6LDY
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6LDW
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6LDV
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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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3QUG
| Structure of heme transport protein IsdH-NEAT3 from S. aureus in complex with Gallium-porphyrin | Descriptor: | GLYCEROL, Iron-regulated surface determinant protein H, PROTOPORPHYRIN IX CONTAINING GA, ... | Authors: | Moriwaki, Y, Caaveiro, J.M.M, Tsumoto, K. | Deposit date: | 2011-02-24 | Release date: | 2011-03-30 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (1.7 Å) | Cite: | Molecular basis of recognition of antibacterial porphyrins by heme-transporter IsdH-NEAT3 of Staphylococcus aureus. Biochemistry, 50, 2011
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3QUH
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3ST7
| Crystal Structure of capsular polysaccharide assembling protein CapF from staphylococcus aureus | Descriptor: | Capsular polysaccharide synthesis enzyme Cap5F, GLYCEROL, ZINC ION | Authors: | Miyafusa, T, Tanaka, Y, Kuroda, M, Yao, M, Watanabe, M, Ohta, T, Tanaka, I, Caaveiro, J.M.M, Tsumoto, K. | Deposit date: | 2011-07-09 | Release date: | 2012-02-15 | Last modified: | 2023-12-06 | Method: | X-RAY DIFFRACTION (2.45 Å) | Cite: | Crystal structure of the enzyme CapF of Staphylococcus aureus reveals a unique architecture composed of two functional domains. Biochem.J., 443, 2012
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1C08
| CRYSTAL STRUCTURE OF HYHEL-10 FV-HEN LYSOZYME COMPLEX | Descriptor: | ANTI-HEN EGG WHITE LYSOZYME ANTIBODY (HYHEL-10), LYSOZYME | Authors: | Shiroishi, M, Kondo, H, Matsushima, M, Tsumoto, K, Kumagai, I. | Deposit date: | 1999-07-15 | Release date: | 2000-07-19 | Last modified: | 2023-05-31 | Method: | X-RAY DIFFRACTION (2.3 Å) | Cite: | Crystal structure of anti-Hen egg white lysozyme antibody (HyHEL-10) Fv-antigen complex. Local structural changes in the protein antigen and water-mediated interactions of Fv-antigen and light chain-heavy chain interfaces. J.Biol.Chem., 274, 1999
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6AFE
| DJ-1 with compound 7 | Descriptor: | 7-(trifluoromethyl)-1~{H}-indole-2,3-dione, CHLORIDE ION, Protein/nucleic acid deglycase DJ-1 | Authors: | Caaveiro, J.M.M, Tashiro, S, Tsumoto, K. | Deposit date: | 2018-08-08 | Release date: | 2018-08-29 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (1.5 Å) | Cite: | Discovery and Optimization of Inhibitors of the Parkinson's Disease Associated Protein DJ-1. ACS Chem. Biol., 13, 2018
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6AF9
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6AFJ
| DJ-1 with compound 13 | Descriptor: | CHLORIDE ION, Protein/nucleic acid deglycase DJ-1, butyl 2-[2,3-bis(oxidanylidene)indol-1-yl]ethanoate | Authors: | Caaveiro, J.M.M, Tashiro, S, Tsumoto, K. | Deposit date: | 2018-08-08 | Release date: | 2018-08-29 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (1.48 Å) | Cite: | Discovery and Optimization of Inhibitors of the Parkinson's Disease Associated Protein DJ-1. ACS Chem. Biol., 13, 2018
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6AFF
| DJ-1 with compound 8 | Descriptor: | CHLORIDE ION, Protein/nucleic acid deglycase DJ-1, methyl 2,3-bis(oxidanylidene)-1~{H}-indole-7-carboxylate | Authors: | Caaveiro, J.M.M, Tashiro, S, Tsumoto, K. | Deposit date: | 2018-08-08 | Release date: | 2018-08-29 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (1.6 Å) | Cite: | Discovery and Optimization of Inhibitors of the Parkinson's Disease Associated Protein DJ-1. ACS Chem. Biol., 13, 2018
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7W81
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7WKI
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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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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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8J81
