PDB: 190 件ウェブページステータス検索Chemie searchBIRD

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4LFB	Crystal Structure of 30S ribosomal subunit from Thermus thermophilus 分子名称: 16S rRNA, MAGNESIUM ION, NEOMYCIN, ... 著者 Demirci, H, Belardinelli, R, Carr, J, Murphy IV, F, Jogl, G, Dahlberg, A.E, Gregory, S.T. 登録日 2013-06-26 公開日 2014-07-02 実験手法 X-RAY DIFFRACTION (3.009 Å) 主引用文献 Crystal Structure of 30S ribosomal subunit from Thermus thermophilus to be published, 2013
4W29	70S ribosome translocation intermediate containing elongation factor EFG/GDP/fusidic acid, mRNA, and tRNAs trapped in the AP/AP pe/E chimeric hybrid state. 分子名称: 16S Ribosomal RNA, 23S Ribosomal RNA, 30S ribosomal protein S10, ... 著者 Zhou, J, Lancaster, L, Donohue, J.P, Noller, H.F. 登録日 2014-07-02 公開日 2014-10-01 最終更新日 2023-09-20 実験手法 X-RAY DIFFRACTION (3.8 Å) 主引用文献 How the ribosome hands the A-site tRNA to the P site during EF-G-catalyzed translocation. Science, 345, 2014
2ET8	Complex Between Neamine and the 16S-RRNA A-Site 分子名称: (1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl 2,6-diamino-2,6-dideoxy-alpha-D-glucopyranoside, 5'-R(*CP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*C)-3' 著者 Westhof, E. 登録日 2005-10-27 公開日 2005-12-13 最終更新日 2023-08-23 実験手法 X-RAY DIFFRACTION (2.5 Å) 主引用文献 Crystal structures of complexes between aminoglycosides and decoding A site oligonucleotides: role of the number of rings and positive charges in the specific binding leading to miscoding. Nucleic Acids Res., 33, 2005
8VTT	Meis1 homeobox domain bound to neomycin fragment 分子名称: Homeobox protein Meis1, RIBOSTAMYCIN, SULFATE ION 著者 Tomchick, D.R, Ahmed, M.S, Nguyen, N.U.N, Sadek, H.A. 登録日 2024-01-27 公開日 2024-02-14 実験手法 X-RAY DIFFRACTION (2.45 Å) 主引用文献 Identification of FDA-Approved Drugs That Induce Heart Regeneration in Mammals to be published
5NDV	Crystal structure of Paromomycin bound to the yeast 80S ribosome 分子名称: 18S ribosomal RNA, 25S ribosomal RNA, 40S ribosomal protein S0-A, ... 著者 Prokhorova, I, Djumagulov, M, Urzhumtsev, A, Yusupov, M, Yusupova, G. 登録日 2017-03-09 公開日 2017-12-13 最終更新日 2024-05-08 実験手法 X-RAY DIFFRACTION (3.3 Å) 主引用文献 Aminoglycoside interactions and impacts on the eukaryotic ribosome. Proc. Natl. Acad. Sci. U.S.A., 114, 2017
7K00	Structure of the Bacterial Ribosome at 2 Angstrom Resolution 分子名称: 16S rRNA, 23S rRNA, 30S ribosomal protein S10, ... 著者 Watson, Z.L, Ward, F.R, Meheust, R, Ad, O, Schepartz, A, Banfield, J.F, Cate, J.H.D. 登録日 2020-09-02 公開日 2020-09-23 最終更新日 2023-11-15 実験手法 ELECTRON MICROSCOPY (1.98 Å) 主引用文献 Structure of the bacterial ribosome at 2 angstrom resolution. Elife, 9, 2020
8G7Q	Structure of the Escherichia coli 70S ribosome in complex with EF-Tu and Ile-tRNAIle(LAU) bound to the near-cognate AUG codon (Structure II) 分子名称: 16S Ribosomal RNA, 23S Ribosomal RNA, 30S ribosomal protein S10, ... 著者 Rybak, M.Y, Gagnon, M.G. 登録日 2023-02-16 公開日 2024-03-06 最終更新日 2024-04-10 実験手法 ELECTRON MICROSCOPY (3.1 Å) 主引用文献 Structures of the ribosome bound to EF-Tu-isoleucine tRNA elucidate the mechanism of AUG avoidance. Nat.Struct.Mol.Biol., 2024
