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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3WTQ
 | | Crystal structure of VDR-LBD complexed with 22S-butyl-2-methylidene-19-nor-1a,25-dihydroxyvitamin D3 | | Descriptor: | (1R,3R,7E,17beta)-17-[(2R,3S)-3-butyl-6-hydroxy-6-methylheptan-2-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, Inaba, Y, Itoh, T, Anami, Y, Ikura, T, Ito, N, Yamamoto, K. | | Deposit date: | 2014-04-15 | | Release date: | 2015-04-15 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Crystal structure of VDR-LBD complexed with 22S-butyl-2-methylidene-19-nor-1a,25-dihydroxyvitamin D3
To be Published
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3AFR
 | | Crystal Structure of VDR-LBD/22S-Butyl-1a,24R-dihydroxyvitamin D3 complex | | Descriptor: | (1R,3S,5Z)-5-[(2E)-2-{(1R,3aS,7aR)-1-[(1R,2S,4R)-2-butyl-4-hydroxy-1,5-dimethylhexyl]-7a-methyloctahydro-4H-inden-4-yli dene}ethylidene]-4-methylidenecyclohexane-1,3-diol, 13-meric peptide from Mediator of RNA polymerase II transcription subunit 1, Vitamin D3 receptor | | Authors: | Inaba, Y, Nakabayashi, M, Itoh, T, Ikura, T, Ito, N, Yamamoto, K. | | Deposit date: | 2010-03-10 | | Release date: | 2010-03-31 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | 22S-Butyl-1alpha,24R-dihydroxyvitamin D(3): Recovery of vitamin D receptor agonistic activity
J.Steroid Biochem.Mol.Biol., 121, 2010
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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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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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6LCB
 | | Crystal structure of human Dishevelled1 PDZ domain with its inhibitor NPL3009 | | Descriptor: | 2-[[3-[(2E)-2-[1,3-bis(oxidanylidene)-1-phenyl-butan-2-ylidene]hydrazinyl]phenyl]sulfonylamino]benzoic acid, SULFATE ION, Segment polarity protein dishevelled homolog DVL-1 | | Authors: | Yasukochi, S, Numoto, N, Tenno, N, Tenno, T, Ito, N, Hiroaki, H. | | Deposit date: | 2019-11-18 | | Release date: | 2020-11-25 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.4 Å) | | Cite: | Crystal structure of human Dishevelled1 PDZ domain with its inhibitor NPL3009
To Be Published
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1URN
 | | U1A MUTANT/RNA COMPLEX + GLYCEROL | | Descriptor: | CHLORIDE ION, GLYCEROL, PROTEIN (U1A), ... | | Authors: | Oubridge, C, Ito, N, Evans, P.R, Teo, C.-H, Nagai, K. | | Deposit date: | 1995-01-04 | | Release date: | 1996-03-08 | | Last modified: | 2024-02-14 | | Method: | X-RAY DIFFRACTION (1.92 Å) | | Cite: | Crystal structure at 1.92 A resolution of the RNA-binding domain of the U1A spliceosomal protein complexed with an RNA hairpin.
