1HMK
 
 | | RECOMBINANT GOAT ALPHA-LACTALBUMIN | | Descriptor: | CALCIUM ION, PROTEIN (ALPHA-LACTALBUMIN) | | Authors: | Horii, K, Matsushima, M, Tsumoto, K, Kumagai, I. | | Deposit date: | 1998-11-26 | | Release date: | 1999-11-26 | | Last modified: | 2024-04-03 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Effect of the extra n-terminal methionine residue on the stability and folding of recombinant alpha-lactalbumin expressed in Escherichia coli.
J.Mol.Biol., 285, 1999
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1IC4
 | | CRYSTAL STRUCTURE OF HYHEL-10 FV MUTANT(HD32A)-HEN LYSOZYME COMPLEX | | Descriptor: | IGG1 FAB CHAIN H, LYSOZYME BINDING IG KAPPA CHAIN, LYSOZYME C | | Authors: | Shiroishi, M, Yokota, A, Tsumoto, K, Kondo, H, Nishimiya, Y, Horii, K, Matsushima, M, Ogasahara, K, Yutani, K, Kumagai, I. | | Deposit date: | 2001-03-30 | | Release date: | 2001-07-18 | | Last modified: | 2021-11-10 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Structural evidence for entropic contribution of salt bridge formation to a protein antigen-antibody interaction: the case of hen lysozyme-HyHEL-10 Fv complex.
J.Biol.Chem., 276, 2001
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1IC7
 | | CRYSTAL STRUCTURE OF HYHEL-10 FV MUTANT(HD32A99A)-HEN LYSOZYME COMPLEX | | Descriptor: | IGG1 FAB CHAIN H, LYSOZYME BINDING IG KAPPA CHAIN, LYSOZYME C | | Authors: | Shiroishi, M, Yokota, A, Tsumoto, K, Kondo, H, Nishimiya, Y, Horii, K, Matsushima, M, Ogasahara, K, Yutani, K, Kumagai, I. | | Deposit date: | 2001-03-30 | | Release date: | 2001-07-18 | | Last modified: | 2021-11-10 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Structural evidence for entropic contribution of salt bridge formation to a protein antigen-antibody interaction: the case of hen lysozyme-HyHEL-10 Fv complex.
J.Biol.Chem., 276, 2001
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1IC5
 | | CRYSTAL STRUCTURE OF HYHEL-10 FV MUTANT(HD99A)-HEN LYSOZYME COMPLEX | | Descriptor: | IGG1 FAB CHAIN H, LYSOZYME BINDING IG KAPPA CHAIN, LYSOZYME C | | Authors: | Shiroishi, M, Yokota, A, Tsumoto, K, Kondo, H, Nishimiya, Y, Horii, K, Matsushima, M, Ogasahara, K, Yutani, K, Kumagai, I. | | Deposit date: | 2001-03-30 | | Release date: | 2001-07-18 | | Last modified: | 2021-11-10 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Structural evidence for entropic contribution of salt bridge formation to a protein antigen-antibody interaction: the case of hen lysozyme-HyHEL-10 Fv complex.
J.Biol.Chem., 276, 2001
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4G5H
 | | Crystal structure of capsular polysaccharide synthesizing enzyme CapE from Staphylococcus aureus in complex with by-product | | Descriptor: | Capsular polysaccharide synthesis enzyme Cap8E, FORMIC ACID, NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE, ... | | Authors: | Miyafusa, T, Caaveiro, J.M.M, Tanaka, Y, Tsumoto, K. | | Deposit date: | 2012-07-18 | | Release date: | 2013-08-28 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (1.88 Å) | | Cite: | Dynamic elements govern the catalytic activity of CapE, a capsular polysaccharide-synthesizing enzyme from Staphylococcus aureus.
Febs Lett., 587, 2013
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8GQ1
 | | HyHEL10 Fab complexed with hen egg lysozyme carrying arginine cluster in framework region of light chain. | | Descriptor: | Heavy Chain of HyHel10 Antibody Fragment (Fab), Light Chain of HyHel10 Antibody Fragment (Fab), Lysozyme C, ... | | Authors: | Matsuura, H, Hirata, K, Sakai, N, Nakakido, M, Tsumoto, K. | | Deposit date: | 2022-08-28 | | Release date: | 2023-08-30 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (3.13 Å) | | Cite: | Arginine cluster introduction on framework region in anti-lysozyme antibody improved association rate constant by changing conformational diversity of CDR loops.
