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PDB: 100 件

6JB5
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Crystal structure of nanobody D3-L11 mutant Y102A in complex with hen egg-white lysozyme (form II)
分子名称: CHLORIDE ION, GLYCEROL, Lysozyme C, ...
著者Caaveiro, J.M.M, Tamura, H, Akiba, H, Tsumoto, K.
登録日2019-01-25
公開日2019-11-06
最終更新日2023-11-22
実験手法X-RAY DIFFRACTION (1.55 Å)
主引用文献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
6K2G
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BU of 6k2g by Molmil
Structure of FraE in the monomer state
分子名称: FraE
著者Caaveiro, J.M.M, Morante, K, Tsumoto, K.
登録日2019-05-14
公開日2020-03-25
最終更新日2023-11-22
実験手法X-RAY DIFFRACTION (2.22 Å)
主引用文献The Isolation of New Pore-Forming Toxins from the Sea AnemoneActinia fragaceaProvides Insights into the Mechanisms of Actinoporin Evolution.
Toxins, 11, 2019
7CUE
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BU of 7cue by Molmil
Crystal structure of HID2 bound to human Hemoglobin
分子名称: Amino acid ABC transporter substrate-binding protein, Hemoglobin subunit alpha, Hemoglobin subunit beta, ...
著者Caaveiro, J.M.M, Hoshino, M, Tsumoto, K.
登録日2020-08-22
公開日2021-07-07
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (2.75 Å)
主引用文献Structural basis for the recognition of human hemoglobin by the Shr protein from Streptococcus pyogenes
To Be Published
7CUD
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BU of 7cud by Molmil
Crystal structure of HID in the unbound form
分子名称: Amino acid ABC transporter substrate-binding protein, BROMIDE ION
著者Caaveiro, J.M.M, Hoshino, M, Tsumoto, K.
登録日2020-08-22
公開日2021-07-07
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (1.8 Å)
主引用文献Structural basis for the recognition of human hemoglobin by the Shr protein from Streptococcus pyogenes
To Be Published
7W81
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BU of 7w81 by Molmil
Crystal structure of the heme-bound form of the linker-NEAT3 region of IsdH from Staphylococcus aureus
分子名称: Iron-regulated surface determinant protein H, PROTOPORPHYRIN IX CONTAINING FE
著者Caaveiro, J.M.M, Vu, N, Tsumoto, K.
登録日2021-12-07
公開日2022-10-19
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (1.8 Å)
主引用文献Structure and role of the linker domain of the iron surface-determinant protein IsdH in heme transportation in Staphylococcus aureus.
J.Biol.Chem., 298, 2022
7WKI
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BU of 7wki by Molmil
Structure of the ultra-affinity complex between CFH and a nanobody
分子名称: Anti-CFH nanobody (VHH), Complement factor H
著者Caaveiro, J.M.M, Yokoo, T, Tsumoto, K.
登録日2022-01-10
公開日2022-11-23
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (2.6 Å)
主引用文献Antibody recognition of complement factor H reveals a flexible loop involved in atypical hemolytic uremic syndrome pathogenesis.
J.Biol.Chem., 298, 2022
7EV1
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Crystal structure of LI-Cadherin EC1-2
分子名称: ACETATE ION, CALCIUM ION, Cadherin-17, ...
著者Caaveiro, J.M.M, Yui, A, Tsumoto, K.
登録日2021-05-19
公開日2021-06-16
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (1.38 Å)
主引用文献Mechanism of dimerization and structural features of human LI-cadherin.
J.Biol.Chem., 297, 2021
7XAR
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BU of 7xar by Molmil
Crystal structure of 3C-like protease from SARS-CoV-2 in complex with covalent inhibitor
分子名称: 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, ...
著者Caaveiro, J.M.M, Ochi, J, Takahashi, D, Ueda, T, Ojida, A.
登録日2022-03-18
公開日2022-11-09
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (1.6 Å)
主引用文献Discovery of Chlorofluoroacetamide-Based Covalent Inhibitors for Severe Acute Respiratory Syndrome Coronavirus 2 3CL Protease.
J.Med.Chem., 65, 2022
7XL0
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BU of 7xl0 by Molmil
Crystal structure of Vobarilizumab at 1.70 Angstrom
分子名称: GLYCEROL, Nanobody Vobarilizumab, SULFATE ION
著者Caaveiro, J.M.M, Mori, C, Kinoshita, S, Nakakido, M, Tsumoto, K.
