8JXC
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![BU of 8jxc by Molmil](/molmil-images/mine/8jxc) | rat megalin wingB | Descriptor: | 2-acetamido-2-deoxy-alpha-D-galactopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ... | Authors: | Goto, S, Tsutsumi, A, Lee, Y, Hosojima, M, Kabasawa, H, Komochi, K, Yun-san, L, Nagatoshi, S, Tsumoto, K, Nishizawa, T, Kikkawa, M, Saito, A. | Deposit date: | 2023-06-30 | Release date: | 2024-06-19 | Method: | ELECTRON MICROSCOPY (3.7 Å) | Cite: | Cryo-EM structures elucidate the multiligand receptor nature of megalin. Proc.Natl.Acad.Sci.USA, 121, 2024
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8JXI
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![BU of 8jxi by Molmil](/molmil-images/mine/8jxi) | rat megalin RAP complex wingB | Descriptor: | 2-acetamido-2-deoxy-alpha-D-galactopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ... | Authors: | Goto, S, Tsutsumi, A, Lee, Y, Hosojima, M, Kabasawa, H, Komochi, K, Yun-san, L, Nagatoshi, S, Tsumoto, K, Nishizawa, T, Kikkawa, M, Saito, A. | Deposit date: | 2023-06-30 | Release date: | 2024-06-19 | Method: | ELECTRON MICROSCOPY (3.4 Å) | Cite: | Cryo-EM structures elucidate the multiligand receptor nature of megalin. Proc.Natl.Acad.Sci.USA, 121, 2024
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8JXG
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![BU of 8jxg by Molmil](/molmil-images/mine/8jxg) | rat megalin RAP complex bodyB | Descriptor: | 2-acetamido-2-deoxy-alpha-D-galactopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose, CALCIUM ION, ... | Authors: | Goto, S, Tsutsumi, A, Lee, Y, Hosojima, M, Kabasawa, H, Komochi, K, Yun-san, L, Nagatoshi, S, Tsumoto, K, Nishizawa, T, Kikkawa, M, Saito, A. | Deposit date: | 2023-06-30 | Release date: | 2024-06-19 | Method: | ELECTRON MICROSCOPY (3.2 Å) | Cite: | Cryo-EM structures elucidate the multiligand receptor nature of megalin. Proc.Natl.Acad.Sci.USA, 121, 2024
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8JXA
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![BU of 8jxa by Molmil](/molmil-images/mine/8jxa) | cryo-EM structure of rat megalin bodyB | Descriptor: | 2-acetamido-2-deoxy-alpha-D-galactopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ... | Authors: | Goto, S, Tsutsumi, A, Lee, Y, Hosojima, M, Kabasawa, H, Komochi, K, Yun-san, L, Nagatoshi, S, Tsumoto, K, Nishizawa, T, Kikkawa, M, Saito, A. | Deposit date: | 2023-06-30 | Release date: | 2024-06-19 | Method: | ELECTRON MICROSCOPY (3.8 Å) | Cite: | Cryo-EM structures elucidate the multiligand receptor nature of megalin. Proc.Natl.Acad.Sci.USA, 121, 2024
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8JXB
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![BU of 8jxb by Molmil](/molmil-images/mine/8jxb) | Cryo-EM structure of rat megalin wingAc | Descriptor: | 2-acetamido-2-deoxy-alpha-D-galactopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ... | Authors: | Goto, S, Tsutsumi, A, Lee, Y, Hosojima, M, Kabasawa, H, Komochi, K, Yun-san, L, Nagatoshi, S, Tsumoto, K, Nishizawa, T, Kikkawa, M, Saito, A. | Deposit date: | 2023-06-30 | Release date: | 2024-06-19 | Method: | ELECTRON MICROSCOPY (3.7 Å) | Cite: | Cryo-EM structures elucidate the multiligand receptor nature of megalin. Proc.Natl.Acad.Sci.USA, 121, 2024
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3VTM
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![BU of 3vtm by Molmil](/molmil-images/mine/3vtm) | Structure of heme transport protein IsdH-NEAT3 from S. aureus in complex with Indium-porphyrin | Descriptor: | GLYCEROL, Iron-regulated surface determinant protein H, PROTOPORPHYRIN IX CONTAINING INDIUM | Authors: | Vu, N.T, Caaveiro, J.M.M, Moriwaki, Y, Tsumoto, K. | Deposit date: | 2012-05-31 | Release date: | 2013-05-15 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.8 Å) | Cite: | Selective binding of antimicrobial porphyrins to the heme-receptor IsdH-NEAT3 of Staphylococcus aureus Protein Sci., 22, 2013
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1UFU
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![BU of 1ufu by Molmil](/molmil-images/mine/1ufu) | Crystal structure of ligand binding domain of immunoglobulin-like transcript 2 (ILT2; LIR-1) | Descriptor: | Immunoglobulin-like transcript 2 | Authors: | Shiroishi, M, Amano, K, Rasubala, L, Tsumoto, K, Kumagai, I, Kohda, D, Maenaka, K. | Deposit date: | 2003-06-10 | Release date: | 2004-08-10 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (3 Å) | Cite: | Kinetic and thermodynamic properties of the interaction between Immunoglobulin like transcript (ILT) and MHC class I To be Published
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5CI9
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![BU of 5ci9 by Molmil](/molmil-images/mine/5ci9) | Crystal structure of human Tob in complex with inhibitor fragment 6 | Descriptor: | 1-(propan-2-yl)-1H-benzimidazole-5-carboxylic acid, Protein Tob1, SODIUM ION | Authors: | Bai, Y, Tashiro, S, Nagatoishi, S, Suzuki, T, Tsumoto, K, Bartlam, M, Yamamoto, T. | Deposit date: | 2015-07-11 | Release date: | 2015-11-18 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (2.3 Å) | Cite: | Structural basis for inhibition of the Tob-CNOT7 interaction by a fragment screening approach Protein Cell, 6, 2015
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5CI8
