7VIS
 
 | | Crystal structure of Au(200EQ)-apo-R168H/L169C-rHLFr | | Descriptor: | 1,2-ETHANEDIOL, CADMIUM ION, CHLORIDE ION, ... | | Authors: | Lu, C, Peng, X, Maity, B, Ito, N, Abe, S, Ueno, T, Lu, D. | | Deposit date: | 2021-09-27 | | Release date: | 2022-06-08 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.85 Å) | | Cite: | Design of a gold clustering site in an engineered apo-ferritin cage.
Commun Chem, 5, 2022
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7VIT
 | | Crystal structure of Au(400EQ)-apo-R168H/L169C-rHLFr | | Descriptor: | CADMIUM ION, CHLORIDE ION, Ferritin light chain, ... | | Authors: | Lu, C, Peng, X, Maity, B, Ito, N, Abe, S, Ueno, T, Lu, D. | | Deposit date: | 2021-09-27 | | Release date: | 2022-06-08 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Design of a gold clustering site in an engineered apo-ferritin cage.
Commun Chem, 5, 2022
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7VIR
 | | Crystal structure of Au(100EQ)-apo-R168H/L169C-rHLFr | | Descriptor: | CADMIUM ION, Ferritin light chain, GOLD ION, ... | | Authors: | Lu, C, Peng, X, Maity, B, Ito, N, Abe, S, Ueno, T, Lu, D. | | Deposit date: | 2021-09-27 | | Release date: | 2022-06-08 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Design of a gold clustering site in an engineered apo-ferritin cage.
Commun Chem, 5, 2022
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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: | 2024-10-30 | | 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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3VJT
 | | Vitamin D receptor complex with a carborane compound | | Descriptor: | 1-(2-[(R)-2,4-Dihydroxybutoxy]ethyl)-12-(5-ethyl-5-hydroxyheptyl)-1,12-dicarba-closo-dodecaborane, Vitamin D3 receptor, peptide from Mediator of RNA polymerase II transcription subunit 1 | | Authors: | Fujii, S, Masuno, M, Kagechika, H, Nakabayashi, M, Ito, N. | | Deposit date: | 2011-10-31 | | Release date: | 2012-02-08 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Boron Cluster-based Development of Potent Nonsecosteroidal Vitamin D Receptor Ligands: Direct Observation of Hydrophobic Interaction between Protein Surface and Carborane
J.Am.Chem.Soc., 133, 2011
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3VT7
 | | Crystal structures of rat VDR-LBD with W282R mutation | | Descriptor: | 5-{2-[1-(5-HYDROXY-1,5-DIMETHYL-HEXYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-4-METHYLENE-CYCLOHEXANE-1,3-DIOL, COACTIVATOR PEPTIDE DRIP, Vitamin D3 receptor | | Authors: | Nakabayashi, M, Shimizu, M, Ikura, T, Ito, N. | | Deposit date: | 2012-05-19 | | Release date: | 2013-05-22 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.65 Å) | | Cite: | Crystal structures of hereditary vitamin D-resistant rickets-associated vitamin D receptor mutants R270L and W282R bound to 1,25-dihydroxyvitamin D3 and synthetic ligands.
J.Med.Chem., 56, 2013
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3VT5
 | | Crystal structures of rat VDR-LBD with R270L mutation | | Descriptor: | (1R,2E,3R,5Z,7E)-17-{(1S)-1-[(2-ethyl-2-hydroxybutyl)sulfanyl]ethyl}-2-(2-hydroxyethylidene)-9,10-secoestra-5,7,16-triene-1,3-diol, COACTIVATOR PEPTIDE DRIP, Vitamin D3 receptor | | Authors: | Nakabayashi, M, Shimizu, M, Ikura, T, Ito, N. | | Deposit date: | 2012-05-19 | | Release date: | 2013-05-22 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.11 Å) | | Cite: | Crystal structures of hereditary vitamin D-resistant rickets-associated vitamin D receptor mutants R270L and W282R bound to 1,25-dihydroxyvitamin D3 and synthetic ligands.
