5XQW
 
 | | Catalytic antibody 7B9 | | Descriptor: | Fab fragment of catalytic antibody 7B9, heavy chain, light chain, ... | | Authors: | Ito, N, Fujii, I, Tsumuraya, T. | | Deposit date: | 2017-06-07 | | Release date: | 2018-04-18 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Structural basis of the broad substrate tolerance of the antibody 7B9-catalyzed hydrolysis of p-nitrobenzyl esters.
Bioorg. Med. Chem., 26, 2018
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1V33
 | | Crystal structure of DNA primase from Pyrococcus horikoshii | | Descriptor: | DNA primase small subunit, PHOSPHATE ION, ZINC ION | | Authors: | Ito, N, Nureki, O, Shirouzu, M, Yokoyama, S, Hanaoka, F, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2003-10-25 | | Release date: | 2004-03-23 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Crystal structure of the Pyrococcus horikoshii DNA primase-UTP complex: implications for the mechanism of primer synthesis.
Genes Cells, 8, 2003
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1V34
 | | Crystal structure of Pyrococcus horikoshii DNA primase-UTP complex | | Descriptor: | DNA primase small subunit, URIDINE 5'-TRIPHOSPHATE, ZINC ION | | Authors: | Ito, N, Nureki, O, Shirouzu, M, Yokoyama, S, Hanaoka, F, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2003-10-25 | | Release date: | 2004-03-23 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (2.7 Å) | | Cite: | Crystal structure of the Pyrococcus horikoshii DNA primase-UTP complex: implications for the mechanism of primer synthesis.
Genes Cells, 8, 2003
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2Z8H
 | | Structure of mouse Bach1 BTB domain | | Descriptor: | Transcription regulator protein BACH1 | | Authors: | Ito, N, Murayama, K. | | Deposit date: | 2007-09-05 | | Release date: | 2008-09-09 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Structure of mouse Bach1 BTB domain
To be Published
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7E0D
 | | Structure of L-glutamate oxidase R305E mutant in complex with L-arginine | | Descriptor: | ARGININE, FLAVIN-ADENINE DINUCLEOTIDE, L-glutamate oxidase | | Authors: | Ito, N, Matsuo, S, Inagaki, K, Imada, K. | | Deposit date: | 2021-01-27 | | Release date: | 2021-04-07 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.7 Å) | | Cite: | A new l-arginine oxidase engineered from l-glutamate oxidase.
Protein Sci., 30, 2021
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7E0C
 | | Structure of L-glutamate oxidase R305E mutant | | Descriptor: | FLAVIN-ADENINE DINUCLEOTIDE, L-glutamate oxidase | | Authors: | Ito, N, Matsuo, S, Inagaki, K, Imada, K. | | Deposit date: | 2021-01-27 | | Release date: | 2021-04-07 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.65 Å) | | Cite: | A new l-arginine oxidase engineered from l-glutamate oxidase.
Protein Sci., 30, 2021
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7D4C
 | | Structure of L-lysine oxidase precursor | | Descriptor: | FLAVIN-ADENINE DINUCLEOTIDE, L-Lysine alpha-oxidase, PHOSPHATE ION | | Authors: | Ito, N, Kitagawa, M, 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 (1.97 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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1GOH
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1GOG
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1GOF
 | | NOVEL THIOETHER BOND REVEALED BY A 1.7 ANGSTROMS CRYSTAL STRUCTURE OF GALACTOSE OXIDASE | | Descriptor: | ACETIC ACID, COPPER (II) ION, GALACTOSE OXIDASE, ... | | Authors: | Ito, N, Phillips, S.E.V, Knowles, P.F. | | Deposit date: | 1993-09-30 | | Release date: | 1994-01-31 | | Last modified: | 2024-10-30 | | Method: | X-RAY DIFFRACTION (1.7 Å) | | Cite: | Novel thioether bond revealed by a 1.7 A crystal structure of galactose oxidase.
