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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6LDX
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6LDY
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5Y78
 | | Crystal structure of the triose-phosphate/phosphate translocator in complex with inorganic phosphate | | Descriptor: | (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, PHOSPHATE ION, Putative hexose phosphate translocator | | Authors: | Lee, Y, Nishizawa, T, Takemoto, M, Kumazaki, K, Yamashita, K, Hirata, K, Minoda, A, Nagatoishi, S, Tsumoto, K, Ishitani, R, Nureki, O. | | Deposit date: | 2017-08-16 | | Release date: | 2017-10-04 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Structure of the triose-phosphate/phosphate translocator reveals the basis of substrate specificity
Nat Plants, 3, 2017
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5Y79
 | | Crystal structure of the triose-phosphate/phosphate translocator in complex with 3-phosphoglycerate | | Descriptor: | (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, 3-PHOSPHOGLYCERIC ACID, CITRATE ANION, ... | | Authors: | Lee, Y, Nishizawa, T, Takemoto, M, Kumazaki, K, Yamashita, K, Hirata, K, Minoda, A, Nagatoishi, S, Tsumoto, K, Ishitani, R, Nureki, O. | | Deposit date: | 2017-08-16 | | Release date: | 2017-10-04 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Structure of the triose-phosphate/phosphate translocator reveals the basis of substrate specificity
Nat Plants, 3, 2017
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3WYQ
 | | Crystal structure of the low-immunogenic core streptavidin mutant LISA-314 (Y22S/Y83S/R84K/E101D/R103K/E116N) at 1.0 A resolution | | Descriptor: | BIOTIN, GLYCEROL, SULFATE ION, ... | | Authors: | Kawato, T, Mizohata, E, Meshizuka, T, Doi, H, Kawamura, T, Matsumura, H, Yumura, K, Tsumoto, K, Kodama, T, Inoue, T, Sugiyama, A. | | Deposit date: | 2014-09-05 | | Release date: | 2014-12-24 | | Last modified: | 2024-05-29 | | Method: | X-RAY DIFFRACTION (1 Å) | | Cite: | Crystal structure of streptavidin mutant with low immunogenicity.
J.Biosci.Bioeng., 119, 2015
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3WYP
 | | Crystal structure of wild-type core streptavidin in complex with D-biotin/biotin-D-sulfoxide at 1.3 A resolution | | Descriptor: | BIOTIN, BIOTIN-D-SULFOXIDE, GLYCEROL, ... | | Authors: | Kawato, T, Mizohata, E, Meshizuka, T, Doi, H, Kawamura, T, Matsumura, H, Yumura, K, Tsumoto, K, Kodama, T, Inoue, T, Sugiyama, A. | | Deposit date: | 2014-09-05 | | Release date: | 2014-12-24 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.3 Å) | | Cite: | Crystal structure of streptavidin mutant with low immunogenicity.
J.Biosci.Bioeng., 119, 2015
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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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2Z91
 | | Crystal structure of the Fab fragment of anti-ciguatoxin antibody 10C9 | | Descriptor: | Anti-ciguatoxin antibody 10C9 FAB heavy chain, Anti-ciguatoxin antibody 10C9 FAB light chain | | Authors: | Ui, M, Tanaka, Y, Tsumoto, K. | | Deposit date: | 2007-09-14 | | Release date: | 2008-05-06 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2.6 Å) | | Cite: | How Protein Recognizes Ladder-like Polycyclic Ethers: INTERACTIONS BETWEEN CIGUATOXIN (CTX3C) FRAGMENTS AND ITS SPECIFIC ANTIBODY 10C9
J.Biol.Chem., 283, 2008
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2Z93
 | | Crystal structure of Fab fragment of anti-ciguatoxin antibody 10C9 in complex with CTX3C-ABCD | | Descriptor: | 1,6:5,9:8,12:11,16-TETRAANHYDRO-2,3,4,10,13,14-HEXADEOXY-D-GLYCERO-D-ALLO-D-GULO-HEPTADECA-2,13-DIENITOL, Anti-ciguatoxin antibody 10C9 Fab heavy chain, Anti-ciguatoxin antibody 10C9 Fab light chain | | Authors: | Ui, M, Tanaka, Y, Tsumoto, K. | | Deposit date: | 2007-09-14 | | Release date: | 2008-05-06 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | How Protein Recognizes Ladder-like Polycyclic Ethers: INTERACTIONS BETWEEN CIGUATOXIN (CTX3C) FRAGMENTS AND ITS SPECIFIC ANTIBODY 10C9
J.Biol.Chem., 283, 2008
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2ZKL
 | | 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, Yao, M, Tanaka, I, Tsumoto, K. | | Deposit date: | 2008-03-25 | | Release date: | 2009-03-31 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (2.61 Å) | | Cite: | Crystal structure of capsular polysaccharide assembling protein from Staphylococcus aureus
to be published
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3A67
 | | Crystal Structure of HyHEL-10 Fv mutant LN31D complexed with hen egg white lysozyme | | Descriptor: | IG VH, anti-lysozyme, Lysozyme C, ... | | Authors: | Yokota, A, Tsumoto, K, Shiroishi, M, Nakanishi, T, Kondo, H, Kumagai, I. | | Deposit date: | 2009-08-24 | | Release date: | 2009-12-22 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Contribution of asparagine residues to the stabilization of a proteinaceous antigen-antibody complex, HyHEL-10-hen egg white lysozyme
