2YZO
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![BU of 2yzo by Molmil](/molmil-images/mine/2yzo) | Crystal structure of uncharacterized conserved protein from Thermotoga maritima | Descriptor: | D-MALATE, Probable 2-phosphosulfolactate phosphatase | Authors: | Nakagawa, N, Nakamura, Y, Bessho, Y, Yokoyama, S, Kuramitsu, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2007-05-06 | Release date: | 2007-11-06 | Last modified: | 2012-02-15 | Method: | X-RAY DIFFRACTION (1.85 Å) | Cite: | Crystal structure of uncharacterized conserved protein from Thermotoga maritima To be Published
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8IFE
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![BU of 8ife by Molmil](/molmil-images/mine/8ife) | Arbekacin-added human 80S ribosome | Descriptor: | 18S ribosomal RNA, 28S ribosomal RNA, 40S ribosomal protein S10, ... | Authors: | Tomono, J, Asano, K, Chiashi, T, Tanaka, Y, Yokoyama, T. | Deposit date: | 2023-02-17 | Release date: | 2024-02-14 | Last modified: | 2024-06-19 | Method: | ELECTRON MICROSCOPY (2.57 Å) | Cite: | Direct visualization of ribosomes in the cell-free system revealed the functional evolution of aminoglycoside. J.Biochem., 175, 2024
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8IFD
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![BU of 8ifd by Molmil](/molmil-images/mine/8ifd) | Dibekacin-added human 80S ribosome | Descriptor: | 18S ribosomal RNA, 28S ribosomal RNA, 40S ribosomal protein S10, ... | Authors: | Tomono, J, Asano, K, Chiashi, T, Tanaka, Y, Yokoyama, T. | Deposit date: | 2023-02-17 | Release date: | 2024-02-14 | Last modified: | 2024-06-19 | Method: | ELECTRON MICROSCOPY (2.59 Å) | Cite: | Direct visualization of ribosomes in the cell-free system revealed the functional evolution of aminoglycoside. J.Biochem., 175, 2024
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8IFB
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![BU of 8ifb by Molmil](/molmil-images/mine/8ifb) | Dibekacin-bound E.coli 70S ribosome in the PURE system | Descriptor: | 16S ribosomal RNA, 23S ribosomal RNA, 30S ribosomal protein S10, ... | Authors: | Tomono, J, Asano, K, Chiashi, T, Tanaka, Y, Yokoyama, T. | Deposit date: | 2023-02-17 | Release date: | 2024-02-14 | Last modified: | 2024-06-19 | Method: | ELECTRON MICROSCOPY (2.43 Å) | Cite: | Direct visualization of ribosomes in the cell-free system revealed the functional evolution of aminoglycoside. J.Biochem., 175, 2024
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4Z3B
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![BU of 4z3b by Molmil](/molmil-images/mine/4z3b) | Crystal structure of MnCO/apo-R52CFr | Descriptor: | CADMIUM ION, Ferritin light chain, GLYCEROL, ... | Authors: | Fujita, K, Tanaka, Y, Abe, S, Ueno, T. | Deposit date: | 2015-03-31 | Release date: | 2015-10-21 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.42 Å) | Cite: | A Photoactive Carbon-Monoxide-Releasing Protein Cage for Dose-Regulated Delivery in Living Cells Angew.Chem.Int.Ed.Engl., 55, 2016
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4ZD6
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![BU of 4zd6 by Molmil](/molmil-images/mine/4zd6) | Halohydrin hydrogen-halide-lyase, HheB | Descriptor: | 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, CHLORIDE ION, Halohydrin epoxidase B, ... | Authors: | Watanabe, F, Yu, F, Ohtaki, A, Yamanaka, Y, Noguchi, K, Yohda, M, Odaka, M. | Deposit date: | 2015-04-17 | Release date: | 2015-11-04 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (1.6 Å) | Cite: | Crystal structures of halohydrin hydrogen-halide-lyases from Corynebacterium sp. N-1074 Proteins, 83, 2015
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4ZKC
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![BU of 4zkc by Molmil](/molmil-images/mine/4zkc) | The chemokine binding protein of orf virus complexed with CCL7 | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, C-C motif chemokine 7, Chemokine binding protein, ... | Authors: | Knapp, K.M, Nakatani, Y, Krause, K.L. | Deposit date: | 2015-04-30 | Release date: | 2015-07-08 | Last modified: | 2023-09-27 | Method: | X-RAY DIFFRACTION (3.15 Å) | Cite: | Structures of Orf Virus Chemokine Binding Protein in Complex with Host Chemokines Reveal Clues to Broad Binding Specificity. Structure, 23, 2015