8G7R	Structure of the Escherichia coli 70S ribosome in complex with A-site tRNAIle(LAU) bound to the cognate AUA codon (Structure III) 分子名称: 16S Ribosomal RNA, 23S Ribosomal RNA, 30S ribosomal protein S10, ... 著者 Rybak, M.Y, Gagnon, M.G. 登録日 2023-02-16 公開日 2024-03-06 最終更新日 2024-04-10 実験手法 ELECTRON MICROSCOPY (2.8 Å) 主引用文献 Structures of the ribosome bound to EF-Tu-isoleucine tRNA elucidate the mechanism of AUG avoidance. Nat.Struct.Mol.Biol., 2024
7UUM	Crystal structure of aminoglycoside resistance enzyme ApmA, complex with paromomycin and coenzyme A 分子名称: Aminocyclitol acetyltransferase ApmA, COENZYME A, GLYCEROL, ... 著者 Stogios, P.J, Evdokimova, E, Osipiuk, J, Di Leo, R, Bordeleau, E, Wright, G.D, Savchenko, A, Joachimiak, A, Satchell, K.J.F, Center for Structural Genomics of Infectious Diseases (CSGID), Center for Structural Biology of Infectious Diseases (CSBID) 登録日 2022-04-28 公開日 2022-11-02 最終更新日 2024-02-14 実験手法 X-RAY DIFFRACTION (2.74 Å) 主引用文献 Mechanistic plasticity in ApmA enables aminoglycoside promiscuity for resistance. Nat.Chem.Biol., 20, 2024
7ZNO	Crystal Structure of Unlinked NS2B_NS3 Protease from Zika Virus in Complex with Boronate Inhibitor MI-2270 分子名称: Serine protease NS3, Serine protease subunit NS2B, [(1R)-1-[[(2S)-6-azanyl-2-[[(2S)-6-azanyl-2-[2-[3-(4-carbamimidamido-3-oxidanylidene-pentyl)phenyl]ethanoylamino]hexanoyl]amino]hexanoyl]amino]-3-methyl-butyl]boronic acid 著者 Huber, S, Heine, A, Steinmetzer, T. 登録日 2022-04-21 公開日 2022-06-22 最終更新日 2024-02-07 実験手法 X-RAY DIFFRACTION (1.7 Å) 主引用文献 Boroleucine-Derived Covalent Inhibitors of the ZIKV Protease. Chemmedchem, 18, 2023
7ZUM	Crystal Structure of Unlinked NS2B-NS3 Protease from Zika Virus in Complex with Inhibitor MI-2130 分子名称: 1-[(5R,8R,15S,18S)-15-(4-azanylbutyl)-5-(cyclohexylmethyl)-18-(1H-indol-3-ylmethyl)-4,7,14,17,20-pentakis(oxidanylidene)-3,6,13,16,19-pentazabicyclo[20.3.1]hexacosa-1(25),22(26),23-trien-8-yl]guanidine, Serine protease NS3, Serine protease subunit NS2B 著者 Huber, S, Steinmetzer, T. 登録日 2022-05-12 公開日 2023-03-22 最終更新日 2024-02-07 実験手法 X-RAY DIFFRACTION (1.75 Å) 主引用文献 Crystal Structure of Unlinked NS2B-NS3 Protease from Zika Virus in Complex with Inhibitor MI-2130 To Be Published
8EIU	E. coli 70S ribosome with A-loop mutations U2554C and U2555C 分子名称: 16S rRNA, 23S rRNA, 3'-amino-3'-deoxyadenosine 5'-(dihydrogen phosphate), ... 著者 Nissley, A.J, Penev, P.I, Watson, Z.L, Banfield, J.F, Cate, J.H.D. 登録日 2022-09-15 公開日 2023-02-01 最終更新日 2023-11-15 実験手法 ELECTRON MICROSCOPY (2.24 Å) 主引用文献 Rare ribosomal RNA sequences from archaea stabilize the bacterial ribosome. Nucleic Acids Res., 51, 2023
8EMM	Composite 70S ribosome structure for "Atomistic simulations of the E. coli ribosome provide selection criteria for translationally active substrates 分子名称: 16S rRNA, 23S rRNA, 30S ribosomal protein S10, ... 著者 Watson, Z.L, Cate, J.H.D. 登録日 2022-09-28 公開日 2023-05-31 最終更新日 2023-11-15 実験手法 ELECTRON MICROSCOPY (2.1 Å) 主引用文献 Atomistic simulations of the Escherichia coli ribosome provide selection criteria for translationally active substrates. Nat.Chem., 15, 2023