Nature, 350, 1991
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1HBH
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2DLA
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3VYC
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2JK7
 | | XIAP BIR3 bound to a Smac Mimetic | | Descriptor: | (3S,6S,7Z,10AS)-N-(DIPHENYLMETHYL)-6-{[(2S)-2-(METHYLIDENEAMINO)BUTANOYL]AMINO}-5-OXO-1,2,3,5,6,9,10,10A-OCTAHYDROPYRROLO[1,2-A]AZOCINE-3-CARBOXAMIDE, BACULOVIRAL IAP REPEAT-CONTAINING PROTEIN 4, ZINC ION | | Authors: | Saito, N.G, Meagher, J.L, Stuckey, J.A. | | Deposit date: | 2008-08-21 | | Release date: | 2008-11-04 | | Last modified: | 2024-05-01 | | Method: | X-RAY DIFFRACTION (2.82 Å) | | Cite: | Structure-Based Design, Synthesis, Evaluation, and Crystallographic Studies of Conformationally Constrained Smac Mimetics as Inhibitors of the X-Linked Inhibitor of Apoptosis Protein (Xiap).
J.Med.Chem., 51, 2008
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4RQ9
 | | Crystal structure of the chromophore-binding domain of Stigmatella aurantiaca bacteriophytochrome (Thr289His mutant) in the Pr state | | Descriptor: | 1,2-ETHANEDIOL, BILIVERDINE IX ALPHA, GLYCEROL, ... | | Authors: | Woitowich, N.C, Halavaty, A.S, Gallagher, K.D, Nugent, A.C, Patel, H, Duong, P, Kovaleva, S.E, St.Peter, S, Ozarowski, W.B, Hernandez, C.N, Stojkovic, E.A. | | Deposit date: | 2014-10-31 | | Release date: | 2016-05-11 | | Last modified: | 2023-09-20 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Crystal structure of the chromophore-binding domain of Stigmatella aurantiaca bacteriophytochrome (Thr289His mutant) in the Pr state
To be Published
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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: | 2024-10-16 | | 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
 | | 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: | 2024-10-16 | | 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
 | | 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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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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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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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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4WUA
 | | Crystal structure of human SRPK1 complexed to an inhibitor SRPIN340 | | Descriptor: | CITRIC ACID, N-[2-(1-piperidinyl)-5-(trifluoromethyl)phenyl]-4-pyridinecarboxamide, SRSF protein kinase 1, ... | | Authors: | Hoshina, M, Ikura, T, Hosoya, T, Hagiwara, M, Ito, N. | | Deposit date: | 2014-10-31 | | Release date: | 2015-09-16 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Identification of a Dual Inhibitor of SRPK1 and CK2 That Attenuates Pathological Angiogenesis of Macular Degeneration in Mice
Mol.Pharmacol., 88, 2015
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4X42
 | | Crystal structure of DEN4 ED3 mutant with epitope two residues substituted from DEN3 ED3 | | Descriptor: | Envelope protein E, SULFATE ION | | Authors: | Kulkarni, M.R, Islam, M.M, Numoto, N, Elahi, M.M, Ito, N, Kuroda, Y. | | Deposit date: | 2014-12-02 | | Release date: | 2015-09-09 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.78 Å) | | Cite: | Structural and biophysical analysis of sero-specific immune responses using epitope grafted Dengue ED3 mutants.
Biochim.Biophys.Acta, 1854, 2015
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5ZQU
 | | Crystal structure of tetrameric RXRalpha-LBD complexed with partial agonist CBt-PMN | | Descriptor: | 1-(3,5,5,8,8-pentamethyl-6,7-dihydronaphthalen-2-yl)benzotriazole-5-carboxylic acid, BROMIDE ION, Retinoic acid receptor RXR-alpha | | Authors: | Miyashita, Y, Numoto, N, Arulmozhiraja, S, Nakano, S, Matsuo, N, Shimizu, K, Kakuta, H, Ito, S, Ikura, T, Ito, N, Tokiwa, H. | | Deposit date: | 2018-04-20 | | Release date: | 2019-02-27 | | Last modified: | 2024-10-16 | | Method: | X-RAY DIFFRACTION (2.60038781 Å) | | Cite: | Dual conformation of the ligand induces the partial agonistic activity of retinoid X receptor alpha (RXR alpha ).
FEBS Lett., 593, 2019
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