2UYR
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2DTM
| Thermodynamic and structural analyses of hydrolytic mechanism by catalytic antibodies | Descriptor: | IMMUNOGLOBULIN 6D9 | Authors: | Oda, M, Ito, N, Tsumuraya, T, Suzuki, K, Fujii, I. | Deposit date: | 2006-07-13 | Release date: | 2007-05-29 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (2.25 Å) | Cite: | Thermodynamic and structural basis for transition-state stabilization in antibody-catalyzed hydrolysis J.Mol.Biol., 369, 2007
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7VGO
| Hen egg lysozyme | Descriptor: | CHLORIDE ION, Lysozyme C, SODIUM ION | Authors: | Oda, M, Ikura, T, Ito, N. | Deposit date: | 2021-09-17 | Release date: | 2022-02-23 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (1.2 Å) | Cite: | Structural Analysis of Hen Egg Lysozyme Refolded after Denaturation at Acidic pH. Protein J., 41, 2022
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7VGP
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3ATG
| endo-1,3-beta-glucanase from Cellulosimicrobium cellulans | Descriptor: | CALCIUM ION, GLUCANASE, GLYCEROL, ... | Authors: | Tanabe, Y, Pang, Z, Oda, M, Mikami, B. | Deposit date: | 2011-01-04 | Release date: | 2012-01-18 | Last modified: | 2024-03-13 | Method: | X-RAY DIFFRACTION (1.66 Å) | Cite: | Structural and thermodynamic characterization of endo-1,3-beta-glucanase: Insights into the substrate recognition mechanism. Biochim. Biophys. Acta, 1866, 2018
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4H0X
| Crystal structure of NAD+-Ia(E380A)-actin complex | Descriptor: | 1,2-ETHANEDIOL, ADENOSINE-5'-TRIPHOSPHATE, Actin, ... | Authors: | Tsurumura, T, Oda, M, Nagahama, M, Tsuge, H. | Deposit date: | 2012-09-10 | Release date: | 2013-02-20 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.33 Å) | Cite: | Arginine ADP-ribosylation mechanism based on structural snapshots of iota-toxin and actin complex Proc.Natl.Acad.Sci.USA, 110, 2013
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4H0T
| Crystal structure of Ia-ADPR-actin complex | Descriptor: | 1,2-ETHANEDIOL, ADENOSINE-5'-TRIPHOSPHATE, Actin, ... | Authors: | Tsurumura, T, Oda, M, Nagahama, M, Tsuge, H. | Deposit date: | 2012-09-10 | Release date: | 2013-02-20 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.2 Å) | Cite: | Arginine ADP-ribosylation mechanism based on structural snapshots of iota-toxin and actin complex Proc.Natl.Acad.Sci.USA, 110, 2013
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4H0Y
| Crystal structure of NAD+-Ia(E380S)-actin complex | Descriptor: | 1,2-ETHANEDIOL, ADENOSINE-5'-TRIPHOSPHATE, Actin, ... | Authors: | Tsurumura, T, Oda, M, Nagahama, M, Tsuge, H. | Deposit date: | 2012-09-10 | Release date: | 2013-02-20 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.94 Å) | Cite: | Arginine ADP-ribosylation mechanism based on structural snapshots of iota-toxin and actin complex Proc.Natl.Acad.Sci.USA, 110, 2013
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4GY2
| Crystal structure of apo-Ia-actin complex | Descriptor: | ADENOSINE-5'-TRIPHOSPHATE, Actin, alpha skeletal muscle, ... | Authors: | Tsurumura, T, Oda, M, Nagahama, M, Tsuge, H. | Deposit date: | 2012-09-05 | Release date: | 2013-02-20 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.71 Å) | Cite: | Arginine ADP-ribosylation mechanism based on structural snapshots of iota-toxin and actin complex Proc.Natl.Acad.Sci.USA, 110, 2013
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4H0V