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4Z9F
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![BU of 4z9f by Molmil](/molmil-images/mine/4z9f) | Halohydrin hydrogen-halide-lyase, HheA | Descriptor: | CHLORIDE ION, Halohydrin epoxidase A | Authors: | Watanabe, F, Yu, F, Ohtaki, A, Yamanaka, Y, Noguchi, K, Yohda, M, Odaka, M. | Deposit date: | 2015-04-10 | Release date: | 2015-11-04 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.75 Å) | Cite: | Crystal structures of halohydrin hydrogen-halide-lyases from Corynebacterium sp. N-1074 Proteins, 83, 2015
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4ZK9
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![BU of 4zk9 by Molmil](/molmil-images/mine/4zk9) | The chemokine binding protein of orf virus complexed with CCL2 | Descriptor: | C-C motif chemokine 2, Chemokine binding protein, beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Authors: | Knapp, K.M, Nakatani, Y, Krause, K.L. | Deposit date: | 2015-04-30 | Release date: | 2015-07-08 | Last modified: | 2023-09-27 | Method: | X-RAY DIFFRACTION (2.6 Å) | Cite: | Structures of Orf Virus Chemokine Binding Protein in Complex with Host Chemokines Reveal Clues to Broad Binding Specificity. Structure, 23, 2015
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3WB5
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![BU of 3wb5 by Molmil](/molmil-images/mine/3wb5) | Crystal Structure of beta secetase in complex with (6S)-2-amino-3,6-dimethyl-6-[(1R,2R)-2-phenylcyclopropyl]-3,4,5,6-tetrahydropyrimidin-4-one | Descriptor: | (6S)-2-amino-3,6-dimethyl-6-[(1R,2R)-2-phenylcyclopropyl]-5,6-dihydropyrimidin-4(3H)-one, Beta-secretase 1, DIMETHYL SULFOXIDE, ... | Authors: | Yonezawa, S, Fujiwara, K, Yamamoto, T, Hattori, K, Yamakawa, H, Muto, C, Hosono, M, Tanaka, Y, Nakano, T, Takemoto, H, Arisawa, M, Shuto, S. | Deposit date: | 2013-05-13 | Release date: | 2013-10-02 | Last modified: | 2017-11-22 | Method: | X-RAY DIFFRACTION (2.501 Å) | Cite: | Conformational restriction approach to beta-secretase (BACE1) inhibitors III: Effective investigation of the binding mode by combinational use of X-ray analysis, isothermal titration calorimetry and theoretical calculations Bioorg.Med.Chem., 21, 2013
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3WB4
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![BU of 3wb4 by Molmil](/molmil-images/mine/3wb4) | Crystal Structure of beta secetase in complex with 2-amino-3,6-dimethyl-6-(2-phenylethyl)-3,4,5,6-tetrahydropyrimidin-4-one | Descriptor: | (6R)-2-amino-3,6-dimethyl-6-(2-phenylethyl)-5,6-dihydropyrimidin-4(3H)-one, Beta-secretase 1, GLYCEROL, ... | Authors: | Yonezawa, S, Fujiwara, K, Yamamoto, T, Hattori, K, Yamakawa, H, Muto, C, Hosono, M, Tanaka, Y, Nakano, T, Takemoto, H, Arisawa, M, Shuto, S. | Deposit date: | 2013-05-13 | Release date: | 2013-10-02 | Last modified: | 2017-11-22 | Method: | X-RAY DIFFRACTION (2.25 Å) | Cite: | Conformational restriction approach to beta-secretase (BACE1) inhibitors III: Effective investigation of the binding mode by combinational use of X-ray analysis, isothermal titration calorimetry and theoretical calculations Bioorg.Med.Chem., 21, 2013
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4OYQ
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![BU of 4oyq by Molmil](/molmil-images/mine/4oyq) | (6-isothiocyanatohexyl)benzene inhibitor complexed with Macrophage Migration Inhibitory Factor | Descriptor: | 6-isothiocyanatohexylbenzene, GLYCEROL, Macrophage migration inhibitory factor, ... | Authors: | Spencer, E.S, Dale, E.J, Gommans, A.L, Vo, C.T, Rutledge, M.T, Nakatani, Y, Gamble, A.B, Smith, R.A.J, Wilbanks, S.M, Hampton, M.B, Tyndall, J.D.A. | Deposit date: | 2014-02-12 | Release date: | 2014-03-05 | Last modified: | 2023-09-27 | Method: | X-RAY DIFFRACTION (1.7 Å) | Cite: | To be published To be published
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4OSF