Nature, 372, 1994
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6LCA
 | | Crystal structure of human Dishevelled1 PDZ domain homotrimer | | Descriptor: | SULFATE ION, Segment polarity protein dishevelled homolog DVL-1 | | Authors: | Yasukochi, S, Numoto, N, Tenno, N, Tenno, T, Ito, N, Hiroaki, H. | | Deposit date: | 2019-11-18 | | Release date: | 2020-11-25 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | Crystal structure of human Dishevelled1 PDZ domain homotrimer
To Be Published
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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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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: | 2024-11-13 | | 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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6LB5
 | | Crystal structure of dimeric RXR-LBD complexed with full agonist NEt-3IB and TIF2 co-activator | | Descriptor: | 6-[ethyl-[3-(2-methylpropoxy)-4-propan-2-yl-phenyl]amino]pyridine-3-carboxylic acid, Nuclear receptor coactivator 2, Retinoic acid receptor RXR-alpha | | Authors: | Imai, D, Numoto, N, Nakano, S, Kakuta, H, Ito, N. | | Deposit date: | 2019-11-13 | | Release date: | 2020-11-18 | | Last modified: | 2024-10-02 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | Structural basis for the full and partial agonist activities of retinoid X receptor alpha ligands with an iso-butoxy and an isopropyl group
Biochem.Biophys.Res.Commun., 734, 2024
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6L6K
 | | Crystal structure of dimeric RXRalpha-LBD complexed with partial agonist CBt-PMN and SRC1 | | Descriptor: | 1-(3,5,5,8,8-pentamethyl-6,7-dihydronaphthalen-2-yl)benzotriazole-5-carboxylic acid, CALCIUM ION, Nuclear receptor coactivator 1, ... | | Authors: | Shimizu, K, Numoto, N, Nakano, S, Makishima, M, Kakuta, H, Ito, N. | | Deposit date: | 2019-10-29 | | Release date: | 2020-11-04 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Crystal structure of dimeric RXRalpha-LBD complexed with partial agonist CBt-PMN and SRC1
To Be Published
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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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6LB4
 | | Crystal structure of dimeric RXR-LBD complexed with NEt-3ME and TIF2 co-activator | | Descriptor: | 1,2-ETHANEDIOL, 6-[ethyl-[3-(2-methoxyethoxy)-4-propan-2-yl-phenyl]amino]pyridine-3-carboxylic acid, Nuclear receptor coactivator 2, ... | | Authors: | Imai, D, Numoto, N, Nakano, S, Kakuta, H, Ito, N. | | Deposit date: | 2019-11-13 | | Release date: | 2020-11-18 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.5 Å) | | Cite: | Crystal structure of dimeric RXR-LBD complexed with NEt-3ME and TIF2 co-activator
To Be Published
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6LB6
 | | Crystal structure of dimeric RXR-LBD complexed with partial agonist NEt-4IB and TIF2 co-activator | | Descriptor: | 6-[ethyl-[4-(2-methylpropoxy)-3-propan-2-yl-phenyl]amino]pyridine-3-carboxylic acid, Nuclear receptor coactivator 2, Retinoic acid receptor RXR-alpha | | Authors: | Imai, D, Numoto, N, Nakano, S, Kakuta, H, Ito, N. | | Deposit date: | 2019-11-13 | | Release date: | 2020-11-18 | | Last modified: | 2024-10-02 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | Structural basis for the full and partial agonist activities of retinoid X receptor alpha ligands with an iso-butoxy and an isopropyl group
Biochem.Biophys.Res.Commun., 734, 2024
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6JEF
 | | Crystal structure of apo-R168C/L169C-Fr | | Descriptor: | CADMIUM ION, CHLORIDE ION, Ferritin light chain, ... | | Authors: | Abe, S, Ito, N, Maity, B, Lu, C, Lu, D, Ueno, T. | | Deposit date: | 2019-02-05 | | Release date: | 2019-12-11 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.58 Å) | | Cite: | Coordination design of cadmium ions at the 4-fold axis channel of the apo-ferritin cage.
Dalton Trans, 48, 2019
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6K5O
 | | Development of Novel Lithocholic Acid Derivatives as Vitamin D Receptor Agonists | | Descriptor: | (4~{R})-4-[(3~{R},5~{R},8~{R},9~{S},10~{S},13~{R},14~{S},17~{R})-10,13-dimethyl-3-methylsulfonyloxy-2,3,4,5,6,7,8,9,11,12,14,15,16,17-tetradecahydro-1~{H}-cyclopenta[a]phenanthren-17-yl]pentanoic acid, Mediator of RNA polymerase II transcription subunit 1, Vitamin D3 receptor | | Authors: | Masuno, H, Kagechika, H, Ito, N. | | Deposit date: | 2019-05-29 | | Release date: | 2019-07-24 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Development of novel lithocholic acid derivatives as vitamin D receptor agonists.