| Crystal structure of NAD+-Ia(E378S)-actin complex | Descriptor: | 1,2-ETHANEDIOL, ADENOSINE-5'-TRIPHOSPHATE, Actin, ... | Authors: | Tsurumura, T, Oda, M, Nagahama, M, Tsuge, H. | Deposit date: | 2012-09-10 | Release date: | 2013-02-20 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.03 Å) | Cite: | Arginine ADP-ribosylation mechanism based on structural snapshots of iota-toxin and actin complex Proc.Natl.Acad.Sci.USA, 110, 2013
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4H03
| Crystal structure of NAD+-Ia-actin complex | Descriptor: | 1,2-ETHANEDIOL, ADENOSINE-5'-TRIPHOSPHATE, Actin, ... | Authors: | Tsurumura, T, Oda, M, Nagahama, M, Tsuge, H. | Deposit date: | 2012-09-07 | Release date: | 2013-02-20 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.75 Å) | Cite: | Arginine ADP-ribosylation mechanism based on structural snapshots of iota-toxin and actin complex Proc.Natl.Acad.Sci.USA, 110, 2013
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1IDZ
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1IDY
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1VEA
| Crystal Structure of HutP, an RNA binding antitermination protein | Descriptor: | Hut operon positive regulatory protein, N-(2-NAPHTHYL)HISTIDINAMIDE | Authors: | Kumarevel, T.S, Fujimoto, Z, Karthe, P, Oda, M, Mizuno, H, Kumar, P.K.R. | Deposit date: | 2004-03-29 | Release date: | 2004-07-20 | Last modified: | 2023-12-27 | Method: | X-RAY DIFFRACTION (2.8 Å) | Cite: | Crystal Structure of Activated HutP; An RNA Binding Protein that Regulates Transcription of the hut Operon in Bacillus subtilis Structure, 12, 2004
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7CIO
| Molecular interactions of cytoplasmic region of CTLA-4 with SH2 domains of PI3-kinase | Descriptor: | Cytotoxic T-lymphocyte protein 4, Phosphatidylinositol 3-kinase regulatory subunit alpha | Authors: | Iiyama, M, Numoto, N, Ogawa, S, Kuroda, M, Morii, H, Abe, R, Ito, N, Oda, M. | Deposit date: | 2020-07-08 | Release date: | 2020-12-09 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (1.1 Å) | Cite: | Molecular interactions of the CTLA-4 cytoplasmic region with the phosphoinositide 3-kinase SH2 domains. Mol.Immunol., 131, 2021
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3BUZ
| Crystal structure of ia-bTAD-actin complex | Descriptor: | ADENOSINE-5'-TRIPHOSPHATE, Actin, alpha skeletal muscle, ... | Authors: | Tsuge, H, Nagahama, M, Oda, M, Iwamoto, S, Utsunomiya, H, Marquez, V.E, Katunuma, N, Nishizawa, M, Sakurai, J. | Deposit date: | 2008-01-04 | Release date: | 2008-05-13 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (2.81 Å) | Cite: | Structural basis of actin recognition and arginine ADP-ribosylation by Clostridium perfringens iota-toxin Proc.Natl.Acad.Sci.Usa, 105, 2008
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8ISN
| HLA-A24 in complex with modified 9mer WT1 peptide | Descriptor: | Beta-2-microglobulin, CYS-TYR-THR-TRP-ASN-GLN-MET-ASN-LEU, GLYCEROL, ... | Authors: | Bekker, G.J, Numoto, N, Kawasaki, M, Hayashi, T, Yabuno, S, Kozono, Y, Shimizu, T, Kozono, H, Ito, N, Oda, M, Kamiya, N. | Deposit date: | 2023-03-21 | Release date: | 2023-09-13 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (2.48 Å) | Cite: | Elucidation of binding mechanism, affinity, and complex structure between mWT1 tumor-associated antigen peptide and HLA-A*24:02. Protein Sci., 32, 2023
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7F1L
| Designed enzyme RA61 M48K/I72D mutant: form V | Descriptor: | CHLORIDE ION, Engineered Retroaldolase, IMIDAZOLE | Authors: | Fujioka, T, Oka, M, Numoto, N, Ito, N, Oda, M, Tanaka, F. | Deposit date: | 2021-06-09 | Release date: | 2021-11-24 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (1.7 Å) | Cite: | Varying the Directionality of Protein Catalysts for Aldol and Retro-Aldol Reactions. Chembiochem, 23, 2022
