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3AAM
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BU of 3aam by Molmil
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
3AAL
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BU of 3aal by Molmil
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
1WT5
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BU of 1wt5 by Molmil
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
1J05
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BU of 1j05 by Molmil
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
9IPA
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BU of 9ipa by Molmil
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
9IPE
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BU of 9ipe by Molmil
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
9IP8
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BU of 9ip8 by Molmil
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
9IP9
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BU of 9ip9 by Molmil
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
9IPC
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BU of 9ipc by Molmil
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
9IP7
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BU of 9ip7 by Molmil
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
9IPD
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BU of 9ipd by Molmil
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
9IPB
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BU of 9ipb by Molmil
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
2Z4Q
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BU of 2z4q by Molmil
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
8YX1
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BU of 8yx1 by Molmil
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
8YX9
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BU of 8yx9 by Molmil
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
8YJ7
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BU of 8yj7 by Molmil
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
8YJ8
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BU of 8yj8 by Molmil
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
8YJ5
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BU of 8yj5 by Molmil
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
8YJ6
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BU of 8yj6 by Molmil
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
6M73
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BU of 6m73 by Molmil
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
6M74
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BU of 6m74 by Molmil
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
6KR0
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BU of 6kr0 by Molmil
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
7V5N
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BU of 7v5n by Molmil
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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