7C7V
 
 | | Vitamin D3 receptor/lithochoric acid derivative complex | | Descriptor: | (4R)-4-[(3R,5R,8R,9S,10S,13R,14S,17R)-10,13-dimethyl-3-(2-methyl-2-oxidanyl-propyl)-2,3,4,5,6,7,8,9,11,12,14,15,16,17-tetradecahydro-1H-cyclopenta[a]phenanthren-17-yl]pentanoic acid, FORMIC ACID, Mediator of RNA polymerase II transcription subunit 1, ... | | Authors: | Masuno, H, Numoto, N, Kagechika, H, Ito, N. | | Deposit date: | 2020-05-26 | | Release date: | 2021-01-20 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Lithocholic Acid Derivatives as Potent Vitamin D Receptor Agonists.
J.Med.Chem., 64, 2021
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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: | 2024-11-13 | | 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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7C7W
 | | Vitamin D3 receptor/lithochoric acid derivative complex | | Descriptor: | (4R)-4-[(3S,5R,8R,9S,10S,13R,14S,17R)-10,13-dimethyl-3-(2-methyl-2-oxidanyl-propyl)-2,3,4,5,6,7,8,9,11,12,14,15,16,17-tetradecahydro-1H-cyclopenta[a]phenanthren-17-yl]pentanoic acid, FORMIC ACID, Mediator of RNA polymerase II transcription subunit 1, ... | | Authors: | Masuno, H, Numoto, N, Kagechika, H, Ito, N. | | Deposit date: | 2020-05-26 | | Release date: | 2021-01-20 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Lithocholic Acid Derivatives as Potent Vitamin D Receptor Agonists.
J.Med.Chem., 64, 2021
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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: | 2024-11-06 | | 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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6ICH
 | | Grb2 SH2 domain in domain swapped dimer form | | Descriptor: | Growth factor receptor-bound protein 2 | | Authors: | Hosoe, Y, Numoto, N, Inaba, S, Ogawa, S, Morii, H, Abe, R, Ito, N, Oda, M. | | Deposit date: | 2018-09-06 | | Release date: | 2019-07-17 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Structural and functional properties of Grb2 SH2 dimer in CD28 binding.
Biophys Physicobio., 16, 2019
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6ICG
 | | Grb2 SH2 domain in phosphopeptide free form | | Descriptor: | GLYCEROL, Growth factor receptor-bound protein 2, SULFATE ION | | Authors: | Hosoe, Y, Numoto, N, Inaba, S, Ogawa, S, Morii, H, Abe, R, Ito, N, Oda, M. | | Deposit date: | 2018-09-06 | | Release date: | 2019-07-17 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.15 Å) | | Cite: | Structural and functional properties of Grb2 SH2 dimer in CD28 binding.
Biophys Physicobio., 16, 2019
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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: | 2024-10-30 | | 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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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: | 2024-10-16 | | 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
 | | 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: | 2024-10-30 | | 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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7E99
 | | Oxy-deoxy intermediate of 400 kDa giant hemoglobin at 13% oxygen saturation | | Descriptor: | Extracellular giant hemoglobin major globin subunit A1, Extracellular giant hemoglobin major globin subunit A2, Extracellular giant hemoglobin major globin subunit B2, ... | | Authors: | Numoto, N, Kawano, Y, Okumura, H, Baba, S, Fukumori, Y, Miki, K, Ito, N. | | Deposit date: | 2021-03-03 | | Release date: | 2021-10-06 | | Last modified: | 2024-10-09 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Coarse snapshots of oxygen-dissociation intermediates of a giant hemoglobin elucidated by determining the oxygen saturation in individual subunits in the crystalline state.
Iucrj, 8, 2021
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7E97
 | | Oxy-deoxy intermediate of 400 kDa giant hemoglobin at 58% oxygen saturation | | Descriptor: | Extracellular giant hemoglobin major globin subunit A1, Extracellular giant hemoglobin major globin subunit A2, Extracellular giant hemoglobin major globin subunit B2, ... | | Authors: | Numoto, N, Kawano, Y, Okumura, H, Baba, S, Fukumori, Y, Miki, K, Ito, N. | | Deposit date: | 2021-03-03 | | Release date: | 2021-10-06 | | Last modified: | 2024-11-20 | | Method: | X-RAY DIFFRACTION (2.7 Å) | | Cite: | Coarse snapshots of oxygen-dissociation intermediates of a giant hemoglobin elucidated by determining the oxygen saturation in individual subunits in the crystalline state.