J.Med.Chem., 56, 2013
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3VTB
 | | Crystal structure of rat vitamin D receptor bound to a partial agonist 25-adamantyl-23-yne-19-norvitammin D ADTK1 | | Descriptor: | (1R,3R,7E,17beta)-17-{(2R,6S)-6-hydroxy-6-[(3S,5S,7S)-tricyclo[3.3.1.1~3,7~]dec-1-yl]hex-4-yn-2-yl}-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol, COACTIVATOR PEPTIDE DRIP, Vitamin D3 receptor | | Authors: | Nakabayashi, M, Kudo, T, Tokiwa, H, Makishima, M, Yamada, S, Ikura, T, Ito, N. | | Deposit date: | 2012-05-26 | | Release date: | 2013-06-12 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Combination of Triple Bond and Adamantane Ring on the Vitamin D Side Chain Produced Partial Agonists for Vitamin D Receptor.
J.Med.Chem., 2014
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3VT6
 | | Crystal structure of rat VDR-LBD with 2-Substituted-16-ene-22-thia-1alpha,25-dihydroxy-26,27-dimethyl-19-norvitamin D3 | | Descriptor: | (1R,2Z,3R,5E,7E)-17-{(1S)-1-[(2-ethyl-2-hydroxybutyl)sulfanyl]ethyl}-2-(2-hydroxyethylidene)-9,10-secoestra-5,7,16-triene-1,3-diol, COACTIVATOR PEPTIDE DRIP, Vitamin D3 receptor | | Authors: | Nakabayashi, M, Shimizu, M, Ikura, T, Ito, N. | | Deposit date: | 2012-05-19 | | Release date: | 2013-05-22 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Crystal structures of hereditary vitamin D-resistant rickets-associated vitamin D receptor mutants R270L and W282R bound to 1,25-dihydroxyvitamin D3 and synthetic ligands.
J.Med.Chem., 56, 2013
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3VTC
 | | Crystal structure of rat vitamin D receptor bound to a partial agonist 26-adamantyl-23-yne-19-norvitammin D ADTK3 | | Descriptor: | (1R,3R,7E,17beta)-17-{(2R,6R)-6-hydroxy-7-[(3S,5S,7S)-tricyclo[3.3.1.1~3,7~]dec-1-yl]hept-4-yn-2-yl}-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol, 1,2-ETHANEDIOL, COACTIVATOR PEPTIDE DRIP, ... | | Authors: | Nakabayashi, M, Kudo, T, Tokiwa, H, Makishima, M, Yamada, S, Ikura, T, Ito, N. | | Deposit date: | 2012-05-26 | | Release date: | 2013-06-12 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.5 Å) | | Cite: | Combination of Triple Bond and Adamantane Ring on the Vitamin D Side Chain Produced Partial Agonists for Vitamin D Receptor.
J.Med.Chem., 2014
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3VT3
 | | Crystal structures of rat VDR-LBD with R270L mutation | | Descriptor: | 1,2-ETHANEDIOL, 5-{2-[1-(5-HYDROXY-1,5-DIMETHYL-HEXYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-4-METHYLENE-CYCLOHEXANE-1,3-DIOL, COACTIVATOR PEPTIDE DRIP, ... | | Authors: | Nakabayashi, M, Shimizu, M, Ikura, T, Ito, N. | | Deposit date: | 2012-05-19 | | Release date: | 2013-05-22 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.7 Å) | | Cite: | Crystal structures of hereditary vitamin D-resistant rickets-associated vitamin D receptor mutants R270L and W282R bound to 1,25-dihydroxyvitamin D3 and synthetic ligands.
J.Med.Chem., 56, 2013
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3VT9
 | | Crystal structures of rat VDR-LBD with W282R mutation | | Descriptor: | (1R,2Z,3R,5E,7E,9beta,17beta)-2-(2-hydroxyethylidene)-17-[(2R)-6-hydroxy-6-methylheptan-2-yl]-9-(prop-2-en-1-yl)-9,10-secoestra-5,7-diene-1,3-diol, COACTIVATOR PEPTIDE DRIP, Vitamin D3 receptor | | Authors: | Nakabayashi, M, Shimizu, M, Ikura, T, Ito, N. | | Deposit date: | 2012-05-19 | | Release date: | 2013-05-22 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.35 Å) | | Cite: | Crystal structures of hereditary vitamin D-resistant rickets-associated vitamin D receptor mutants R270L and W282R bound to 1,25-dihydroxyvitamin D3 and synthetic ligands.
