. | | Deposit date: | 2018-08-08 | | Release date: | 2018-08-29 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.5 Å) | | Cite: | Discovery and Optimization of Inhibitors of the Parkinson's Disease Associated Protein DJ-1.
ACS Chem. Biol., 13, 2018
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6AFH
 | | DJ-1 with compound 10 | | Descriptor: | 1-(2-phenylethyl)indole-2,3-dione, CHLORIDE ION, Protein/nucleic acid deglycase DJ-1 | | Authors: | Caaveiro, J.M.M, Tashiro, S, Tsumoto, K. | | Deposit date: | 2018-08-08 | | Release date: | 2018-08-29 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.65 Å) | | Cite: | Discovery and Optimization of Inhibitors of the Parkinson's Disease Associated Protein DJ-1.
ACS Chem. Biol., 13, 2018
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6AFA
 | | DJ-1 with isatin (low concentration) | | Descriptor: | CHLORIDE ION, ISATIN, Protein/nucleic acid deglycase DJ-1 | | Authors: | Caaveiro, J.M.M, Tashiro, S, Tsumoto, K. | | Deposit date: | 2018-08-08 | | Release date: | 2018-08-29 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.65 Å) | | Cite: | Discovery and Optimization of Inhibitors of the Parkinson's Disease Associated Protein DJ-1.
ACS Chem. Biol., 13, 2018
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6AFE
 | | DJ-1 with compound 7 | | Descriptor: | 7-(trifluoromethyl)-1~{H}-indole-2,3-dione, CHLORIDE ION, Protein/nucleic acid deglycase DJ-1 | | Authors: | Caaveiro, J.M.M, Tashiro, S, Tsumoto, K. | | Deposit date: | 2018-08-08 | | Release date: | 2018-08-29 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.5 Å) | | Cite: | Discovery and Optimization of Inhibitors of the Parkinson's Disease Associated Protein DJ-1.
ACS Chem. Biol., 13, 2018
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6AF9
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6AFF
 | | DJ-1 with compound 8 | | Descriptor: | CHLORIDE ION, Protein/nucleic acid deglycase DJ-1, methyl 2,3-bis(oxidanylidene)-1~{H}-indole-7-carboxylate | | Authors: | Caaveiro, J.M.M, Tashiro, S, Tsumoto, K. | | Deposit date: | 2018-08-08 | | Release date: | 2018-08-29 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.6 Å) | | Cite: | Discovery and Optimization of Inhibitors of the Parkinson's Disease Associated Protein DJ-1.
ACS Chem. Biol., 13, 2018
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