3AAM
 
 | | Crystal structure of endonuclease IV from Thermus thermophilus HB8 | | Descriptor: | Endonuclease IV, MANGANESE (II) ION, PHOSPHATE ION | | Authors: | Asano, R, Ishikawa, H, Nakane, S, Baba, S, Nakagawa, N, Kuramitsu, S, Masui, R, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2009-11-20 | | Release date: | 2010-12-01 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (1.58 Å) | | Cite: | An additional C-terminal loop in endonuclease IV, an apurinic/apyrimidinic endonuclease, controls binding affinity to DNA
Acta Crystallogr.,Sect.D, 67, 2011
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3AAL
 | | Crystal Structure of endonuclease IV from Geobacillus kaustophilus | | Descriptor: | CACODYLATE ION, FE (III) ION, Probable endonuclease 4, ... | | Authors: | Asano, R, Ishikawa, H, Nakane, S, Nakagawa, N, Kuramitsu, S, Masui, R, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2009-11-20 | | Release date: | 2010-12-01 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (1.6 Å) | | Cite: | An additional C-terminal loop in endonuclease IV, an apurinic/apyrimidinic endonuclease, controls binding affinity to DNA
Acta Crystallogr.,Sect.D, 67, 2011
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1WT5
 | | The Crystal Structure Of A Humanized Antibody Fv 528 | | Descriptor: | ANTI EGFR ANTIBODY FV REGION | | Authors: | Makabe, K, Tsumoto, K, Asano, R, Kondo, H, Kumagai, I. | | Deposit date: | 2004-11-16 | | Release date: | 2005-05-16 | | Last modified: | 2024-11-13 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Thermodynamic consequences of mutations in vernier zone residues of a humanized anti-human epidermal growth factor receptor murine antibody, 528
J.Biol.Chem., 283, 2008
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1J05
 | | The crystal structure of anti-carcinoembryonic antigen monoclonal antibody T84.66 Fv fragment | | Descriptor: | GLYCEROL, PHOSPHATE ION, anti-CEA mAb T84.66, ... | | Authors: | Kondo, H, Nishimura, Y, Shiroishi, M, Asano, R, Noro, N, Tsumoto, K, Kumagai, I. | | Deposit date: | 2002-11-01 | | Release date: | 2003-12-16 | | Last modified: | 2024-10-23 | | Method: | X-RAY DIFFRACTION (1.5 Å) | | Cite: | The crystal structure of anti-carcinoembryonic antigen monoclonal antibody T84.66 Fv fragment
To be Published
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9IPA
 | | Poly-alanine model for HL-type bispecific diabody Ex3 composed of 528 and OKT3 Fvs in ternary complex with sEGFR and CD3gamma-epsilon (open conformation) | | Descriptor: | Epidermal growth factor receptor, HL-type bispecific diabody Ex3, T-cell surface glycoprotein CD3 gamma chain,T-cell surface glycoprotein CD3 epsilon chain | | Authors: | Sato, K, Uehara, S, Tsugita, A, Matsui, T, Asano, R, Makabe, K, Yokoyama, T, Tanaka, Y. | | Deposit date: | 2024-07-10 | | Release date: | 2025-05-28 | | Last modified: | 2025-06-25 | | Method: | ELECTRON MICROSCOPY (3.85 Å) | | Cite: | Bispecific antibody-antigen complex structures reveal activity enhancement by domain rearrangement
Cell Rep, 2025
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9IPE
 | | Poly-alanine model for LH-type bispecific diabody Ex3 composed of 528 and OKT3 Fvs in ternary complex with sEGFR and CD3gamma-epsilon (open conformation) | | Descriptor: | Epidermal growth factor receptor, LH-type bispecific diabody Ex3, T-cell surface glycoprotein CD3 gamma chain,T-cell surface glycoprotein CD3 epsilon chain | | Authors: | Sato, K, Uehara, S, Tsugita, A, Matsui, T, Asano, R, Makabe, K, Yokoyama, T, Tanaka, Y. | | Deposit date: | 2024-07-10 | | Release date: | 2025-05-28 | | Last modified: | 2025-07-02 | | Method: | ELECTRON MICROSCOPY (3.31 Å) | | Cite: | Bispecific antibody-antigen complex structures reveal activity enhancement by domain rearrangement