| MDM2 bound with a peptoid | Descriptor: | (2S)-2-[[(2S)-2-[(6-chloranyl-1H-indol-3-yl)methyl-[(2S)-2-[[(2S)-2-[ethanoyl-(phenylmethyl)amino]propanoyl]-methyl-amino]propanoyl]amino]propanoyl]-methyl-amino]-N-(3,3-dimethylbutyl)-N-[(2S)-1-oxidanylidene-1-piperazin-1-yl-propan-2-yl]propanamide, CHLORIDE ION, E3 ubiquitin-protein ligase Mdm2 | Authors: | Yokomine, M, Fukuda, Y, Ago, H, Matsuura, H, Ueno, G, Nagatoishi, S, Yamamoto, M, Tsumoto, K, Jumpei, M, Sando, S. | Deposit date: | 2023-04-28 | Release date: | 2024-05-01 | Method: | X-RAY DIFFRACTION (1.35 Å) | Cite: | A structural and physicochemical study of how a peptoid binds to a protein To Be Published
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8HYI
| Crystal structure of human P-cadherin MEC12 (X dimer) in complex with 2-(2-methyl-5-phenyl-1H-indole-3-yl)ethan-1-amine | Descriptor: | 2-(2-methyl-5-phenyl-1H-indole-3-yl)ethan-1-amine, CALCIUM ION, Cadherin-3, ... | Authors: | Senoo, A, Ito, S, Ueno, G, Nagatoishi, S, Tsumoto, K. | Deposit date: | 2023-01-06 | Release date: | 2023-08-30 | Last modified: | 2023-10-11 | Method: | X-RAY DIFFRACTION (2.85 Å) | Cite: | Modulation of a conformational ensemble by a small molecule that inhibits key protein-protein interactions involved in cell adhesion. Protein Sci., 32, 2023
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5GHW
| Crystal structure of broad neutralizing antibody 10E8 with long epitope bound | Descriptor: | Endogenous retrovirus group K member 8 Env polyprotein, FAB 10E8 HEAVY CHAIN, FAB 10E8 LIGHT CHAIN, ... | Authors: | Caaveiro, J.M.M, Rujas, E, Morante, K, Nieva, J.L, Tsumoto, K. | Deposit date: | 2016-06-21 | Release date: | 2016-11-23 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.4 Å) | Cite: | Structural basis for broad neutralization of HIV-1 through the molecular recognition of 10E8 helical epitope at the membrane interface Sci Rep, 6, 2016
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4TSO
| Crystal structure of FraC with DHPC bound (crystal form I) | Descriptor: | 1,2-dihexanoyl-sn-glycero-3-phosphocholine, Fragaceatoxin C, PHOSPHATE ION, ... | Authors: | Caaveiro, J.M.M, Tanaka, K, Tsumoto, K. | Deposit date: | 2014-06-19 | Release date: | 2015-03-04 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.3 Å) | Cite: | Structural basis for self-assembly of a cytolytic pore lined by protein and lipid Nat Commun, 6, 2015
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4TSP
| Crystal structure of FraC with DHPC bound (crystal form II) | Descriptor: | 1,2-dihexanoyl-sn-glycero-3-phosphocholine, Fragaceatoxin C, PHOSPHATE ION, ... | Authors: | Caaveiro, J.M.M, Tanaka, K, Tsumoto, K. | Deposit date: | 2014-06-19 | Release date: | 2015-03-04 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.15 Å) | Cite: | Structural basis for self-assembly of a cytolytic pore lined by protein and lipid Nat Commun, 6, 2015
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6M5O
| Co-crystal structure of human serine hydroxymethyltransferase 2 in complex with Pyridoxal 5'-phosphate (PLP) and glycodeoxycholic acid | Descriptor: | (3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OIC ACID, GLYCINE, Serine hydroxymethyltransferase, ... | Authors: | Ota, T, Senoo, A, Ito, S, Ueno, G, Nagatoishi, S, Tsumoto, K, Sando, S. | Deposit date: | 2020-03-11 | Release date: | 2021-01-20 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.30000663 Å) | Cite: | Structural basis for selective inhibition of human serine hydroxymethyltransferase by secondary bile acid conjugate. Iscience, 24, 2021
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6M5E
| Human serum albumin with cyclic peptide dalbavancin | Descriptor: | (2S,5S)-5-azanyl-3,4,6-tris(oxidanyl)oxane-2-carboxylic acid, 10-METHYLUNDECANOIC ACID, 2-amino-2-deoxy-beta-D-altropyranuronic acid, ... | Authors: | Ito, S, Senoo, A, Nagatoishi, S, Ohue, M, Yamamoto, M, Tsumoto, K, Wakui, N. | Deposit date: | 2020-03-10 | Release date: | 2020-11-18 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.8 Å) | Cite: | Structural Basis for the Binding Mechanism of Human Serum Albumin Complexed with Cyclic Peptide Dalbavancin. J.Med.Chem., 63, 2020
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6M5D
| Human serum albumin (apo form) | Descriptor: | PHOSPHATE ION, Serum albumin | Authors: | Ito, S, Senoo, A, Nagatoishi, S, Yamamoto, M, Tsumoto, K, Wakui, N. | Deposit date: | 2020-03-10 | Release date: | 2020-11-18 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.6 Å) | Cite: | Structural Basis for the Binding Mechanism of Human Serum Albumin Complexed with Cyclic Peptide Dalbavancin. J.Med.Chem., 63, 2020
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