6M5W
 
 | | Co-crystal structure of human serine hydroxymethyltransferase 1 in complex with Pyridoxal 5'-phosphate (PLP) and glycodeoxycholic acid | | Descriptor: | (3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OIC ACID, GLYCINE, PYRIDOXAL-5'-PHOSPHATE, ... | | 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 (3.1 Å) | | Cite: | Structural basis for selective inhibition of human serine hydroxymethyltransferase by secondary bile acid conjugate.
Iscience, 24, 2021
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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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3WII
 | | Crystal structure of the Fab fragment of B2212A, a murine monoclonal antibody specific for the third fibronectin domain (Fn3) of human ROBO1. | | Descriptor: | anti-human ROBO1 antibody B2212A Fab heavy chain, anti-human ROBO1 antibody B2212A Fab light chain | | Authors: | Nakayama, T, Mizohata, E, Yamashita, T, Nagatoishi, S, Nakakido, M, Iwanari, H, Mochizuki, Y, Kado, Y, Yokota, Y, Sato, R, Tsumoto, K, Fujitani, H, Kodama, T, Hamakubo, T, Inoue, T. | | Deposit date: | 2013-09-12 | | Release date: | 2015-01-21 | | Last modified: | 2017-11-22 | | Method: | X-RAY DIFFRACTION (1.6 Å) | | Cite: | Structural features of interfacial tyrosine residue in ROBO1 fibronectin domain-antibody complex: Crystallographic, thermodynamic, and molecular dynamic analyses
Protein Sci., 24, 2015
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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
 | | 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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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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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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5E8D
 | | Crystal structure of human epiregulin in complex with the Fab fragment of murine monoclonal antibody 9E5 | | Descriptor: | CHLORIDE ION, GLYCEROL, Proepiregulin, ... | | 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: | 2015-10-14 | | Release date: | 2015-12-09 | | Last modified: | 2020-02-19 | | Method: | X-RAY DIFFRACTION (2.5 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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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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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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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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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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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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5Y78
 | | Crystal structure of the triose-phosphate/phosphate translocator in complex with inorganic phosphate | | Descriptor: | (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, PHOSPHATE ION, Putative hexose phosphate translocator | | Authors: | Lee, Y, Nishizawa, T, Takemoto, M, Kumazaki, K, Yamashita, K, Hirata, K, Minoda, A, Nagatoishi, S, Tsumoto, K, Ishitani, R, Nureki, O. | | Deposit date: | 2017-08-16 | | Release date: | 2017-10-04 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Structure of the triose-phosphate/phosphate translocator reveals the basis of substrate specificity
Nat Plants, 3, 2017
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5Y79
 | | Crystal structure of the triose-phosphate/phosphate translocator in complex with 3-phosphoglycerate | | Descriptor: | (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, 3-PHOSPHOGLYCERIC ACID, CITRATE ANION, ... | | Authors: | Lee, Y, Nishizawa, T, Takemoto, M, Kumazaki, K, Yamashita, K, Hirata, K, Minoda, A, Nagatoishi, S, Tsumoto, K, Ishitani, R, Nureki, O. | | Deposit date: | 2017-08-16 | | Release date: | 2017-10-04 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Structure of the triose-phosphate/phosphate translocator reveals the basis of substrate specificity
Nat Plants, 3, 2017
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6FEK
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7FB7
 | | Crystal structure of human UHRF1 TTD in complex with 5-amino-2,4-dimethylpyridine | | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, 5-amino-2,4-dimethylpyridine, DIMETHYL SULFOXIDE, ... | | Authors: | Kori, S, Arita, K, Yoshimi, S. | | Deposit date: | 2021-07-08 | | Release date: | 2022-01-05 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.45 Å) | | Cite: | Structure-based screening combined with computational and biochemical analyses identified the inhibitor targeting the binding of DNA Ligase 1 to UHRF1.
Bioorg.Med.Chem., 52, 2021
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3WIH
 | | Crystal structure of the third fibronectin domain (Fn3) of human ROBO1 in complex with the Fab fragment of murine monoclonal antibody B2212A. | | Descriptor: | GLYCEROL, Roundabout homolog 1, anti-human ROBO1 antibody B2212A Fab heavy chain, ... | | Authors: | Nakayama, T, Mizohata, E, Yamashita, T, Nagatoishi, M, Iwanari, H, Mochizuki, Y, Kado, Y, Yokota, Y, Sato, R, Tsumoto, K, Fujitani, H, Kodama, T, Hamakubo, T, Inoue, T. | | Deposit date: | 2013-09-12 | | Release date: | 2015-01-21 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.701 Å) | | Cite: | Structural features of interfacial tyrosine residue in ROBO1 fibronectin domain-antibody complex: Crystallographic, thermodynamic, and molecular dynamic analyses
Protein Sci., 24, 2015
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5I20
 | | Crystal structure of protein | | Descriptor: | (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, SULFATE ION, Uncharacterized protein | | Authors: | Ishitani, R, Nureki, O. | | Deposit date: | 2016-02-08 | | Release date: | 2016-06-01 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | Structural basis for amino acid export by DMT superfamily transporter YddG.
Nature, 534, 2016
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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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7W81
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5EW1
 | | Human thrombin sandwiched between two DNA aptamers: HD22 and HD1-deltaT3 | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide, HD1-deltaT3, ... | | Authors: | Pica, A, Russo Krauss, I, Parente, V, Sica, F. | | Deposit date: | 2015-11-20 | | Release date: | 2016-11-30 | | Last modified: | 2024-01-10 | | Method: | X-RAY DIFFRACTION (2.95 Å) | | Cite: | Through-bond effects in the ternary complexes of thrombin sandwiched by two DNA aptamers.
Nucleic Acids Res., 45, 2017
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5EW2
 | | Human thrombin sandwiched between two DNA aptamers: HD22 and HD1-deltaT12 | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide, HD1-deltaT12, ... | | Authors: | Pica, A, Russo Krauss, I, Parente, V, Sica, F. | | Deposit date: | 2015-11-20 | | Release date: | 2016-11-30 | | Last modified: | 2020-07-29 | | Method: | X-RAY DIFFRACTION (3.59 Å) | | Cite: | Through-bond effects in the ternary complexes of thrombin sandwiched by two DNA aptamers.
Nucleic Acids Res., 45, 2017
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4LZ4
 | | X-ray structure of the complex between human thrombin and the TBA deletion mutant lacking thymine 3 nucleobase | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide, POTASSIUM ION, ... | | Authors: | Pica, A, Russo Krauss, I, Merlino, A, Sica, F. | | Deposit date: | 2013-07-31 | | Release date: | 2014-01-08 | | Last modified: | 2020-07-29 | | Method: | X-RAY DIFFRACTION (2.56 Å) | | Cite: | Dissecting the contribution of thrombin exosite I in the recognition of thrombin binding aptamer.
Febs J., 280, 2013
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