Cell Rep, 2025
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9IP8
 | | Poly-alanine model for HL-type bispecific diabody Ex3 composed of 528 and OKT3 Fvs in ternary complex with sEGFR and CD3gamma-epsilon (closed conformation) | | Descriptor: | Epidermal growth factor receptor, HL-type bispecific diabody Ex3, T-cell surface glycoprotein CD3 gamma chain,T-cell surface glycoprotein CD3 epsilon chain | | Authors: | Sato, K, Uehara, S, Tsugita, A, Matsui, T, Asano, R, Makabe, K, Yokoyama, T, Tanaka, Y. | | Deposit date: | 2024-07-10 | | Release date: | 2025-05-28 | | Last modified: | 2025-07-02 | | Method: | ELECTRON MICROSCOPY (3.91 Å) | | Cite: | Bispecific antibody-antigen complex structures reveal activity enhancement by domain rearrangement
Cell Rep, 2025
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9IP9
 | | Poly-alanine model for HL-type bispecific diabody Ex3 composed of 528 and OKT3 Fvs in ternary complex with sEGFR and CD3gamma-epsilon (middle conformation) | | Descriptor: | Epidermal growth factor receptor, HL-type bispecific diabody Ex3, T-cell surface glycoprotein CD3 gamma chain,T-cell surface glycoprotein CD3 epsilon chain | | Authors: | Sato, K, Uehara, S, Tsugita, A, Matsui, T, Asano, R, Makabe, K, Yokoyama, T, Tanaka, Y. | | Deposit date: | 2024-07-10 | | Release date: | 2025-05-28 | | Last modified: | 2025-06-18 | | Method: | ELECTRON MICROSCOPY (3.64 Å) | | Cite: | Bispecific antibody-antigen complex structures reveal activity enhancement by domain rearrangement
Cell Rep, 2025
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9IPC
 | | Poly-alanine model for LH-type bispecific diabody Ex3 composed of 528 and OKT3 Fvs in ternary complex with sEGFR and CD3gamma-epsilon (closed conformation) | | Descriptor: | Epidermal growth factor receptor, LH-type bispecific diabody Ex3, T-cell surface glycoprotein CD3 gamma chain,T-cell surface glycoprotein CD3 epsilon chain | | Authors: | Sato, K, Uehara, S, Tsugita, A, Matsui, T, Asano, R, Makabe, K, Yokoyama, T, Tanaka, Y. | | Deposit date: | 2024-07-10 | | Release date: | 2025-05-28 | | Last modified: | 2025-07-02 | | Method: | ELECTRON MICROSCOPY (3.4 Å) | | Cite: | Bispecific antibody-antigen complex structures reveal activity enhancement by domain rearrangement
Cell Rep, 2025
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9IP7
 | | Local refinement structure of sEGFR and 528 Fv (from HL-type bispecific diabody Ex3) complex | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 528 Fv from HL-type bispecific diabody Ex3, ... | | Authors: | Sato, K, Uehara, S, Tsugita, A, Matsui, T, Asano, R, Makabe, K, Yokoyama, T, Tanaka, Y. | | Deposit date: | 2024-07-10 | | Release date: | 2025-05-28 | | Last modified: | 2025-06-25 | | Method: | ELECTRON MICROSCOPY (3.21 Å) | | Cite: | Bispecific antibody-antigen complex structures reveal activity enhancement by domain rearrangement
Cell Rep, 2025
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9IPD
 | | Poly-alanine model for LH-type bispecific diabody Ex3 composed of 528 and OKT3 Fvs in ternary complex with sEGFR and CD3gamma-epsilon (middle conformation) | | Descriptor: | Epidermal growth factor receptor, LH-type bispecific diabody Ex3, T-cell surface glycoprotein CD3 gamma chain,T-cell surface glycoprotein CD3 epsilon chain | | Authors: | Sato, K, Uehara, S, Tsugita, A, Matsui, T, Asano, R, Makabe, K, Yokoyama, T, Tanaka, Y. | | Deposit date: | 2024-07-10 | | Release date: | 2025-05-28 | | Last modified: | 2025-06-18 | | Method: | ELECTRON MICROSCOPY (3.29 Å) | | Cite: | Bispecific antibody-antigen complex structures reveal activity enhancement by domain rearrangement