J.Biol.Chem., 285, 2010
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3A6C
 | | Crystal Structure of HyHEL-10 Fv mutant LN92D complexed with hen egg white lysozyme | | Descriptor: | IG VH, anti-lysozyme, Lysozyme C, ... | | Authors: | Yokota, A, Tsumoto, K, Shiroishi, M, Nakanishi, T, Kondo, H, Kumagai, I. | | Deposit date: | 2009-08-28 | | Release date: | 2009-12-22 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Contribution of asparagine residues to the stabilization of a proteinaceous antigen-antibody complex, HyHEL-10-hen egg white lysozyme
J.Biol.Chem., 285, 2010
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3A6B
 | | Crystal Structure of HyHEL-10 Fv mutant LN32D complexed with hen egg white lysozyme | | Descriptor: | IG VH, anti-lysozyme, Lysozyme C, ... | | Authors: | Yokota, A, Tsumoto, K, Shiroishi, M, Nakanishi, T, Kondo, H, Kumagai, I. | | Deposit date: | 2009-08-28 | | Release date: | 2009-12-22 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Contribution of asparagine residues to the stabilization of a proteinaceous antigen-antibody complex, HyHEL-10-hen egg white lysozyme
J.Biol.Chem., 285, 2010
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2Z92
 | | Crystal structure of the Fab fragment of anti-ciguatoxin antibody 10C9 in complex with CTX3C_ABCDE | | Descriptor: | (4Z)-2,8:7,12:11,15:14,18:17,22-PENTAANHYDRO-4,5,6,9,10,13,19,20,21-NONADEOXY-D-ARABINO-D-ALLO-D-ALLO-DOCOSA-4,9,20-TRIENITOL, Anti-ciguatoxin antibody 10C9 Fab heavy chain, Anti-ciguatoxin antibody 10C9 Fab light chain, ... | | Authors: | Ui, M, Tanaka, Y, Tsumoto, K. | | Deposit date: | 2007-09-14 | | Release date: | 2008-05-06 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | How Protein Recognizes Ladder-like Polycyclic Ethers: INTERACTIONS BETWEEN CIGUATOXIN (CTX3C) FRAGMENTS AND ITS SPECIFIC ANTIBODY 10C9
J.Biol.Chem., 283, 2008
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2Z6F
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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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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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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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3VVB
 | | Crystal Structure of Capsular Polysaccharide Synthesizing Enzyme CapE from Staphylococcus aureus in apo form | | Descriptor: | CapE, NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE | | Authors: | Miyafusa, T, Caaveiro, J.M, Tanaka, Y, Tsumoto, K. | | Deposit date: | 2012-07-18 | | Release date: | 2013-06-12 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.8 Å) | | Cite: | Crystal structure of the capsular polysaccharide synthesizing protein CapE of Staphylococcus aureus.
Biosci.Rep., 33, 2013
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3VVC
 | | Crystal Structure of Capsular Polysaccharide Synthesizing Enzyme CapE , K126E, in apo form | | Descriptor: | Capsular polysaccharide synthesis enzyme Cap8E, NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE, SULFATE ION | | Authors: | Miyafusa, T, Caaveiro, J.M, Tanaka, Y, Tsumoto, K. | | Deposit date: | 2012-07-18 | | Release date: | 2013-06-12 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Crystal structure of the capsular polysaccharide synthesizing protein CapE of Staphylococcus aureus.
Biosci.Rep., 33, 2013
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3W1V
 | | Crystal Structure of Capsular Polysaccharide Synthesizing Enzyme CapE from Staphylococcus aureus in complex with inihibitor | | Descriptor: | 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, Capsular polysaccharide synthesis enzyme Cap8E, SODIUM ION, ... | | Authors: | Miyafusa, T, Caaveiro, J.M, Tanaka, Y, Tsumoto, K. | | Deposit date: | 2012-11-21 | | Release date: | 2013-06-12 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Crystal structure of the capsular polysaccharide synthesizing protein CapE of Staphylococcus aureus.
Biosci.Rep., 33, 2013
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3WII
 | | Crystal structure of the Fab fragment of B2212A, a murine monoclonal antibody specific for the third fibronectin domain (Fn3) of human ROBO1. | | Descriptor: | anti-human ROBO1 antibody B2212A Fab heavy chain, anti-human ROBO1 antibody B2212A Fab light chain | | Authors: | Nakayama, T, Mizohata, E, Yamashita, T, Nagatoishi, S, Nakakido, M, Iwanari, H, Mochizuki, Y, Kado, Y, Yokota, Y, Sato, R, Tsumoto, K, Fujitani, H, Kodama, T, Hamakubo, T, Inoue, T. | | Deposit date: | 2013-09-12 | | Release date: | 2015-01-21 | | Last modified: | 2017-11-22 | | Method: | X-RAY DIFFRACTION (1.6 Å) | | Cite: | Structural features of interfacial tyrosine residue in ROBO1 fibronectin domain-antibody complex: Crystallographic, thermodynamic, and molecular dynamic analyses
Protein Sci., 24, 2015
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