登録日2022-04-20
公開日2022-11-09
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (1.7 Å)
主引用文献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
7XL1
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BU of 7xl1 by Molmil
Crystal structure of chimeric 7D12-Vob nanobody at 1.65 Angstrom
分子名称: Chimeric 7D12-Vob nanobody, MALONATE ION
著者Caaveiro, J.M.M, Kinoshita, S, Mori, C, Nakakido, M, Tsumoto, K.
登録日2022-04-20
公開日2022-11-09
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (1.65 Å)
主引用文献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
7CYM
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BU of 7cym by Molmil
Crystal structure of LI-Cadherin EC1-4
分子名称: 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, ...
著者Caaveiro, J.M.M, Yui, A, Tsumoto, K.
登録日2020-09-03
公開日2021-08-18
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (2.7 Å)
主引用文献Mechanism of dimerization and structural features of human LI-cadherin.
J.Biol.Chem., 297, 2021
7XLI
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BU of 7xli by Molmil
Crystal structure of IsdB linker-NEAT2 bound to a nanobody (VHH)
分子名称: CALCIUM ION, CHLORIDE ION, Iron-regulated surface determinant protein B, ...
著者Caaveiro, J.M.M, Valenciano-Bellido, S, Tsumoto, K.
登録日2022-04-21
公開日2023-05-31
最終更新日2024-03-06
実験手法X-RAY DIFFRACTION (1.7 Å)
主引用文献Targeting hemoglobin receptors IsdH and IsdB of Staphylococcus aureus with a single VHH antibody inhibits bacterial growth.
J.Biol.Chem., 299, 2023
7EKB
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BU of 7ekb by Molmil
Crystal structure of 4E10 modified with pyrene acetamide
分子名称: 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, ...
著者Caaveiro, J.M.M, Rujas, E, Nieva, J.L.
登録日2021-04-05
公開日2021-08-11
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (1.45 Å)
主引用文献Focal accumulation of aromaticity at the CDRH3 loop mitigates 4E10 polyreactivity without altering its HIV neutralization profile.
Iscience, 24, 2021
7EKK
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BU of 7ekk by Molmil
Anti-HIV-1 broadly neutralizing antibody delta-loop 4E10 modified with pyrene acetamide
分子名称: AMMONIUM ION, CHLORIDE ION, GLYCEROL, ...
著者Caaveiro, J.M.M, Rujas, E, Nieva, J.L.
登録日2021-04-05
公開日2021-08-11
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (1.7 Å)
主引用文献Focal accumulation of aromaticity at the CDRH3 loop mitigates 4E10 polyreactivity without altering its HIV neutralization profile.
Iscience, 24, 2021
5YD4
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BU of 5yd4 by Molmil
Crystal structure of the scFv antibody 4B08 with epitope peptide (mutation T6A)
分子名称: Epitope peptide (mutation T6A), SULFATE ION, scFv 4B08
著者Caaveiro, J.M.M, Miyanabe, K, Tsumoto, K.
登録日2017-09-11
公開日2018-06-06
最終更新日2023-11-22
実験手法X-RAY DIFFRACTION (1.35 Å)
主引用文献Intramolecular H-bonds govern the recognition of a flexible peptide by an antibody
J. Biochem., 164, 2018
5YQ5
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BU of 5yq5 by Molmil
Crystal structure of human osteomodulin
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Osteomodulin, PHOSPHATE ION
著者Caaveiro, J.M.M, Tashima, T, Tsumoto, K.
登録日2017-11-05
公開日2018-04-25
最終更新日2023-11-22
実験手法X-RAY DIFFRACTION (2.17 Å)
主引用文献Molecular basis for governing the morphology of type-I collagen fibrils by Osteomodulin.
Commun Biol, 1, 2018
5YD5
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BU of 5yd5 by Molmil
Crystal structure of the scFv antibody 4B08 with epitope peptide (mutation N3A)
分子名称: Peptide epitope (mutation N3A), SULFATE ION, scFv 4B08
著者Caaveiro, J.M.M, Miyanabe, K, Tsumoto, K.
登録日2017-09-11
公開日2018-06-06
最終更新日2023-11-22
実験手法X-RAY DIFFRACTION (1.96 Å)
主引用文献Intramolecular H-bonds govern the recognition of a flexible peptide by an antibody
J. Biochem., 164, 2018
5YD3
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BU of 5yd3 by Molmil
Crystal structure of the scFv antibody 4B08 with epitope peptide
分子名称: Epitope peptide, GLYCEROL, SULFATE ION, ...
著者Caaveiro, J.M.M, Miyanabe, K, Tsumoto, K.