Cell Rep, 2025
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9IPB
 | | Local refinement structure of sEGFR and 528 Fv (from LH-type bispecific diabody Ex3) complex | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 528 Fv from LH-type bispecific diabody Ex3, ... | | Authors: | Sato, K, Uehara, S, Tsugita, A, Matsui, T, Asano, R, Makabe, K, Yokoyama, T, Tanaka, Y. | | Deposit date: | 2024-07-10 | | Release date: | 2025-05-28 | | Last modified: | 2025-07-02 | | Method: | ELECTRON MICROSCOPY (2.93 Å) | | Cite: | Bispecific antibody-antigen complex structures reveal activity enhancement by domain rearrangement
Cell Rep, 2025
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2Z4Q
 | | Crystal structure of a murine antibody FAB 528 | | Descriptor: | CADMIUM ION, CHLORIDE ION, anti egfr antibody fab, ... | | Authors: | Nakanishi, T, Tsumoto, K, Asano, R, Kondo, H, Kumagai, I. | | Deposit date: | 2007-06-22 | | Release date: | 2007-10-30 | | Last modified: | 2024-11-13 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Thermodynamic consequences of mutations in vernier zone residues of a humanized anti-human epidermal growth factor receptor murine antibody, 528
J.Biol.Chem., 283, 2008
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8YX1
 | | CD40 in complex with Bleselumab Fab | | Descriptor: | Bleselumab, heavy chain, light chain, ... | | Authors: | Caaveiro, J.M.M, Fernandez-Perez, J, Tsumoto, K. | | Deposit date: | 2024-04-01 | | Release date: | 2024-05-08 | | Last modified: | 2024-11-06 | | Method: | X-RAY DIFFRACTION (2.7 Å) | | Cite: | Crystal structures of human CD40 in complex with monoclonal antibodies dacetuzumab and bleselumab.
Biochem.Biophys.Res.Commun., 714, 2024
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8YX9
 | | CD40 in complex with Dacetuzumab Fab | | Descriptor: | Dacetuzumab, Heavy chain, light chain, ... | | Authors: | Caaveiro, J.M.M, Fernandez-Perez, J, Tsumoto, K. | | Deposit date: | 2024-04-02 | | Release date: | 2024-05-08 | | Last modified: | 2024-10-16 | | Method: | X-RAY DIFFRACTION (2.8 Å) | | Cite: | Crystal structures of human CD40 in complex with monoclonal antibodies dacetuzumab and bleselumab.
Biochem.Biophys.Res.Commun., 714, 2024
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8YJ7
 | | Characerization of a novel format scFvXVHH single-chain Biparatopic antibody against a metal binding protein, MtsA | | Descriptor: | Iron ABC transporter substrate-binding lipoprotein MtsA, ZINC ION, scFv13 | | Authors: | Ito, S, Nagatoishi, S, Nakakido, M, Tsumoto, K. | | Deposit date: | 2024-03-01 | | Release date: | 2024-06-19 | | Last modified: | 2024-11-06 | | Method: | X-RAY DIFFRACTION (2.8 Å) | | Cite: | Characterization of a novel format scFv×VHH single-chain biparatopic antibody against metal binding protein MtsA.
Protein Sci., 33, 2024
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8YJ8
 | | Characerization of a novel format scFvXVHH single-chain Biparatopic antibody against a metal binding protein, MtsA | | Descriptor: | Iron ABC transporter substrate-binding lipoprotein MtsA, VHH43, ZINC ION | | Authors: | Ito, S, Nagatoishi, S, Nakakido, M, Tsumoto, K. | | Deposit date: | 2024-03-01 | | Release date: | 2024-06-19 | | Last modified: | 2024-10-23 | | Method: | X-RAY DIFFRACTION (1.65 Å) | | Cite: | Characterization of a novel format scFv×VHH single-chain biparatopic antibody against metal binding protein MtsA.