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7F1H
| Designed enzyme RA61 M48K/I72D mutant: form I | Descriptor: | Engineered Retroaldolase, FORMIC ACID, GLYCEROL | Authors: | Fujioka, T, Oka, M, Numoto, N, Ito, N, Oda, M, Tanaka, F. | Deposit date: | 2021-06-09 | Release date: | 2021-11-24 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (1.14 Å) | Cite: | Varying the Directionality of Protein Catalysts for Aldol and Retro-Aldol Reactions. Chembiochem, 23, 2022
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7F1K
| Designed enzyme RA61 M48K/I72D mutant: form IV | Descriptor: | Engineered Retroaldolase | Authors: | Fujioka, T, Oka, M, Numoto, N, Ito, N, Oda, M, Tanaka, F. | Deposit date: | 2021-06-09 | Release date: | 2021-11-24 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (1.05 Å) | Cite: | Varying the Directionality of Protein Catalysts for Aldol and Retro-Aldol Reactions. Chembiochem, 23, 2022
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7F1J
| Designed enzyme RA61 M48K/I72D mutant: form III | Descriptor: | Engineered Retroaldolase | Authors: | Fujioka, T, Oka, M, Numoto, N, Ito, N, Oda, M, Tanaka, F. | Deposit date: | 2021-06-09 | Release date: | 2021-11-24 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (1.6 Å) | Cite: | Varying the Directionality of Protein Catalysts for Aldol and Retro-Aldol Reactions. Chembiochem, 23, 2022
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7F1I
| Designed enzyme RA61 M48K/I72D mutant: form II | Descriptor: | Engineered Retroaldolase | Authors: | Fujioka, T, Oka, M, Numoto, N, Ito, N, Oda, M, Tanaka, F. | Deposit date: | 2021-06-09 | Release date: | 2021-11-24 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (1.4 Å) | Cite: | Varying the Directionality of Protein Catalysts for Aldol and Retro-Aldol Reactions. Chembiochem, 23, 2022
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4WFJ
| Crystal structure of PET-degrading cutinase Cut190 S226P mutant in Ca(2+)-bound state at 1.75 angstrom resolution | Descriptor: | CALCIUM ION, CHLORIDE ION, Cutinase | Authors: | Miyakawa, T, Mizushima, H, Ohtsuka, J, Oda, M, Kawai, F, Tanokura, M. | Deposit date: | 2014-09-15 | Release date: | 2014-12-24 | Last modified: | 2020-01-29 | Method: | X-RAY DIFFRACTION (1.75 Å) | Cite: | Structural basis for the Ca(2+)-enhanced thermostability and activity of PET-degrading cutinase-like enzyme from Saccharomonospora viridis AHK190. Appl.Microbiol.Biotechnol., 99, 2015
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4WFK
| Crystal structure of PET-degrading cutinase Cut190 S226P mutant in Ca(2+)-bound state at 2.35 angstrom resolution | Descriptor: | CALCIUM ION, CHLORIDE ION, Cutinase | Authors: | Miyakawa, T, Mizushima, H, Ohtsuka, J, Oda, M, Kawai, F, Tanokura, M. | Deposit date: | 2014-09-15 | Release date: | 2014-12-24 | Last modified: | 2020-01-29 | Method: | X-RAY DIFFRACTION (2.35 Å) | Cite: | Structural basis for the Ca(2+)-enhanced thermostability and activity of PET-degrading cutinase-like enzyme from Saccharomonospora viridis AHK190. Appl.Microbiol.Biotechnol., 99, 2015
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4WFI
| Crystal structure of PET-degrading cutinase Cut190 S226P mutant in Ca(2+)-free state | Descriptor: | Cutinase | Authors: | Miyakawa, T, Mizushima, H, Ohtsuka, J, Oda, M, Kawai, F, Tanokura, M. | Deposit date: | 2014-09-15 | Release date: | 2014-12-24 | Last modified: | 2020-01-29 | Method: | X-RAY DIFFRACTION (1.446 Å) | Cite: | Structural basis for the Ca(2+)-enhanced thermostability and activity of PET-degrading cutinase-like enzyme from Saccharomonospora viridis AHK190. Appl.Microbiol.Biotechnol., 99, 2015
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