5YD4
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5YD5
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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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5AZ2
| Crystal structure of the Fab fragment of 9E5, a murine monoclonal antibody specific for human epiregulin | Descriptor: | anti-human epiregulin antibody 9E5 Fab heavy chain, anti-human epiregulin antibody 9E5 Fab light chain | 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: | 2015-09-16 | Release date: | 2015-12-09 | Last modified: | 2020-02-26 | Method: | X-RAY DIFFRACTION (1.603 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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3VWI
| High resolution crystal structure of FraC in the monomeric form | Descriptor: | AMMONIUM ION, CHLORIDE ION, Fragaceatoxin C, ... | Authors: | Tanaka, K, Morante, K, Caaveiro, J.M.M, Gonzalez-Manas, J.M, Tsumoto, K. | Deposit date: | 2012-08-23 | Release date: | 2013-08-28 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.7 Å) | Cite: | Structural basis for self-assembly of a cytolytic pore lined by protein and lipid Nat Commun, 6, 2015
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5BTQ
| Crystal structure of human heme oxygenase 1 H25R with biliverdin bound | Descriptor: | BILIVERDINE IX ALPHA, Heme oxygenase 1, SULFATE ION | Authors: | Caaveiro, J.M.M, Morante, K, Sigala, P, Tsumoto, K. | Deposit date: | 2015-06-03 | Release date: | 2016-06-08 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.08 Å) | Cite: | In-Cell Enzymology To Probe His-Heme Ligation in Heme Oxygenase Catalysis Biochemistry, 55, 2016
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2D31
| Crystal structure of disulfide-linked HLA-G dimer | Descriptor: | 9-mer peptide from Histone H2A, Beta-2-microglobulin, HLA class I histocompatibility antigen, ... | Authors: | Shiroishi, M, Kuroki, K, Ose, T, Rasubala, L, Shiratori, I, Arase, H, Tsumoto, K, Kumagai, I, Kohda, D, Maenaka, K. | Deposit date: | 2005-09-23 | Release date: | 2006-03-14 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (3.2 Å) | Cite: | Efficient Leukocyte Ig-like Receptor Signaling and Crystal Structure of Disulfide-linked HLA-G Dimer J.Biol.Chem., 281, 2006
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5BPG
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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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3W9P
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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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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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6K2G
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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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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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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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6JB2
| Crystal structure of nanobody D3-L11 mutant Y102A in complex with hen egg-white lysozyme | Descriptor: | CHLORIDE ION, GLYCEROL, Lysozyme C, ... | Authors: | Caaveiro, J.M.M, Tamura, H, Akiba, H, Tsumoto, K. | Deposit date: | 2019-01-25 | Release date: | 2019-11-06 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (1.5 Å) | Cite: | Structural and thermodynamic basis for the recognition of the substrate-binding cleft on hen egg lysozyme by a single-domain antibody. Sci Rep, 9, 2019
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6JB9
| Crystal structure of nanobody D3-L11 (unbound form) | Descriptor: | Nanobody D3-L11, SULFATE ION | Authors: | Caaveiro, J.M.M, Tamura, H, Akiba, H, Tsumoto, K. | Deposit date: | 2019-01-25 | Release date: | 2019-11-06 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (1.15 Å) | Cite: | Structural and thermodynamic basis for the recognition of the substrate-binding cleft on hen egg lysozyme by a single-domain antibody. Sci Rep, 9, 2019
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6JB8
| Crystal structure of nanobody D3-L11 in complex with hen egg-white lysozyme | Descriptor: | CHLORIDE ION, GLYCEROL, Lysozyme C, ... | Authors: | Caaveiro, J.M.M, Tamura, H, Akiba, H, Tsumoto, K. | Deposit date: | 2019-01-25 | Release date: | 2019-11-06 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (1.65 Å) | Cite: | Structural and thermodynamic basis for the recognition of the substrate-binding cleft on hen egg lysozyme by a single-domain antibody. Sci Rep, 9, 2019
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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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