Iucrj, 8, 2021
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7E98
 | | Oxy-deoxy intermediate of 400 kDa giant hemoglobin at 21% oxygen saturation | | Descriptor: | Extracellular giant hemoglobin major globin subunit A1, Extracellular giant hemoglobin major globin subunit A2, Extracellular giant hemoglobin major globin subunit B2, ... | | Authors: | Numoto, N, Kawano, Y, Okumura, H, Baba, S, Fukumori, Y, Miki, K, Ito, N. | | Deposit date: | 2021-03-03 | | Release date: | 2021-10-06 | | Last modified: | 2024-10-23 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Coarse snapshots of oxygen-dissociation intermediates of a giant hemoglobin elucidated by determining the oxygen saturation in individual subunits in the crystalline state.
Iucrj, 8, 2021
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7E96
 | | Oxy-deoxy intermediate of 400 kDa giant hemoglobin at 69% oxygen saturation | | Descriptor: | CALCIUM ION, Extracellular giant hemoglobin major globin subunit A1, Extracellular giant hemoglobin major globin subunit A2, ... | | Authors: | Numoto, N, Kawano, Y, Okumura, H, Baba, S, Fukumori, Y, Miki, K, Ito, N. | | Deposit date: | 2021-03-03 | | Release date: | 2021-10-06 | | Last modified: | 2024-11-20 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | Coarse snapshots of oxygen-dissociation intermediates of a giant hemoglobin elucidated by determining the oxygen saturation in individual subunits in the crystalline state.
Iucrj, 8, 2021
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7BON
 | | Crystal structure of recombinant horse spleen apo-R52C/E56C/R59C/E63C-Fr | | Descriptor: | 1,2-ETHANEDIOL, CADMIUM ION, CHLORIDE ION, ... | | Authors: | Hishikawa, Y, Maity, B, Ito, N, Abe, S, Lu, D, Ueno, T. | | Deposit date: | 2020-03-19 | | Release date: | 2021-01-27 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.48 Å) | | Cite: | Design of Multinuclear Gold Binding Site at the Two-fold Symmetric Interface of the Ferritin Cage
Chem Lett., 49, 2021
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7BOM
 | | Crystal structure of recombinant horse spleen apo-R52C/E56C/R59C/E63C-Fr immobilized with gold ions. | | Descriptor: | 1,2-ETHANEDIOL, CADMIUM ION, CHLORIDE ION, ... | | Authors: | Hishikawa, Y, Maity, B, Ito, N, Abe, S, Lu, D, Ueno, T. | | Deposit date: | 2020-03-19 | | Release date: | 2021-01-27 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.93 Å) | | Cite: | Design of Multinuclear Gold Binding Site at the Two-fold Symmetric Interface of the Ferritin Cage
Chem Lett., 49, 2021
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5GJI
 | | PI3K p85 N-terminal SH2 domain/CD28-derived peptide complex | | Descriptor: | GLYCEROL, Phosphatidylinositol 3-kinase regulatory subunit alpha, SULFATE ION, ... | | Authors: | Inaba, S, Numoto, N, Morii, H, Ogawa, S, Ikura, T, Abe, R, Ito, N, Oda, M. | | Deposit date: | 2016-06-30 | | Release date: | 2016-12-14 | | Last modified: | 2024-11-20 | | Method: | X-RAY DIFFRACTION (0.9 Å) | | Cite: | Crystal Structures and Thermodynamic Analysis Reveal Distinct Mechanisms of CD28 Phosphopeptide Binding to the Src Homology 2 (SH2) Domains of Three Adaptor Proteins
J. Biol. Chem., 292, 2017
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5GJH
 | | Gads SH2 domain/CD28-derived peptide complex | | Descriptor: | GRB2-related adapter protein 2, T-cell-specific surface glycoprotein CD28 | | Authors: | Inaba, S, Numoto, N, Morii, H, Ogawa, S, Ikura, T, Abe, R, Ito, N, Oda, M. | | Deposit date: | 2016-06-30 | | Release date: | 2016-12-14 | | Last modified: | 2024-11-13 | | Method: | X-RAY DIFFRACTION (1.2 Å) | | Cite: | Crystal Structures and Thermodynamic Analysis Reveal Distinct Mechanisms of CD28 Phosphopeptide Binding to the Src Homology 2 (SH2) Domains of Three Adaptor Proteins
J. Biol. Chem., 292, 2017
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2YM4
 | | Crystal structure of checkpoint kinase 1 (Chk1) in complex with inhibitors | | Descriptor: | 1,2-ETHANEDIOL, SERINE/THREONINE-PROTEIN KINASE CHK1, ethyl 4-[(2R)-2-(aminomethyl)morpholin-4-yl]-3-(3-cyanophenyl)-1H-pyrazolo[3,4-b]pyridine-5-carboxylate | | Authors: | Reader, J.C, Matthews, T.P, Klair, S, Cheung, K.M.J, Scanlon, J, Proisy, N, Addison, G, Ellard, J, Piton, N, Taylor, S, Cherry, M, Fisher, M, Boxall, K, Burns, S, Walton, M.I, Westwood, I.M, Hayes, A, Eve, P, Valenti, M, Brandon, A.H, Box, G, vanMontfort, R.L.M, Williams, D.H, Aherne, G.W, Raynaud, F.I, Eccles, S.A, Garrett, M.D, Collins, I. | | Deposit date: | 2011-06-06 | | Release date: | 2012-01-11 | | Last modified: | 2023-12-20 | | Method: | X-RAY DIFFRACTION (2.35 Å) | | Cite: | Structure-Guided Evolution of Potent and Selective Chk1 Inhibitors Through Scaffold Morphing.
