7CUE
 
 | | Crystal structure of HID2 bound to human Hemoglobin | | Descriptor: | Amino acid ABC transporter substrate-binding protein, Hemoglobin subunit alpha, Hemoglobin subunit beta, ... | | Authors: | Caaveiro, J.M.M, Hoshino, M, Tsumoto, K. | | Deposit date: | 2020-08-22 | | Release date: | 2021-07-07 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.75 Å) | | Cite: | Structural basis for the recognition of human hemoglobin by the Shr protein from Streptococcus pyogenes
To Be Published
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7CUD
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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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3FZW
 | | Crystal Structure of Ketosteroid Isomerase D40N-D103N from Pseudomonas putida (pKSI) with bound equilenin | | Descriptor: | EQUILENIN, GLYCEROL, ISOPROPYL ALCOHOL, ... | | Authors: | Caaveiro, J.M.M, Ringe, D, Petsko, G.A. | | Deposit date: | 2009-01-26 | | Release date: | 2009-06-02 | | Last modified: | 2023-09-06 | | Method: | X-RAY DIFFRACTION (1.32 Å) | | Cite: | Hydrogen bond coupling in the ketosteroid isomerase active site.
Biochemistry, 48, 2009
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3CPO
 | | Crystal structure of ketosteroid isomerase D40N with bound 2-fluorophenol | | Descriptor: | 2-fluorophenol, Delta(5)-3-ketosteroid isomerase | | Authors: | Caaveiro, J.M.M, Pybus, B, Ringe, D, Petsko, G. | | Deposit date: | 2008-03-31 | | Release date: | 2008-09-23 | | Last modified: | 2023-08-30 | | Method: | X-RAY DIFFRACTION (1.24 Å) | | Cite: | Testing geometrical discrimination within an enzyme active site: constrained hydrogen bonding in the ketosteroid isomerase oxyanion hole
J.Am.Chem.Soc., 130, 2008
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5JYM
 | | Human P-cadherin EC12 with scFv TSP11 bound | | Descriptor: | Antibody scFv TSP11, CALCIUM ION, Cadherin-3 | | Authors: | Caaveiro, J.M.M, Kudo, S, Tsumoto, K. | | Deposit date: | 2016-05-14 | | Release date: | 2016-12-28 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.45 Å) | | Cite: | Disruption of cell adhesion by an antibody targeting the cell-adhesive intermediate (X-dimer) of human P-cadherin
Sci Rep, 7, 2017
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5JYL
 | | Human P-cadherin MEC1 with scFv TSP7 bound | | Descriptor: | CHLORIDE ION, Cadherin-3, GLYCEROL, ... | | Authors: | Caaveiro, J.M.M, Kudo, S, Tsumoto, K. | | Deposit date: | 2016-05-14 | | Release date: | 2016-12-28 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.55 Å) | | Cite: | Disruption of cell adhesion by an antibody targeting the cell-adhesive intermediate (X-dimer) of human P-cadherin
Sci Rep, 7, 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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4W4N
 | | Crystal structure of human Fc at 1.80 A | | 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)-2-acetamido-2-deoxy-beta-D-glucopyranose, 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, GLYCEROL, ... | | Authors: | Caaveiro, J.M.M, Kiyoshi, M, Tsumoto, K. | | Deposit date: | 2014-08-15 | | Release date: | 2015-04-29 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Structural basis for binding of human IgG1 to its high-affinity human receptor Fc gamma RI
Nat Commun, 6, 2015
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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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5YD4
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5YQ5
 | | Crystal structure of human osteomodulin | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, Osteomodulin, PHOSPHATE ION | | Authors: | Caaveiro, J.M.M, Tashima, T, Tsumoto, K. | | Deposit date: | 2017-11-05 | | Release date: | 2018-04-25 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.17 Å) | | Cite: | Molecular basis for governing the morphology of type-I collagen fibrils by Osteomodulin.
Commun Biol, 1, 2018
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5YD5
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7CYM
 | | Crystal structure of LI-Cadherin EC1-4 | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, CALCIUM ION, ... | | Authors: | Caaveiro, J.M.M, Yui, A, Tsumoto, K. | | Deposit date: | 2020-09-03 | | Release date: | 2021-08-18 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.7 Å) | | Cite: | Mechanism of dimerization and structural features of human LI-cadherin.
J.Biol.Chem., 297, 2021
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7EKB
 | | Crystal structure of 4E10 modified with pyrene acetamide | | Descriptor: | ACETATE ION, Fab region of the heavy chain of broadly neutralizing antibody anti-HIV-1 4E10, Fab region of the light chain of the broadly neutralizing anti-HIV-1 antibody 4E10, ... | | Authors: | Caaveiro, J.M.M, Rujas, E, Nieva, J.L. | | Deposit date: | 2021-04-05 | | Release date: | 2021-08-11 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.45 Å) | | Cite: | Focal accumulation of aromaticity at the CDRH3 loop mitigates 4E10 polyreactivity without altering its HIV neutralization profile.
Iscience, 24, 2021
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7EKK
 | | Anti-HIV-1 broadly neutralizing antibody delta-loop 4E10 modified with pyrene acetamide | | Descriptor: | AMMONIUM ION, CHLORIDE ION, GLYCEROL, ... | | Authors: | Caaveiro, J.M.M, Rujas, E, Nieva, J.L. | | Deposit date: | 2021-04-05 | | Release date: | 2021-08-11 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.7 Å) | | Cite: | Focal accumulation of aromaticity at the CDRH3 loop mitigates 4E10 polyreactivity without altering its HIV neutralization profile.
Iscience, 24, 2021
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7EV1
 | | Crystal structure of LI-Cadherin EC1-2 | | Descriptor: | ACETATE ION, CALCIUM ION, Cadherin-17, ... | | Authors: | Caaveiro, J.M.M, Yui, A, Tsumoto, K. | | Deposit date: | 2021-05-19 | | Release date: | 2021-06-16 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.38 Å) | | Cite: | Mechanism of dimerization and structural features of human LI-cadherin.
J.Biol.Chem., 297, 2021
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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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7XAR
 | | Crystal structure of 3C-like protease from SARS-CoV-2 in complex with covalent inhibitor | | Descriptor: | 3C-like proteinase, 4-fluoranyl-~{N}-[(2~{S})-1-[2-(2-fluoranylethanoyl)-2-[[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]methyl]hydrazinyl]-4-methyl-1-oxidanylidene-pentan-2-yl]-1~{H}-indole-2-carboxamide, CHLORIDE ION, ... | | Authors: | Caaveiro, J.M.M, Ochi, J, Takahashi, D, Ueda, T, Ojida, A. | | Deposit date: | 2022-03-18 | | Release date: | 2022-11-09 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.6 Å) | | Cite: | Discovery of Chlorofluoroacetamide-Based Covalent Inhibitors for Severe Acute Respiratory Syndrome Coronavirus 2 3CL Protease.
J.Med.Chem., 65, 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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