7D4C
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 7d4c by Molmil](/molmil-images/mine/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
|
|
1GOG
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 1gog by Molmil](/molmil-images/mine/1gog) | |
1GOF
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 1gof by Molmil](/molmil-images/mine/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: | 2023-07-26 | 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
|
|
1GOH
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 1goh by Molmil](/molmil-images/mine/1goh) | |
1HBH
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 1hbh by Molmil](/molmil-images/mine/1hbh) | |
1V33
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 1v33 by Molmil](/molmil-images/mine/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
|
|
1V34
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 1v34 by Molmil](/molmil-images/mine/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
|
|
5XQW
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 5xqw by Molmil](/molmil-images/mine/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
|
|
2Z8H
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 2z8h by Molmil](/molmil-images/mine/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
|
|
7E0D
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 7e0d by Molmil](/molmil-images/mine/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
|
|
7E0C
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 7e0c by Molmil](/molmil-images/mine/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
|
|
2DLA
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 2dla by Molmil](/molmil-images/mine/2dla) | |
4RQ9
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 4rq9 by Molmil](/molmil-images/mine/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
|
|
2JK7
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 2jk7 by Molmil](/molmil-images/mine/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
|
|
3VYC
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 3vyc by Molmil](/molmil-images/mine/3vyc) | |
3VRT
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 3vrt by Molmil](/molmil-images/mine/3vrt) | VDR ligand binding domain in complex with 2-Mehylidene-19,25,26,27-tetranor-1alpha,24-dihydroxyvitaminD3 | Descriptor: | (1R,3R,7E,17beta)-17-[(2R)-5-hydroxypentan-2-yl]-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol, 13-meric peptide from Mediator of RNA polymerase II transcription subunit 1, Vitamin D3 receptor | Authors: | Nakabayashi, M, Yoshimoto, N, Inaba, Y, Itoh, T, Ito, N, Yamamoto, K. | Deposit date: | 2012-04-14 | Release date: | 2012-05-23 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (2.4 Å) | Cite: | Butyl pocket formation in the vitamin d receptor strongly affects the agonistic or antagonistic behavior of ligands J.Med.Chem., 55, 2012
|
|
3VRU
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 3vru by Molmil](/molmil-images/mine/3vru) | VDR ligand binding domain in complex with 2-Methylidene-19,24-dinor-1alpha,25-dihydroxy vitaminD3 | Descriptor: | (1R,3R,7E,17beta)-17-[(2R)-5-hydroxy-5-methylhexan-2-yl]-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol, 13-meric peptide from Mediator of RNA polymerase II transcription subunit 1, Vitamin D3 receptor | Authors: | Yoshimoto, N, Inaba, Y, Itoh, T, Nakabayashi, M, Ito, N, Yamamoto, K. | Deposit date: | 2012-04-14 | Release date: | 2012-05-23 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Butyl pocket formation in the vitamin d receptor strongly affects the agonistic or antagonistic behavior of ligands J.Med.Chem., 55, 2012
|
|
8ISN
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![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
|
|
3VT4
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 3vt4 by Molmil](/molmil-images/mine/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
|
|
3VT7
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 3vt7 by Molmil](/molmil-images/mine/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
|
|
3VT6
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 3vt6 by Molmil](/molmil-images/mine/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
|
|
3VTC
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 3vtc by Molmil](/molmil-images/mine/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
|
|
3VT5
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 3vt5 by Molmil](/molmil-images/mine/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
|
|
3VTB
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 3vtb by Molmil](/molmil-images/mine/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
|
|
8YTN
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![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
|
|