7CIO
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![BU of 7cio by Molmil](/molmil-images/mine/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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7CTR
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![BU of 7ctr by Molmil](/molmil-images/mine/7ctr) | Closed form of PET-degrading cutinase Cut190 with thermostability-improving mutations of S226P/R228S/Q138A/D250C-E296C/Q123H/N202H | Descriptor: | 1,4-DIETHYLENE DIOXIDE, Alpha/beta hydrolase family protein | Authors: | Emori, M, Numoto, N, Senga, A, Bekker, G.J, Kamiya, N, Ito, N, Kawai, F, Oda, M. | Deposit date: | 2020-08-20 | Release date: | 2021-02-03 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (1.2 Å) | Cite: | Structural basis of mutants of PET-degrading enzyme from Saccharomonospora viridis AHK190 with high activity and thermal stability. Proteins, 89, 2021
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7CTS
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![BU of 7cts by Molmil](/molmil-images/mine/7cts) | Open form of PET-degrading cutinase Cut190 with thermostability-improving mutations of S226P/R228S/Q138A/D250C-E296C/Q123H/N202H and S176A inactivation | Descriptor: | 1,4-DIETHYLENE DIOXIDE, Alpha/beta hydrolase family protein, BICINE, ... | Authors: | Emori, M, Numoto, N, Senga, A, Bekker, G.J, Kamiya, N, Ito, N, Kawai, F, Oda, M. | Deposit date: | 2020-08-20 | Release date: | 2021-02-03 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (1.1 Å) | Cite: | Structural basis of mutants of PET-degrading enzyme from Saccharomonospora viridis AHK190 with high activity and thermal stability. Proteins, 89, 2021
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7CEF
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![BU of 7cef by Molmil](/molmil-images/mine/7cef) | Crystal structure of PET-degrading cutinase Cut190 /S226P/R228S/ mutant with the C-terminal three residues deletion | Descriptor: | Alpha/beta hydrolase family protein, CALCIUM ION, ZINC ION | Authors: | Senga, A, Numoto, N, Ito, N, Kawai, F, Oda, M. | Deposit date: | 2020-06-23 | Release date: | 2020-08-26 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (1.6 Å) | Cite: | Multiple structural states of Ca2+-regulated PET hydrolase, Cut190, and its correlation with activity and stability. J.Biochem., 169, 2021
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7CEH
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![BU of 7ceh by Molmil](/molmil-images/mine/7ceh) | Crystal structure of PET-degrading cutinase Cut190 S176A/S226P/R228S/ mutant with the C-terminal three residues deletion in ligand ejecting form | Descriptor: | Alpha/beta hydrolase family protein, CALCIUM ION | Authors: | Senga, A, Numoto, N, Ito, N, Kawai, F, Oda, M. | Deposit date: | 2020-06-23 | Release date: | 2020-08-26 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (1.09 Å) | Cite: | Multiple structural states of Ca2+-regulated PET hydrolase, Cut190, and its correlation with activity and stability. J.Biochem., 169, 2021
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6K4Z
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![BU of 6k4z by Molmil](/molmil-images/mine/6k4z) | Single-chain Fv antibody of C6 COMPLEXED WITH 2-(4-HYDROXY-3-NITROPHENYL)ACETIC ACID | Descriptor: | 2-(4-HYDROXY-3-NITROPHENYL)ACETIC ACID, GLYCEROL, SULFATE ION, ... | Authors: | Nishiguchi, A, Numoto, N, Ito, N, Azuma, T, Oda, M. | Deposit date: | 2019-05-27 | Release date: | 2019-09-18 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (1.65 Å) | Cite: | Three-dimensional structure of a high affinity anti-(4-hydroxy-3-nitrophenyl)acetyl antibody possessing a glycine residue at position 95 of the heavy chain. Mol.Immunol., 114, 2019
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4H0Y
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![BU of 4h0y by Molmil](/molmil-images/mine/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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4H0T
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![BU of 4h0t by Molmil](/molmil-images/mine/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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4GY2
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![BU of 4gy2 by Molmil](/molmil-images/mine/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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4H0X
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![BU of 4h0x by Molmil](/molmil-images/mine/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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4H03
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![BU of 4h03 by Molmil](/molmil-images/mine/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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4H0V
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![BU of 4h0v by Molmil](/molmil-images/mine/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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8ISN
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![BU of 8isn by Molmil](/molmil-images/mine/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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1VEA
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![BU of 1vea by Molmil](/molmil-images/mine/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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8YTN
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![BU of 8ytn by Molmil](/molmil-images/mine/8ytn) | Single-chain Fv antibody of E11 | Descriptor: | GLYCEROL, Single-chain Fv antibody of E11 | Authors: | Yoshida, M, Hanazono, Y, Numoto, N, Ito, N, Oda, M. | Deposit date: | 2024-03-26 | Release date: | 2024-07-03 | Last modified: | 2024-07-10 | Method: | X-RAY DIFFRACTION (1.72 Å) | Cite: | Affinity-matured antibody with a disulfide bond in H-CDR3 loop. Arch.Biochem.Biophys., 758, 2024
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8YTO
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![BU of 8yto by Molmil](/molmil-images/mine/8yto) | Single-chain Fv antibody of E11 complex with NP-glycine | Descriptor: | 2-[2-(3-nitro-4-oxidanyl-phenyl)ethanoylamino]ethanoic acid, 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, GLYCEROL, ... | Authors: | Yoshida, M, Hanazono, Y, Numoto, N, Ito, N, Oda, M. | Deposit date: | 2024-03-26 | Release date: | 2024-07-03 | Last modified: | 2024-07-10 | Method: | X-RAY DIFFRACTION (1.04 Å) | Cite: | Affinity-matured antibody with a disulfide bond in H-CDR3 loop. Arch.Biochem.Biophys., 758, 2024
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8YTP
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![BU of 8ytp by Molmil](/molmil-images/mine/8ytp) | Single-chain Fv antibody of E11 complex with NP-glycine under reducing conditions | Descriptor: | 2-[2-(3-nitro-4-oxidanyl-phenyl)ethanoylamino]ethanoic acid, Single-chain Fv antibody of E11 | Authors: | Yoshida, M, Hanazono, Y, Numoto, N, Ito, N, Oda, M. | Deposit date: | 2024-03-26 | Release date: | 2024-07-03 | Last modified: | 2024-07-10 | Method: | X-RAY DIFFRACTION (1.36 Å) | Cite: | Affinity-matured antibody with a disulfide bond in H-CDR3 loop. Arch.Biochem.Biophys., 758, 2024
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7F1I
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![BU of 7f1i by Molmil](/molmil-images/mine/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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7F1H
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![BU of 7f1h by Molmil](/molmil-images/mine/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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7F1J
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![BU of 7f1j by Molmil](/molmil-images/mine/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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7F1K
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![BU of 7f1k by Molmil](/molmil-images/mine/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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7F1L
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![BU of 7f1l by Molmil](/molmil-images/mine/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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4WFJ
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![BU of 4wfj by Molmil](/molmil-images/mine/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
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![BU of 4wfk by Molmil](/molmil-images/mine/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
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![BU of 4wfi by Molmil](/molmil-images/mine/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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