J.Med.Chem., 56, 2013
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3VTD
 | | Crystal structure of rat vitamin D receptor bound to a partial agonist 26-adamantyl-23-yne-19-norvitammin D ADTK4 | | Descriptor: | (1R,3R,7E,17beta)-17-{(2R,6S)-6-hydroxy-7-[(3S,5S,7S)-tricyclo[3.3.1.1~3,7~]dec-1-yl]hept-4-yn-2-yl}-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol, COACTIVATOR PEPTIDE DRIP, Vitamin D3 receptor | | Authors: | Nakabayashi, M, Kudo, T, Tokiwa, H, Makishima, M, Yamada, S, Ikura, T, Ito, N. | | Deposit date: | 2012-05-26 | | Release date: | 2013-06-12 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.7 Å) | | Cite: | Combination of Triple Bond and Adamantane Ring on the Vitamin D Side Chain Produced Partial Agonists for Vitamin D Receptor.
J.Med.Chem., 2014
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3VT8
 | | Crystal structures of rat VDR-LBD with W282R mutation | | Descriptor: | (1R,3R,7E,9beta,17beta)-9-butyl-17-[(2R)-6-hydroxy-6-methylheptan-2-yl]-9,10-secoestra-5,7-diene-1,3-diol, COACTIVATOR PEPTIDE DRIP, Vitamin D3 receptor | | Authors: | Nakabayashi, M, Shimizu, M, Ikura, T, Ito, N. | | Deposit date: | 2012-05-19 | | Release date: | 2013-05-22 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Crystal structures of hereditary vitamin D-resistant rickets-associated vitamin D receptor mutants R270L and W282R bound to 1,25-dihydroxyvitamin D3 and synthetic ligands.
J.Med.Chem., 56, 2013
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3W5P
 | | Crystal structure of complexes of vitamin D receptor ligand binding domain with lithocholic acid derivatives | | Descriptor: | (3beta,5beta,14beta,17alpha)-3-hydroxycholan-24-oic acid, Mediator of RNA polymerase II transcription subunit 1, Vitamin D3 receptor | | Authors: | Masuno, H, Ikura, T, Ito, N. | | Deposit date: | 2013-02-05 | | Release date: | 2013-06-26 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Crystal structures of complexes of vitamin D receptor ligand-binding domain with lithocholic acid derivatives.
J.Lipid Res., 54, 2013
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3W5Q
 | | Crystal structure of complexes of vitamin D receptor ligand binding domain with lithocholic acid derivatives | | Descriptor: | (5beta,9beta)-3-oxocholan-24-oic acid, Mediator of RNA polymerase II transcription subunit 1, Vitamin D3 receptor | | Authors: | Masuno, H, Ikura, T, Ito, N. | | Deposit date: | 2013-02-05 | | Release date: | 2013-06-26 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Crystal structures of complexes of vitamin D receptor ligand-binding domain with lithocholic acid derivatives.
J.Lipid Res., 54, 2013
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3VT4
 | | Crystal structures of rat VDR-LBD with R270L mutation | | Descriptor: | (1R,2Z,3R,5E,7E)-17-{(1S)-1-[(2-ethyl-2-hydroxybutyl)sulfanyl]ethyl}-2-(2-hydroxyethylidene)-9,10-secoestra-5,7,16-triene-1,3-diol, COACTIVATOR PEPTIDE DRIP, Vitamin D3 receptor | | Authors: | Nakabayashi, M, Shimizu, M, Ikura, T, Ito, N. | | Deposit date: | 2012-05-19 | | Release date: | 2013-05-22 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Crystal structures of hereditary vitamin D-resistant rickets-associated vitamin D receptor mutants R270L and W282R bound to 1,25-dihydroxyvitamin D3 and synthetic ligands.
J.Med.Chem., 56, 2013
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3VJS
 | | Vitamin D receptor complex with a carborane compound | | Descriptor: | 1-(2-[(S)-2,4-Dihydroxybutoxy]ethyl)-12-(5-ethyl-5-hydroxyheptyl)-1,12-dicarba-closo-dodecaborane, Vitamin D3 receptor, peptide from Mediator of RNA polymerase II transcription subunit 1 | | Authors: | Fujii, S, Masuno, M, Kagechika, H, Nakabayashi, M, Ito, N. | | Deposit date: | 2011-10-31 | | Release date: | 2012-02-08 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.93 Å) | | Cite: | Boron Cluster-based Development of Potent Nonsecosteroidal Vitamin D Receptor Ligands: Direct Observation of Hydrophobic Interaction between Protein Surface and Carborane
J.Am.Chem.Soc., 133, 2011
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3W5R
 | | Crystal structure of complexes of vitamin D receptor ligand binding domain with lithocholic acid derivatives | | Descriptor: | (3beta,5beta,9beta)-3-(acetyloxy)cholan-24-oic acid, Mediator of RNA polymerase II transcription subunit 1, Vitamin D3 receptor | | Authors: | Masuno, H, Ikura, T, Ito, N. | | Deposit date: | 2013-02-06 | | Release date: | 2013-06-26 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Crystal structures of complexes of vitamin D receptor ligand-binding domain with lithocholic acid derivatives.