登録日2017-09-11
公開日2018-06-06
最終更新日2023-11-22
実験手法X-RAY DIFFRACTION (1.35 Å)
主引用文献Intramolecular H-bonds govern the recognition of a flexible peptide by an antibody
J. Biochem., 164, 2018
5YC5
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BU of 5yc5 by Molmil
Crystal structure of human IgG-Fc in complex with aglycan and optimized Fc gamma receptor IIIa
分子名称: 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, ...
著者Caaveiro, J.M.M, Tamura, H, Tsumoto, K, Kiyoshi, M.
登録日2017-09-06
公開日2018-03-21
最終更新日2023-11-22
実験手法X-RAY DIFFRACTION (2.71 Å)
主引用文献Assessing the Heterogeneity of the Fc-Glycan of a Therapeutic Antibody Using an engineered Fc gamma Receptor IIIa-Immobilized Column.
Sci Rep, 8, 2018
5YY4
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BU of 5yy4 by Molmil
Crystal structure of the scFv antibody 4B08 with sulfated epitope peptide
分子名称: C-C chemokine receptor type 5, CHLORIDE ION, SULFATE ION, ...
著者Caaveiro, J.M.M, Miyanabe, K, Tsumoto, K.
登録日2017-12-07
公開日2018-07-18
最終更新日2023-11-22
実験手法X-RAY DIFFRACTION (1.59 Å)
主引用文献Tyrosine Sulfation Restricts the Conformational Ensemble of a Flexible Peptide, Strengthening the Binding Affinity for an Antibody
Biochemistry, 57, 2018
3VGN
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BU of 3vgn by Molmil
Crystal Structure of Ketosteroid Isomerase D40N from Pseudomonas putida (pKSI) with bound 3-fluoro-4-nitrophenol
分子名称: 3-fluoro-4-nitrophenol, Steroid Delta-isomerase
著者Caaveiro, J.M.M, Pybus, B, Ringe, D, Petsko, G.A, Sigala, P.A.
登録日2011-08-16
公開日2012-08-22
最終更新日2023-11-08
実験手法X-RAY DIFFRACTION (1.3 Å)
主引用文献Quantitative dissection of hydrogen bond-mediated proton transfer in the ketosteroid isomerase active site
Proc.Natl.Acad.Sci.USA, 110, 2013
3VSY
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BU of 3vsy by Molmil
High-resolution crystal structure of wild-type KSI in the apo form at neutral pH
分子名称: SULFATE ION, Steroid Delta-isomerase
著者Caaveiro, J.M.M, Kobe, A, Tsumoto, K.
登録日2012-05-16
公開日2013-02-27
最終更新日2023-11-08
実験手法X-RAY DIFFRACTION (1.5 Å)
主引用文献Incorporation of rapid thermodynamic data in fragment-based drug discovery.
J.Med.Chem., 56, 2013
3W9P
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BU of 3w9p by Molmil
Crystal structure of monomeric FraC (second crystal form)
分子名称: Fragaceatoxin C
著者Caaveiro, J.M.M, Tanaka, K, Tsumoto, K.
登録日2013-04-09
公開日2014-04-09
最終更新日2023-11-08
実験手法X-RAY DIFFRACTION (2.1 Å)
主引用文献Structural basis for self-assembly of a cytolytic pore lined by protein and lipid
Nat Commun, 6, 2015
6AFB
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DJ-1 C106S incubated with isatin
分子名称: CHLORIDE ION, DIMETHYL SULFOXIDE, ISATIN, ...
著者Caaveiro, J.M.M, Tashiro, S, Tsumoto, K.
登録日2018-08-08
公開日2018-08-29
最終更新日2023-11-22
実験手法X-RAY DIFFRACTION (1.6 Å)
主引用文献Discovery and Optimization of Inhibitors of the Parkinson's Disease Associated Protein DJ-1.
ACS Chem. Biol., 13, 2018
6AFL
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DJ-1 with compound 15
分子名称: 5-fluoranyl-1-(2-phenylethyl)indole-2,3-dione, CHLORIDE ION, Protein/nucleic acid deglycase DJ-1
著者Caaveiro, J.M.M, Tashiro, S, Tsumoto, K.
登録日2018-08-08
公開日2018-08-29
最終更新日2023-11-22
実験手法X-RAY DIFFRACTION (1.6 Å)
主引用文献Discovery and Optimization of Inhibitors of the Parkinson's Disease Associated Protein DJ-1.
ACS Chem. Biol., 13, 2018

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件を2024-07-10に公開中

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