Bioorg.Med.Chem., 27, 2019
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6JEE
 | | Crystal structure of apo-L161C/L165C-Fr | | Descriptor: | 1,2-ETHANEDIOL, CADMIUM ION, CHLORIDE ION, ... | | Authors: | Abe, S, Ito, N, Maity, B, Lu, C, Lu, D, Ueno, T. | | Deposit date: | 2019-02-05 | | Release date: | 2019-12-11 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.3 Å) | | Cite: | Coordination design of cadmium ions at the 4-fold axis channel of the apo-ferritin cage.
Dalton Trans, 48, 2019
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2DQU
 | | Crystal form II: high resolution crystal structure of the complex of the hydrolytic antibody Fab 6D9 and a transition-state analog | | Descriptor: | IMMUNOGLOBULIN 6D9, [1-(3-DIMETHYLAMINO-PROPYL)-3-ETHYL-UREIDO]-[4-(2,2,2-TRIFLUORO-ACETYLAMINO)-BENZYL]PHOSPHINIC ACID-2-(2,2-DIHYDRO-ACETYLAMINO)-3-HYDROXY-1-(4-NITROPHENYL)-PROPYL ESTER | | Authors: | Kristensen, O, Vassylyev, D.G, Tanaka, F, Ito, N, Morikawa, K, Fujii, I. | | Deposit date: | 2006-05-30 | | Release date: | 2006-06-20 | | Last modified: | 2024-10-16 | | Method: | X-RAY DIFFRACTION (1.7 Å) | | Cite: | Thermodynamic and structural basis for transition-state stabilization in antibody-catalyzed hydrolysis
J.Mol.Biol., 369, 2007
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7D4E
 | | Structure of L-lysine oxidase precursor in complex with L-lysine (1.0 M) | | Descriptor: | FLAVIN-ADENINE DINUCLEOTIDE, L-Lysine alpha-oxidase, LYSINE | | Authors: | Kitagawa, M, Ito, N, Matsumoto, Y, Inagaki, K, Imada, K. | | Deposit date: | 2020-09-23 | | Release date: | 2021-02-10 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.85 Å) | | Cite: | Structural basis of enzyme activity regulation by the propeptide of l-lysine alpha-oxidase precursor from Trichoderma viride .
J Struct Biol X, 5, 2021
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7D4D
 | | Structure of L-lysine oxidase precursor in complex with L-lysine (1.24M) | | Descriptor: | FLAVIN-ADENINE DINUCLEOTIDE, L-Lysine alpha-oxidase, LYSINE | | Authors: | Kitagawa, M, Ito, N, Matsumoto, Y, Inagaki, K, Imada, K. | | Deposit date: | 2020-09-23 | | Release date: | 2021-02-10 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.29 Å) | | Cite: | Structural basis of enzyme activity regulation by the propeptide of l-lysine alpha-oxidase precursor from Trichoderma viride .
J Struct Biol X, 5, 2021
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2DQT
 | | High resolution crystal structure of the complex of the hydrolytic antibody Fab 6D9 and a transition-state analog | | Descriptor: | IMMUNOGLOBULIN 6D9, [1-(3-DIMETHYLAMINO-PROPYL)-3-ETHYL-UREIDO]-[4-(2,2,2-TRIFLUORO-ACETYLAMINO)-BENZYL]PHOSPHINIC ACID-2-(2,2-DIHYDRO-ACETYLAMINO)-3-HYDROXY-1-(4-NITROPHENYL)-PROPYL ESTER | | Authors: | Kristensen, O, Vassylyev, D.G, Tanaka, F, Ito, N, Morikawa, K, Fujii, I. | | Deposit date: | 2006-05-30 | | Release date: | 2006-06-20 | | Last modified: | 2024-10-23 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Thermodynamic and structural basis for transition-state stabilization in antibody-catalyzed hydrolysis
J.Mol.Biol., 369, 2007
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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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