8BSQ	Notum Inhibitor ARUK3006561 分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, DIMETHYL SULFOXIDE, Palmitoleoyl-protein carboxylesterase NOTUM, ... 著者 Zhao, Y, Jones, E.Y, Fish, P. 登録日 2022-11-26 公開日 2022-12-14 最終更新日 2023-06-28 実験手法 X-RAY DIFFRACTION (1.45 Å) 主引用文献 Designed switch from covalent to non-covalent inhibitors of carboxylesterase Notum activity. Eur.J.Med.Chem., 251, 2023
7MQL	AAC(3)-IIIa in complex with CoA and neomycin 分子名称: Aminoglycoside N(3)-acetyltransferase III, COENZYME A, FORMIC ACID, ... 著者 Zielinski, M, Berghuis, A.M. 登録日 2021-05-05 公開日 2022-07-06 最終更新日 2022-08-17 実験手法 X-RAY DIFFRACTION (1.6 Å) 主引用文献 Structural elucidation of substrate-bound aminoglycoside acetyltransferase (3)-IIIa. Plos One, 17, 2022
8G6W	Structure of WT E.coli 70S ribosome complexed with mRNA, P-site fMet-NH-tRNAfMet and A-site ortho-aminobenzoic acid charged NH-tRNAPhe 分子名称: 16S rRNA, 2-AMINO-BENZAMIDE, 23S rRNA, ... 著者 Majumdar, C, Cate, J.H.D. 登録日 2023-02-16 公開日 2023-04-05 最終更新日 2023-11-15 実験手法 ELECTRON MICROSCOPY (2.02 Å) 主引用文献 Aminobenzoic Acid Derivatives Obstruct Induced Fit in the Catalytic Center of the Ribosome. Acs Cent.Sci., 9, 2023
2FCZ	HIV-1 DIS kissing-loop in complex with ribostamycin 分子名称: HIV-1 DIS RNA, POTASSIUM ION, RIBOSTAMYCIN 著者 Ennifar, E, Paillart, J.C, Marquet, R, Dumas, P. 登録日 2005-12-13 公開日 2006-05-16 最終更新日 2023-08-30 実験手法 X-RAY DIFFRACTION (2.01 Å) 主引用文献 Targeting the dimerization initiation site of HIV-1 RNA with aminoglycosides: from crystal to cell. Nucleic Acids Res., 34, 2006
2FD0	HIV-1 DIS kissing-loop in complex with lividomycin 分子名称: (2R,3S,4S,5S,6R)-2-((2S,3S,4R,5R,6R)-5-AMINO-2-(AMINOMETHYL)-6-((2R,3S,4R,5S)-5-((1R,2R,3S,5R,6S)-3,5-DIAMINO-2-((2S,3R ,5S,6R)-3-AMINO-5-HYDROXY-6-(HYDROXYMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)-6-HYDROXYCYCLOHEXYLOXY)-4-HYDROXY-2-(HYDROXYMET HYL)-TETRAHYDROFURAN-3-YLOXY)-4-HYDROXY-TETRAHYDRO-2H-PYRAN-3-YLOXY)-6-(HYDROXYMETHYL)-TETRAHYDRO-2H-PYRAN-3,4,5-TRIOL, CHLORIDE ION, HIV-1 DIS RNA, ... 著者 Ennifar, E, Paillart, J.C, Marquet, R, Dumas, P. 登録日 2005-12-13 公開日 2006-05-16 最終更新日 2023-08-30 実験手法 X-RAY DIFFRACTION (1.8 Å) 主引用文献 Targeting the dimerization initiation site of HIV-1 RNA with aminoglycosides: from crystal to cell. Nucleic Acids Res., 34, 2006
4DR2	Crystal structure of the Thermus thermophilus (HB8) 30S ribosomal subunit with multiple copies of paromomycin molecules bound 分子名称: 16S rRNA, 30S ribosomal protein S10, 30S ribosomal protein S11, ... 著者 Demirci, H, Murphy IV, F, Murphy, E, Gregory, S.T, Dahlberg, A.E, Jogl, G. 登録日 2012-02-16 公開日 2012-11-14 最終更新日 2013-01-30 実験手法 X-RAY DIFFRACTION (3.249 Å) 主引用文献 A structural basis for streptomycin-induced misreading of the genetic code. Nat Commun, 4, 2013