J.Lipid Res., 54, 2013
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3WA4
 | | Grb2 SH2 domain/CD28-derived peptide complex | | Descriptor: | ACETIC ACID, CADMIUM ION, Growth factor receptor-bound protein 2, ... | | Authors: | Higo, K, Oda, M, Ito, N. | | Deposit date: | 2013-04-23 | | Release date: | 2014-02-26 | | Last modified: | 2024-10-16 | | Method: | X-RAY DIFFRACTION (1.35 Å) | | Cite: | High Resolution Crystal Structure of the Grb2 SH2 Domain with a Phosphopeptide Derived from CD28
Plos One, 8, 2013
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3W5T
 | | Crystal structure of complexes of vitamin D receptor ligand binding domain with lithocholic acid derivatives | | Descriptor: | (3beta,5beta,9beta)-3-(propanoyloxy)cholan-24-oic acid, Mediator of RNA polymerase II transcription subunit 1, Vitamin D3 receptor | | Authors: | Masuno, H, Ikura, T, Ito, N. | | Deposit date: | 2013-02-06 | | Release date: | 2013-06-26 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.29 Å) | | Cite: | Crystal structures of complexes of vitamin D receptor ligand-binding domain with lithocholic acid derivatives.
J.Lipid Res., 54, 2013
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3WWH
 | | Crystal structure of the first R-stereoselective -transaminase identified from Arthrobacter sp. KNK168 (FERM-BP-5228) | | Descriptor: | (R)-amine transaminase, GLYCEROL, PYRIDOXAL-5'-PHOSPHATE | | Authors: | Guan, L.J, Ohtsuka, J, Okai, M, Miyakawa, T, Mase, T, Zhi, Y, Ito, N, Yasohara, Y, Tanokura, M. | | Deposit date: | 2014-06-18 | | Release date: | 2015-08-12 | | Last modified: | 2018-11-21 | | Method: | X-RAY DIFFRACTION (1.65 Å) | | Cite: | A new target region for changing the substrate specificity of amine transaminases.
Sci Rep, 5, 2015
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3WWI
 | | Crystal structure of the G136F mutant of the first R-stereoselective -transaminase identified from Arthrobacter sp. KNK168 (FERM-BP-5228) | | Descriptor: | (R)-amine transaminase, PYRIDOXAL-5'-PHOSPHATE | | Authors: | Guan, L.J, Ohtsuka, J, Miyakawa, T, Zhi, Y, Ito, N, Yasohara, Y, Tanokura, M. | | Deposit date: | 2014-06-18 | | Release date: | 2015-08-19 | | Last modified: | 2020-01-22 | | Method: | X-RAY DIFFRACTION (2.27 Å) | | Cite: | A new target region for changing the substrate specificity of amine transaminases.
Sci Rep, 5, 2015
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3WWJ
 | | Crystal structure of an engineered sitagliptin-producing transaminase, ATA-117-Rd11 | | Descriptor: | (R)-amine transaminase, PYRIDOXAL-5'-PHOSPHATE | | Authors: | Guan, L.J, Ohtsuka, J, Okai, M, Miyakawa, T, Mase, T, Zhi, Y, Hou, F, Ito, N, Yasohara, Y, Tanokura, M. | | Deposit date: | 2014-06-18 | | Release date: | 2015-08-12 | | Last modified: | 2018-11-21 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | A new target region for changing the substrate specificity of amine transaminases.
Sci Rep, 5, 2015
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1V2Z
 | | Crystal structure of the C-terminal domain of Thermosynechococcus elongatus BP-1 KaiA | | Descriptor: | circadian clock protein KaiA homolog | | Authors: | Uzumaki, T, Fujita, M, Nakatsu, T, Hayashi, F, Shibata, H, Itoh, N, Kato, H, Ishiura, M, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2003-10-20 | | Release date: | 2004-06-01 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Crystal structure of the C-terminal clock-oscillator domain of the cyanobacterial KaiA protein
NAT.STRUCT.MOL.BIOL., 11, 2004
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