Protein Sci., 33, 2024
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8YJ5
 | | Characerization of a novel format scFvXVHH single-chain Biparatopic antibody against a metal binding protein, MtsA | | Descriptor: | Iron ABC transporter substrate-binding lipoprotein MtsA, VHH43 | | Authors: | Ito, S, Nagatoishi, S, Nakakido, M, Tsumoto, K. | | Deposit date: | 2024-03-01 | | Release date: | 2024-06-19 | | Last modified: | 2024-10-30 | | Method: | X-RAY DIFFRACTION (3.66 Å) | | Cite: | Characterization of a novel format scFv×VHH single-chain biparatopic antibody against metal binding protein MtsA.
Protein Sci., 33, 2024
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8YJ6
 | | Characerization of a novel format scFvXVHH single-chain Biparatopic antibody against a metal binding protein, MtsA | | Descriptor: | Iron ABC transporter substrate-binding lipoprotein MtsA, ZINC ION | | Authors: | Ito, S, Nagatoishi, S, Nakakido, M, Tsumoto, K. | | Deposit date: | 2024-03-01 | | Release date: | 2024-06-19 | | Method: | X-RAY DIFFRACTION (1.37 Å) | | Cite: | Characterization of a novel format scFv×VHH single-chain biparatopic antibody against metal binding protein MtsA.
Protein Sci., 33, 2024
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6M73
 | | Crystal structure of Enterococcus hirae L-lactate oxidase in complex with D-lactate form ligand | | Descriptor: | 1,2-ETHANEDIOL, 1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL, 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, ... | | Authors: | Yoshida, H, Hiraka, K, Tsugawa, W, Sode, K. | | Deposit date: | 2020-03-16 | | Release date: | 2021-03-17 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.7 Å) | | Cite: | Structure of lactate oxidase from Enterococcus hirae revealed new aspects of active site loop function: Product-inhibition mechanism and oxygen gatekeeper
Protein Sci., 31, 2022
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6M74
 | | Crystal structure of Enterococcus hirae L-lactate oxidase M207L in complex with D-lactate form ligand | | Descriptor: | 1,2-ETHANEDIOL, 1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL, 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, ... | | Authors: | Yoshida, H, Hiraka, K, Tsugawa, W, Sode, K. | | Deposit date: | 2020-03-16 | | Release date: | 2021-03-17 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.52 Å) | | Cite: | Structure of lactate oxidase from Enterococcus hirae revealed new aspects of active site loop function: Product-inhibition mechanism and oxygen gatekeeper
Protein Sci., 31, 2022
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6KR0
 | | Crystal structure of HL homo-diabody | | Descriptor: | HL diabody | | Authors: | Tanaka, Y. | | Deposit date: | 2019-08-20 | | Release date: | 2020-08-26 | | Last modified: | 2024-11-06 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Association behavior and control of the quality of cancer therapeutic bispecific diabodies expressed in Escherichia coli
Biochem Eng J, 160, 2020
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7V5N
 | | Crystal structure of Fab fragment of bevacizumab bound to DNA aptamer | | Descriptor: | 1,2-ETHANEDIOL, DNA (5'-D(*GP*CP*GP*GP*TP*TP*GP*GP*TP*GP*GP*TP*AP*GP*TP*TP*AP*CP*GP*TP*TP*CP*GP*C)-3'), IMIDAZOLE, ... | | Authors: | Hishiki, A, Tong, J, Todoroki, K, Hashimoto, H. | | Deposit date: | 2021-08-17 | | Release date: | 2022-02-02 | | Last modified: | 2024-11-13 | | Method: | X-RAY DIFFRACTION (1.7 Å) | | Cite: | Development of a DNA aptamer that binds to the complementarity-determining region of therapeutic monoclonal antibody and affinity improvement induced by pH-change for sensitive detection.
Biosens.Bioelectron., 203, 2022
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