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![BU of 4osf by Molmil](/molmil-images/mine/4osf) | 4-(2-isothiocyanatoethyl)phenol inhibitor complexed with Macrophage Migration Inhibitory Factor | Descriptor: | CHLORIDE ION, ISOPROPYL ALCOHOL, Macrophage migration inhibitory factor, ... | Authors: | Spencer, E.S, Dale, E.J, Gommans, A.L, Vo, C.T, Rutledge, M.T, Nakatani, Y, Gamble, A.B, Smith, R.A.J, Wilbanks, S.M, Hampton, M.B, Tyndall, J.D.A. | Deposit date: | 2014-02-12 | Release date: | 2014-03-12 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.62 Å) | Cite: | Multiple binding modes of isothiocyanates that inhibit macrophage migration inhibitory factor Eur.J.Med.Chem., 93, 2015
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4KQ6
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![BU of 4kq6 by Molmil](/molmil-images/mine/4kq6) | Product complex of lumazine synthase from candida glabrata | Descriptor: | 1-deoxy-1-(6,7-dimethyl-2,4-dioxo-3,4-dihydropteridin-8(2H)-yl)-D-ribitol, 6,7-dimethyl-8-ribityllumazine synthase, GLYCEROL, ... | Authors: | Shankar, M, Wilbanks, S.M, Nakatani, Y, Monk, B.C, Tyndall, J.D.A. | Deposit date: | 2013-05-14 | Release date: | 2013-05-29 | Last modified: | 2023-09-20 | Method: | X-RAY DIFFRACTION (2.24 Å) | Cite: | Catalysis product captured in lumazine synthase from the fungal pathogen Candida glabrata. Acta Crystallogr.,Sect.D, 69, 2013
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6L96
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![BU of 6l96 by Molmil](/molmil-images/mine/6l96) | Structure of PPARalpha-LBD/pemafibrate/SRC1 peptide | Descriptor: | (2~{R})-2-[3-[[1,3-benzoxazol-2-yl-[3-(4-methoxyphenoxy)propyl]amino]methyl]phenoxy]butanoic acid, Peroxisome proliferator-activated receptor alpha, SRC1 coactivator peptide | Authors: | Kawasaki, M, Kambe, A, Yamamoto, Y, Arulmozhira, S, Ito, S, Nakagawa, Y, Tokiwa, H, Nakano, S, Shimano, H. | Deposit date: | 2019-11-08 | Release date: | 2020-01-15 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (3.2 Å) | Cite: | Elucidation of Molecular Mechanism of a Selective PPAR alpha Modulator, Pemafibrate, through Combinational Approaches of X-ray Crystallography, Thermodynamic Analysis, and First-Principle Calculations. Int J Mol Sci, 21, 2020
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4L24
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![BU of 4l24 by Molmil](/molmil-images/mine/4l24) | Crystal structure of metallo-DNA duplex containing consecutive T-Hg(II)-T base pairs | Descriptor: | DNA (5'-D(*CP*GP*CP*GP*AP*TP*TP*TP*CP*GP*CP*G)-3'), MERCURY (II) ION | Authors: | Kondo, J, Yamada, T, Hirose, C, Okamoto, I, Tanaka, Y, Ono, A. | Deposit date: | 2013-06-04 | Release date: | 2014-03-05 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.7 Å) | Cite: | Crystal Structure of Metallo DNA Duplex Containing Consecutive Watson-Crick-like T-Hg(II) -T Base Pairs Angew.Chem.Int.Ed.Engl., 53, 2014
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4L26
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![BU of 4l26 by Molmil](/molmil-images/mine/4l26) | Crystal structure of DNA duplex containing consecutive T-T mispairs (Br-derivative) | Descriptor: | DNA (5'-D(*CP*GP*(CBR)P*GP*AP*TP*TP*TP*CP*GP*CP*G)-3') | Authors: | Kondo, J, Yamada, T, Hirose, C, Tanaka, Y, Ono, A. | Deposit date: | 2013-06-04 | Release date: | 2014-03-05 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (1.4 Å) | Cite: | Crystal Structure of Metallo DNA Duplex Containing Consecutive Watson-Crick-like T-Hg(II) -T Base Pairs Angew.Chem.Int.Ed.Engl., 53, 2014
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4L25
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![BU of 4l25 by Molmil](/molmil-images/mine/4l25) | Crystal structure of DNA duplex containing consecutive T-T mispairs | Descriptor: | DNA (5'-D(*CP*GP*CP*GP*AP*TP*TP*TP*CP*GP*CP*G)-3') | Authors: | Kondo, J, Yamada, T, Hirose, C, Tanaka, Y, Ono, A. | Deposit date: | 2013-06-04 | Release date: | 2014-03-05 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.1 Å) | Cite: | Crystal Structure of Metallo DNA Duplex Containing Consecutive Watson-Crick-like T-Hg(II) -T Base Pairs Angew.Chem.Int.Ed.Engl., 53, 2014
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3B0U
