3W9P
 
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5YD3
 | | Crystal structure of the scFv antibody 4B08 with epitope peptide | | Descriptor: | Epitope peptide, GLYCEROL, SULFATE ION, ... | | Authors: | Caaveiro, J.M.M, Miyanabe, K, Tsumoto, K. | | Deposit date: | 2017-09-11 | | Release date: | 2018-06-06 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.35 Å) | | Cite: | Intramolecular H-bonds govern the recognition of a flexible peptide by an antibody
J. Biochem., 164, 2018
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5YY4
 | | Crystal structure of the scFv antibody 4B08 with sulfated epitope peptide | | Descriptor: | C-C chemokine receptor type 5, CHLORIDE ION, SULFATE ION, ... | | Authors: | Caaveiro, J.M.M, Miyanabe, K, Tsumoto, K. | | Deposit date: | 2017-12-07 | | Release date: | 2018-07-18 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.59 Å) | | Cite: | Tyrosine Sulfation Restricts the Conformational Ensemble of a Flexible Peptide, Strengthening the Binding Affinity for an Antibody
Biochemistry, 57, 2018
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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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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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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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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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6AFJ
 | | DJ-1 with compound 13 | | Descriptor: | CHLORIDE ION, Protein/nucleic acid deglycase DJ-1, butyl 2-[2,3-bis(oxidanylidene)indol-1-yl]ethanoate | | 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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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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5CIP
 | | Crystal Structure of Unbound 4E10 | | Descriptor: | FAB 4E10 HEAVY CHAIN, FAB 4E10 LIGHT CHAIN | | Authors: | Caaveiro, J.M.M, Rujas, E, Nieva, J.L, Tsumoto, K. | | Deposit date: | 2015-07-13 | | Release date: | 2015-09-23 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.48 Å) | | Cite: | Structural and Thermodynamic Basis of Epitope Binding by Neutralizing and Nonneutralizing Forms of the Anti-HIV-1 Antibody 4E10
J.Virol., 89, 2015
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5CIL
 | | Crystal Structure of non-neutralizing version of 4E10 (WDWD) with epitope bound | | Descriptor: | ACETATE ION, CHLORIDE ION, FAB 4E10 HEAVY CHAIN, ... | | Authors: | Caaveiro, J.M.M, Rujas, E, Nieva, J.L, Tsumoto, K. | | Deposit date: | 2015-07-13 | | Release date: | 2015-09-23 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.81 Å) | | Cite: | Structural and Thermodynamic Basis of Epitope Binding by Neutralizing and Nonneutralizing Forms of the Anti-HIV-1 Antibody 4E10
J.Virol., 89, 2015
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5CIN
 | | Crystal Structure of non-neutralizing version of 4E10 (DeltaLoop) with epitope bound | | Descriptor: | CHLORIDE ION, FAB 4E10 HEAVY CHAIN, FAB 4E10 LIGHT CHAIN, ... | | Authors: | Caaveiro, J.M.M, Rujas, E, Nieva, J.L, Tsumoto, K. | | Deposit date: | 2015-07-13 | | Release date: | 2015-09-23 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.7 Å) | | Cite: | Structural and Thermodynamic Basis of Epitope Binding by Neutralizing and Nonneutralizing Forms of the Anti-HIV-1 Antibody 4E10
J.Virol., 89, 2015
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1UD9
 | | Crystal Structure of Proliferating Cell Nuclear Antigen (PCNA) Homolog From Sulfolobus tokodaii | | Descriptor: | DNA polymerase sliding clamp A, ZINC ION | | Authors: | Tanabe, E, Yasutake, Y, Tanaka, Y, Yao, M, Tsumoto, K, Kumagai, I, Tanaka, I. | | Deposit date: | 2003-04-28 | | Release date: | 2004-06-15 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (1.68 Å) | | Cite: | Crystal Structure of Proliferating Cell Nuclear Antigen (PCNA) Homolog From Sulfolobus tokodaii
To be published
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5YC5
 | | Crystal structure of human IgG-Fc in complex with aglycan and optimized Fc gamma receptor IIIa | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, CHLORIDE ION, Immunoglobulin gamma-1 heavy chain, ... | | Authors: | Caaveiro, J.M.M, Tamura, H, Tsumoto, K, Kiyoshi, M. | | Deposit date: | 2017-09-06 | | Release date: | 2018-03-21 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.71 Å) | | Cite: | Assessing the Heterogeneity of the Fc-Glycan of a Therapeutic Antibody Using an engineered Fc gamma Receptor IIIa-Immobilized Column.
Sci Rep, 8, 2018
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1UA6
 | | Crystal structure of HYHEL-10 FV MUTANT SFSF complexed with HEN EGG WHITE LYSOZYME complex | | Descriptor: | Ig VH,anti-lysozyme, Lysozyme C, lysozyme binding Ig kappa chain V23-J2 region | | Authors: | Kumagai, I, Nishimiya, Y, Kondo, H, Tsumoto, K. | | Deposit date: | 2003-02-28 | | Release date: | 2004-03-09 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Structural consequences of target epitope-directed functional alteration of an antibody. The case of anti-hen lysozyme antibody, HyHEL-10
J.Biol.Chem., 278, 2003
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3ST7
 | | Crystal Structure of capsular polysaccharide assembling protein CapF from staphylococcus aureus | | Descriptor: | Capsular polysaccharide synthesis enzyme Cap5F, GLYCEROL, ZINC ION | | Authors: | Miyafusa, T, Tanaka, Y, Kuroda, M, Yao, M, Watanabe, M, Ohta, T, Tanaka, I, Caaveiro, J.M.M, Tsumoto, K. | | Deposit date: | 2011-07-09 | | Release date: | 2012-02-15 | | Last modified: | 2023-12-06 | | Method: | X-RAY DIFFRACTION (2.45 Å) | | Cite: | Crystal structure of the enzyme CapF of Staphylococcus aureus reveals a unique architecture composed of two functional domains.
Biochem.J., 443, 2012
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1UKU
 | | Crystal Structure of Pyrococcus horikoshii CutA1 Complexed with Cu2+ | | Descriptor: | COPPER (II) ION, periplasmic divalent cation tolerance protein CutA | | Authors: | Tanaka, Y, Yasutake, Y, Yao, M, Sakai, N, Tanaka, I, Tsumoto, K, Kumagai, I. | | Deposit date: | 2003-09-01 | | Release date: | 2004-01-13 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (1.45 Å) | | Cite: | Structural implications for heavy metal-induced reversible assembly and aggregation of a protein: the case of Pyrococcus horikoshii CutA.
Febs Lett., 556, 2004
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