5TCU	Methicillin sensitive Staphylococcus aureus 70S ribosome 分子名称: 16S RRNA, 23S RRNA, 30S ribosomal protein S10, ... 著者 Eyal, Z, Ahmed, T, Belousoff, N, Mishra, S, Matzov, D, Bashan, A, Zimmerman, E, Lithgow, T, Bhushan, S, Yonath, A. 登録日 2016-09-15 公開日 2017-05-24 最終更新日 2019-12-18 実験手法 ELECTRON MICROSCOPY (3.9 Å) 主引用文献 Structural Basis for Linezolid Binding Site Rearrangement in the Staphylococcus aureus Ribosome. MBio, 8, 2017
4DR4	Crystal structure of the Thermus thermophilus (HB8) 30S ribosomal subunit with codon, cognate transfer RNA anticodon stem-loop and multiple copies of paromomycin molecules bound 分子名称: 16S rRNA, 30S ribosomal protein S10, 30S ribosomal protein S11, ... 著者 Demirci, H, Murphy IV, F, Murphy, E, Gregory, S.T, Dahlberg, A.E, Jogl, G. 登録日 2012-02-16 公開日 2012-11-14 最終更新日 2013-01-30 実験手法 X-RAY DIFFRACTION (3.969 Å) 主引用文献 A structural basis for streptomycin-induced misreading of the genetic code. Nat Commun, 4, 2013
6S0V	The crystal structure of kanamycin B dioxygenase (KanJ) from Streptomyces kanamyceticus in complex with nickel, neamine and sulfate 分子名称: (1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl 2,6-diamino-2,6-dideoxy-alpha-D-glucopyranoside, Kanamycin B dioxygenase, NICKEL (II) ION, ... 著者 Mrugala, B, Niedzialkowska, E, Minor, W, Borowski, T. 登録日 2019-06-18 公開日 2020-07-08 最終更新日 2024-01-24 実験手法 X-RAY DIFFRACTION (3 Å) 主引用文献 A study on the structure, mechanism, and biochemistry of kanamycin B dioxygenase (KanJ)-an enzyme with a broad range of substrates. Febs J., 288, 2021
3C44	Crystal structure of HIV-1 subtype F DIS extended duplex RNA bound to paromomycin 分子名称: CHLORIDE ION, HIV-1 subtype F genomic RNA, PAROMOMYCIN, ... 著者 Freisz, S, Ennifar, E, Dumas, P. 登録日 2008-01-29 公開日 2008-05-06 最終更新日 2023-11-01 実験手法 X-RAY DIFFRACTION (2 Å) 主引用文献 Binding of aminoglycoside antibiotics to the duplex form of the HIV-1 genomic RNA dimerization initiation site. Angew.Chem.Int.Ed.Engl., 47, 2008
3BNQ	Crystal Structure of the Homo sapiens Mitochondrial Ribosomal Decoding Site in the Presence of SrCl2 (A1555G mutant, Br-derivative) 分子名称: A site of human mitochondrial ribosome, A chain, B chain, ... 著者 Kondo, J, Westhof, E. 登録日 2007-12-14 公開日 2008-06-24 最終更新日 2024-02-21 実験手法 X-RAY DIFFRACTION (2 Å) 主引用文献 The bacterial and mitochondrial ribosomal A-site molecular switches possess different conformational substates Nucleic Acids Res., 36, 2008
4GKJ	Structure of the Thermus thermophilus 30S ribosomal subunit complexed with a human mitochondrial anticodon stem loop (ASL) of transfer RNA Methionine (TRNAMET) bound to an mRNA with an AUG-codon in the A-site and paromomycin. 分子名称: 16S rRNA, 30S ribosomal protein S10, 30S ribosomal protein S11, ... 著者 Cantara, W.A, Murphy IV, F.V, Spears, J.L, Demirci, H, Agris, P.F. 登録日 2012-08-11 公開日 2013-06-05 最終更新日 2024-02-28 実験手法 X-RAY DIFFRACTION (3.298 Å) 主引用文献 Expanded use of sense codons is regulated by modified cytidines in tRNA. Proc.Natl.Acad.Sci.USA, 110, 2013

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