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![BU of 5ci8 by Molmil](/molmil-images/mine/5ci8) | Crystal structure of human Tob in complex with inhibitor fragment 1 | Descriptor: | Protein Tob1, pyrrolo[1,2-a]quinoxalin-4(5H)-one | Authors: | Bai, Y, Tashiro, S, Nagatoishi, S, Suzuki, T, Tsumoto, K, Bartlam, M, Yamamoto, T. | Deposit date: | 2015-07-11 | Release date: | 2015-11-18 | Last modified: | 2015-12-09 | Method: | X-RAY DIFFRACTION (2.328 Å) | Cite: | Structural basis for inhibition of the Tob-CNOT7 interaction by a fragment screening approach Protein Cell, 6, 2015
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1WT5
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![BU of 1wt5 by Molmil](/molmil-images/mine/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: | 2011-07-13 | 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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4YRD
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![BU of 4yrd by Molmil](/molmil-images/mine/4yrd) | Crystal structure of CapF with inhibitor 3-isopropenyl-tropolone | Descriptor: | 2-hydroxy-3-(prop-1-en-2-yl)cyclohepta-2,4,6-trien-1-one, Capsular polysaccharide synthesis enzyme Cap5F, ZINC ION | Authors: | Nakano, K, Chigira, T, Miyafusa, T, Nagatoishi, S, Caaveiro, J.M.M, Tsumoto, K. | Deposit date: | 2015-03-15 | Release date: | 2015-10-21 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.44 Å) | Cite: | Discovery and characterization of natural tropolones as inhibitors of the antibacterial target CapF from Staphylococcus aureus. Sci Rep, 5, 2015
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3VUA
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![BU of 3vua by Molmil](/molmil-images/mine/3vua) | Apo IsdH-NEAT3 in space group P3121 at a resolution of 1.85 A | Descriptor: | ACETATE ION, GLYCEROL, Iron-regulated surface determinant protein H, ... | Authors: | Vu, N.T, Caaveiro, J.M.M, Moriwaki, Y, Tsumoto, K. | Deposit date: | 2012-06-26 | Release date: | 2013-06-26 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.85 Å) | Cite: | Structure of heme transport protein IsdH-NEAT3 from S. aureus in complex with Indium-porphyrin To be Published
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2Z4Q
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![BU of 2z4q by Molmil](/molmil-images/mine/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: | 2023-11-01 | 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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5AZ2
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![BU of 5az2 by Molmil](/molmil-images/mine/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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5BTQ
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![BU of 5btq by Molmil](/molmil-images/mine/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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7CME
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![BU of 7cme by Molmil](/molmil-images/mine/7cme) | Crystal structure of human P-cadherin MEC12 (X dimer) in complex with 2-(5-chloro-2-methyl-1H-indol-3-yl)ethan-1-amine (inhibitor) | Descriptor: | 2-(5-chloro-2-methyl-1H-indol-3-yl)ethan-1-amine, CALCIUM ION, Cadherin-3, ... | Authors: | Senoo, A, Ito, S, Ueno, G, Nagatoishi, S, Tsumoto, K. | Deposit date: | 2020-07-27 | Release date: | 2021-09-15 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.45 Å) | Cite: | Regulation of cadherin dimerization by chemical fragments as a trigger to inhibit cell adhesion Commun Biol, 4, 2021
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7CMF
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![BU of 7cmf by Molmil](/molmil-images/mine/7cmf) | Crystal structure of human P-cadherin REC12 (monomer) in complex with 2-(5-chloro-2-methyl-1H-indol-3-yl)ethan-1-amine (inhibitor) | Descriptor: | 2-(5-chloro-2-methyl-1H-indol-3-yl)ethan-1-amine, CALCIUM ION, Cadherin-3 | Authors: | Senoo, A, Ito, S, Ueno, G, Nagatoishi, S, Tsumoto, K. | Deposit date: | 2020-07-27 | Release date: | 2021-09-15 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.3 Å) | Cite: | Regulation of cadherin dimerization by chemical fragments as a trigger to inhibit cell adhesion Commun Biol, 4, 2021
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6K2G
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6LDX
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6LDY
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6LDW
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6LDV
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6JB5
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![BU of 6jb5 by Molmil](/molmil-images/mine/6jb5) | Crystal structure of nanobody D3-L11 mutant Y102A in complex with hen egg-white lysozyme (form II) | 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 (1.55 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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2YSS
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![BU of 2yss by Molmil](/molmil-images/mine/2yss) | Crystal structure of Humanized HYHEL-10 FV mutant(HQ39KW47Y)-HEN lysozyme complex | Descriptor: | ANTI-LYSOZYME ANTIBODY FV REGION, Lysozyme C | Authors: | Nakanishi, T, Tsumoto, K, Yokota, A, Kondo, H, Kumagai, I. | Deposit date: | 2007-04-03 | Release date: | 2008-04-08 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (2.4 Å) | Cite: | Critical contribution of VH-VL interaction to reshaping of an antibody: the case of humanization of anti-lysozyme antibody, HyHEL-10 Protein Sci., 17, 2008
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2Z92
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![BU of 2z92 by Molmil](/molmil-images/mine/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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