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![BU of 3b0u by Molmil](/molmil-images/mine/3b0u) | tRNA-dihydrouridine synthase from Thermus thermophilus in complex with tRNA fragment | Descriptor: | FLAVIN MONONUCLEOTIDE, RNA (5'-R(*GP*GP*(H2U)P*A)-3'), tRNA-dihydrouridine synthase | Authors: | Yu, F, Tanaka, Y, Yamashita, K, Nakamura, A, Yao, M, Tanaka, I. | Deposit date: | 2011-06-14 | Release date: | 2011-12-14 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (1.948 Å) | Cite: | Molecular basis of dihydrouridine formation on tRNA Proc.Natl.Acad.Sci.USA, 108, 2011
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3AZV
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![BU of 3azv by Molmil](/molmil-images/mine/3azv) | Crystal structure of the receptor binding domain | Descriptor: | D/C mosaic neurotoxin, SULFATE ION | Authors: | Nuemket, N, Tanaka, Y, Tsukamoto, K, Tsuji, T, Nakamura, K, Kozaki, S, Yao, M, Tanaka, I. | Deposit date: | 2011-06-02 | Release date: | 2011-12-28 | Last modified: | 2017-10-11 | Method: | X-RAY DIFFRACTION (3.1 Å) | Cite: | Structural and mutational analyses of the receptor binding domain of botulinum D/C mosaic neurotoxin: insight into the ganglioside binding mechanism Biochem.Biophys.Res.Commun., 411, 2011
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3AZW
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![BU of 3azw by Molmil](/molmil-images/mine/3azw) | Crystal structure of the receptor binding domain | Descriptor: | D/C mosaic neurotoxin, SULFATE ION | Authors: | Nuemket, N, Tanaka, Y, Tsukamoto, K, Tsuji, T, Nakamura, K, Kozaki, S, Yao, M, Tanaka, I. | Deposit date: | 2011-06-02 | Release date: | 2011-12-28 | Last modified: | 2024-03-13 | Method: | X-RAY DIFFRACTION (2.99 Å) | Cite: | Structural and mutational analyses of the receptor binding domain of botulinum D/C mosaic neurotoxin: insight into the ganglioside binding mechanism Biochem.Biophys.Res.Commun., 411, 2011
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5FCL
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![BU of 5fcl by Molmil](/molmil-images/mine/5fcl) | Crystal structure of Cas1 from Pectobacterium atrosepticum | Descriptor: | CRISPR-associated endonuclease Cas1 | Authors: | Wilkinson, M.E, Nakatani, Y, Opel-Reading, H.K, Fineran, P.C, Krause, K.L. | Deposit date: | 2015-12-15 | Release date: | 2016-03-16 | Last modified: | 2024-03-06 | Method: | X-RAY DIFFRACTION (2.7 Å) | Cite: | Structural plasticity and in vivo activity of Cas1 from the type I-F CRISPR-Cas system. Biochem.J., 473, 2016
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3B0P
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![BU of 3b0p by Molmil](/molmil-images/mine/3b0p) | tRNA-dihydrouridine synthase from Thermus thermophilus | Descriptor: | FLAVIN MONONUCLEOTIDE, tRNA-dihydrouridine synthase | Authors: | Yu, F, Tanaka, Y, Yamashita, K, Nakamura, A, Yao, M, Tanaka, I. | Deposit date: | 2011-06-12 | Release date: | 2011-12-14 | Last modified: | 2024-03-13 | Method: | X-RAY DIFFRACTION (1.7 Å) | Cite: | Molecular basis of dihydrouridine formation on tRNA Proc.Natl.Acad.Sci.USA, 108, 2011
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5H6O
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![BU of 5h6o by Molmil](/molmil-images/mine/5h6o) | Porphobilinogen deaminase from Vibrio Cholerae | Descriptor: | 3-[5-{[3-(2-carboxyethyl)-4-(carboxymethyl)-5-methyl-1H-pyrrol-2-yl]methyl}-4-(carboxymethyl)-1H-pyrrol-3-yl]propanoic acid, MAGNESIUM ION, Porphobilinogen deaminase | Authors: | Funamizu, T, Chen, M, Tanaka, Y, Ishimori, K, Uchida, T. | Deposit date: | 2016-11-14 | Release date: | 2017-11-15 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.702 Å) | Cite: | Porphobilinogen deaminase from Vibrio Cholerae To Be Published
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3B0V
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![BU of 3b0v by Molmil](/molmil-images/mine/3b0v) | tRNA-dihydrouridine synthase from Thermus thermophilus in complex with tRNA | Descriptor: | FLAVIN MONONUCLEOTIDE, tRNA, tRNA-dihydrouridine synthase | Authors: | Yu, F, Tanaka, Y, Yamashita, K, Nakamura, A, Yao, M, Tanaka, I. | Deposit date: | 2011-06-14 | Release date: | 2011-12-14 | Last modified: | 2017-10-11 | Method: | X-RAY DIFFRACTION (3.51 Å) | Cite: | Molecular basis of dihydrouridine formation on tRNA Proc.Natl.Acad.Sci.USA, 108, 2011
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