J.Med.Chem., 54, 2011
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2YM6
 | | Crystal structure of checkpoint kinase 1 (Chk1) in complex with inhibitors | | Descriptor: | 1,2-ETHANEDIOL, 1-[(2R)-4-(9H-pyrido[4',3':4,5]pyrrolo[2,3-d]pyrimidin-4-yl)morpholin-2-yl]methanamine, SERINE/THREONINE-PROTEIN KINASE CHK1 | | Authors: | Reader, J.C, Matthews, T.P, Klair, S, Cheung, K.M.J, Scanlon, J, Proisy, N, Addison, G, Ellard, J, Piton, N, Taylor, S, Cherry, M, Fisher, M, Boxall, K, Burns, S, Walton, M.I, Westwood, I.M, Hayes, A, Eve, P, Valenti, M, Brandon, A.H, Box, G, vanMontfort, R.L.M, Williams, D.H, Aherne, G.W, Raynaud, F.I, Eccles, S.A, Garrett, M.D, Collins, I. | | Deposit date: | 2011-06-06 | | Release date: | 2012-01-11 | | Last modified: | 2023-12-20 | | Method: | X-RAY DIFFRACTION (2.01 Å) | | Cite: | Structure-Guided Evolution of Potent and Selective Chk1 Inhibitors Through Scaffold Morphing.
J.Med.Chem., 54, 2011
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2YM5
 | | Crystal structure of checkpoint kinase 1 (Chk1) in complex with inhibitors | | Descriptor: | (3-{4-[(2S)-2-(AMINOMETHYL)MORPHOLIN-4-YL]-7H-PYRROLO[2,3-D]PYRIMIDIN-5-YL}PHENYL)METHANOL, 1,2-ETHANEDIOL, SERINE/THREONINE-PROTEIN KINASE CHK1 | | Authors: | Reader, J.C, Matthews, T.P, Klair, S, Cheung, K.M.J, Scanlon, J, Proisy, N, Addison, G, Ellard, J, Piton, N, Taylor, S, Cherry, M, Fisher, M, Boxall, K, Burns, S, Walton, M.I, Westwood, I.M, Hayes, A, Eve, P, Valenti, M, Brandon, A.H, Box, G, vanMontfort, R.L.M, Williams, D.H, Aherne, G.W, Raynaud, F.I, Eccles, S.A, Garrett, M.D, Collins, I. | | Deposit date: | 2011-06-06 | | Release date: | 2012-01-11 | | Last modified: | 2023-12-20 | | Method: | X-RAY DIFFRACTION (2.03 Å) | | Cite: | Structure-Guided Evolution of Potent and Selective Chk1 Inhibitors Through Scaffold Morphing.