Protein Sci., 32, 2023
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7W81
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7WKI
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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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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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5X08
 | | Crystal structure of broadly neutralizing anti-HIV-1 antibody 4E10, mutant Npro, with peptide bound | | Descriptor: | ACETATE ION, CHLORIDE ION, Envelope glycoprotein gp160, ... | | Authors: | Caaveiro, J.M.M, Rujas, E, Nieva, J.L, Tsumoto, K. | | Deposit date: | 2017-01-20 | | Release date: | 2017-04-05 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.49 Å) | | Cite: | Functional Contacts between MPER and the Anti-HIV-1 Broadly Neutralizing Antibody 4E10 Extend into the Core of the Membrane
J. Mol. Biol., 429, 2017
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5GWF
 | | FraC with GlcNAc(6S) bound | | Descriptor: | 2-acetamido-2-deoxy-6-O-sulfo-alpha-D-glucopyranose, CHLORIDE ION, DELTA-actitoxin-Afr1a, ... | | Authors: | Caaveiro, J.M.M, Tsumoto, K. | | Deposit date: | 2016-09-11 | | Release date: | 2017-06-21 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.55 Å) | | Cite: | Haemolytic actinoporins interact with carbohydrates using their lipid-binding module
Philos. Trans. R. Soc. Lond., B, Biol. Sci., 372, 2017
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8H62
 | | Crystal structure of Internalin A from Listeria monocytogenes with human E-cadherin EC12 | | Descriptor: | ACETATE ION, CALCIUM ION, Cadherin-1, ... | | Authors: | Caaveiro, J.M.M, Nagatoish, S, Tsumoto, K. | | Deposit date: | 2022-10-14 | | Release date: | 2023-10-04 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (1.91 Å) | | Cite: | Anti-InlA single-domain antibodies that inhibit the cell invasion of Listeria monocytogenes.
J.Biol.Chem., 299, 2023
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8H64
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8H63
 | | Crystal structure of Internalin A from Listeria monocytogenes with nanobody VHH10 bound | | Descriptor: | 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, GLYCEROL, ISOPROPYL ALCOHOL, ... | | Authors: | Caaveiro, J.M.M, Nagatoish, S, Tsumoto, K. | | Deposit date: | 2022-10-15 | | Release date: | 2023-10-04 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (1.53 Å) | | Cite: | Anti-InlA single-domain antibodies that inhibit the cell invasion of Listeria monocytogenes.
J.Biol.Chem., 299, 2023
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8HYI
 | | Crystal structure of human P-cadherin MEC12 (X dimer) in complex with 2-(2-methyl-5-phenyl-1H-indole-3-yl)ethan-1-amine | | Descriptor: | 2-(2-methyl-5-phenyl-1H-indole-3-yl)ethan-1-amine, CALCIUM ION, Cadherin-3, ... | | Authors: | Senoo, A, Ito, S, Ueno, G, Nagatoishi, S, Tsumoto, K. | | Deposit date: | 2023-01-06 | | Release date: | 2023-08-30 | | Last modified: | 2023-10-11 | | Method: | X-RAY DIFFRACTION (2.85 Å) | | Cite: | Modulation of a conformational ensemble by a small molecule that inhibits key protein-protein interactions involved in cell adhesion.
Protein Sci., 32, 2023
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4P34
 | | Crystal structure of DJ-1 in sulfenic acid form (fresh crystal) | | Descriptor: | PENTAETHYLENE GLYCOL, Protein DJ-1 | | Authors: | Tashiro, S, Wu, C.-X, Hoang, Q.Q, Caaveiro, J.M.M, Tsumoto, K. | | Deposit date: | 2014-03-05 | | Release date: | 2014-04-09 | | Last modified: | 2023-11-15 | | Method: | X-RAY DIFFRACTION (1.55 Å) | | Cite: | Thermodynamic and Structural Characterization of the Specific Binding of Zn(II) to Human Protein DJ-1.
Biochemistry, 53, 2014
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4P2G
 | | Crystal structure of DJ-1 in sulfinic acid form (aged crystal) | | Descriptor: | 1,2-ETHANEDIOL, PENTAETHYLENE GLYCOL, Protein DJ-1 | | Authors: | Tashiro, S, Wu, C.-X, Hoang, Q.Q, Caaveiro, J.M.M, Tsumoto, K. | | Deposit date: | 2014-03-04 | | Release date: | 2014-04-09 | | Last modified: | 2023-09-27 | | Method: | X-RAY DIFFRACTION (1.35 Å) | | Cite: | Thermodynamic and Structural Characterization of the Specific Binding of Zn(II) to Human Protein DJ-1.
Biochemistry, 53, 2014
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4P36
 | | Crystal structure of DJ-1 With Zn(II) bound (crystal 2) | | Descriptor: | 2,5,8,11,14,17-HEXAOXANONADECAN-19-OL, Protein DJ-1, ZINC ION | | Authors: | Tashiro, S, Wu, C.-X, Hoang, Q.Q, Caaveiro, J.M.M, Tsumoto, K. | | Deposit date: | 2014-03-05 | | Release date: | 2014-04-09 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (1.182 Å) | | Cite: | Thermodynamic and Structural Characterization of the Specific Binding of Zn(II) to Human Protein DJ-1.
Biochemistry, 53, 2014
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4P35
 | | Crystal structure of DJ-1 with Zinc(II) bound (crystal I) | | Descriptor: | CHLORIDE ION, GLYCEROL, Protein DJ-1, ... | | Authors: | Tashiro, S, Wu, C.-X, Hoang, Q.Q, Caaveiro, J.M.M, Tsumoto, K. | | Deposit date: | 2014-03-05 | | Release date: | 2014-04-09 | | Last modified: | 2023-09-27 | | Method: | X-RAY DIFFRACTION (1.75 Å) | | Cite: | Thermodynamic and Structural Characterization of the Specific Binding of Zn(II) to Human Protein DJ-1.
Biochemistry, 53, 2014
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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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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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