J.Med.Chem., 54, 2011
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2YM8
 | | Crystal structure of checkpoint kinase 1 (Chk1) in complex with inhibitors | | Descriptor: | (R)-5-(8-CHLOROISOQUINOLIN-3-YLAMINO)-3-(1-(DIMETHYLAMINO)PROPAN-2-YLOXY)PYRAZINE-2-CARBONITRILE, 1,2-ETHANEDIOL, SERINE/THREONINE-PROTEIN KINASE CHK1 | | Authors: | Reader, J.C, Matthews, T.P, Klair, S, Cheung, K.M.J, Scanlon, J, Proisy, N, Addison, G, Ellard, J, Piton, N, Taylor, S, Cherry, M, Fisher, M, Boxall, K, Burns, S, Walton, M.I, Westwood, I.M, Hayes, A, Eve, P, Valenti, M, Brandon, A.H, Box, G, vanMontfort, R.L.M, Williams, D.H, Aherne, G.W, Raynaud, F.I, Eccles, S.A, Garrett, M.D, Collins, I. | | Deposit date: | 2011-06-06 | | Release date: | 2012-01-11 | | Last modified: | 2023-12-20 | | Method: | X-RAY DIFFRACTION (2.07 Å) | | Cite: | Structure-Guided Evolution of Potent and Selective Chk1 Inhibitors Through Scaffold Morphing.
J.Med.Chem., 54, 2011
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2YM3
 | | Crystal structure of checkpoint kinase 1 (Chk1) in complex with inhibitors | | Descriptor: | 1,2-ETHANEDIOL, ETHYL 4-(2-(AMINOMETHYL)MORPHOLINO)-1H-PYRAZOLO[3,4-B]PYRIDINE-5-CARBOXYLATE, SERINE/THREONINE-PROTEIN KINASE CHK1 | | Authors: | Reader, J.C, Matthews, T.P, Klair, S, Cheung, K.M.J, Scanlon, J, Proisy, N, Addison, G, Ellard, J, Piton, N, Taylor, S, Cherry, M, Fisher, M, Boxall, K, Burns, S, Walton, M.I, Westwood, I.M, Hayes, A, Eve, P, Valenti, M, Brandon, A.H, Box, G, vanMontfort, R.L.M, Williams, D.H, Aherne, G.W, Raynaud, F.I, Eccles, S.A, Garrett, M.D, Collins, I. | | Deposit date: | 2011-06-06 | | Release date: | 2012-01-11 | | Last modified: | 2023-12-20 | | Method: | X-RAY DIFFRACTION (2.007 Å) | | Cite: | Structure-Guided Evolution of Potent and Selective Chk1 Inhibitors Through Scaffold Morphing.
J.Med.Chem., 54, 2011
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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: | 2024-10-23 | | 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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2ZMI
 | | Crystal Structure of Rat Vitamin D Receptor Bound to Adamantyl Vitamin D Analogs: Structural Basis for Vitamin D Receptor Antagonism and/or Partial Agonism | | Descriptor: | (1R,3R,7E,17beta)-17-{(1S,2E,5R)-5-hydroxy-1-methyl-5-[(3S,5S,7S)-tricyclo[3.3.1.1~3,7~]dec-1-yl]pent-2-en-1-yl}-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol, 1,2-ETHANEDIOL, FORMIC ACID, ... | | Authors: | Nakabayashi, M, Yamada, S, Tanaka, T, Igarashi, M, Yoshimoto, N, Ikura, T, Ito, N, Makishima, M, Tokiwa, H, DeLuca, H.F, Shimizu, M. | | Deposit date: | 2008-04-19 | | Release date: | 2008-09-02 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (1.7 Å) | | Cite: | Crystal structures of rat vitamin d receptor bound to adamantyl vitamin d analogs: structural basis for vitamin d receptor antagonism and partial agonism
J.Med.Chem., 51, 2008
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2ZMH
 | | Crystal Structure of Rat Vitamin D Receptor Bound to Adamantyl Vitamin D Analogs: Structural Basis for Vitamin D Receptor Antagonism and/or Partial Agonism | | Descriptor: | (1R,3R,7E,17beta)-17-{(1R,2E,4R)-4-hydroxy-1-methyl-4-[(3S,5S,7S)-tricyclo[3.3.1.1~3,7~]dec-1-yl]but-2-en-1-yl}-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol, Mediator of RNA polymerase II transcription subunit 1, Vitamin D3 receptor | | Authors: | Nakabayashi, M, Yamada, S, Tanaka, T, Igarashi, M, Yoshimoto, N, Ikura, T, Ito, N, Makishima, M, Tokiwa, H, DeLuca, H.F, Shimizu, M. | | Deposit date: | 2008-04-18 | | Release date: | 2008-09-02 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Crystal structures of rat vitamin d receptor bound to adamantyl vitamin d analogs: structural basis for vitamin d receptor antagonism and partial agonism
J.Med.Chem., 51, 2008
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