RNA 3D Hub //

Equivalence class NR_all_08124.1 Obsolete

#IFEStandardized nameMoleculeOrganismSourceRfamTitleMethodRes. ÅDate
14IOA|1|X (rep)Large subunit ribosomal RNA23S ribosomal RNADeinococcus radioduransBacteriaRF02541Crystal structure of compound 4e bound to large ribosomal subunit (50S) from Deinococcus radioduransX-ray diffraction3.22013-03-06
24IO9|1|XLarge subunit ribosomal RNA23S ribosomal RNADeinococcus radioduransBacteriaRF02541Crystal structure of compound 4d bound to large ribosomal subunit (50S) from Deinococcus radioduransX-ray diffraction3.22013-03-06
34IOC|1|XLarge subunit ribosomal RNA23S ribosomal RNADeinococcus radioduransBacteriaRF02541Crystal structure of compound 4f bound to large ribosomal subunit (50S) from Deinococcus radioduransX-ray diffraction3.62013-03-06
42ZJR|1|XLarge subunit ribosomal RNAribosomal 23S RNADeinococcus radioduransBacteriaRF02541Refined native structure of the large ribosomal subunit (50S) from Deinococcus radioduransX-ray diffraction2.912008-06-17
53CF5|1|XLarge subunit ribosomal RNARRNA-23S RIBOSOMAL RNADeinococcus radioduransBacteriaRF02541Thiopeptide antibiotic Thiostrepton bound to the large ribosomal subunit of Deinococcus radioduransX-ray diffraction3.32008-06-17
62ZJQ|1|XLarge subunit ribosomal RNAribosomal 23S RNADeinococcus radioduransBacteriaRF02541Interaction of L7 with L11 induced by Microccocin binding to the Deinococcus radiodurans 50S subunitX-ray diffraction3.32008-06-17
72ZJP|1|XLarge subunit ribosomal RNARIBOSOMAL 23S RNADeinococcus radioduransBacteriaRF02541Thiopeptide antibiotic Nosiheptide bound to the large ribosomal subunit of Deinococcus radioduransX-ray diffraction3.72008-06-17
83DLL|1|XLarge subunit ribosomal RNArRNA-23S ribosomal RNADeinococcus radioduransBacteriaRF02541The oxazolidinone antibiotics perturb the ribosomal peptidyl-transferase center and effect tRNA positioningX-ray diffraction3.52008-09-16
92AAR|1|0Large subunit ribosomal RNA23S ribosomal RNADeinococcus radioduransBacteriaRF02541Structure of trigger factor binding domain in biologically homologous complex with eubacterial ribosome.X-ray diffraction3.52005-08-23
102OGM|1|0Large subunit ribosomal RNA23S ribosomal RNADeinococcus radioduransBacteriaRF02541The crystal structure of the large ribosomal subunit from Deinococcus radiodurans complexed with the pleuromutilin derivative SB-571519X-ray diffraction3.52007-05-01
113PIO|1|XLarge subunit ribosomal RNARIBOSOMAL 23S RNADeinococcus radioduransBacteriaRF02541Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunitX-ray diffraction3.252011-02-23
123JQ4|1|ALarge subunit ribosomal RNA23S ribosomal RNADeinococcus radioduransBacteriaRF02541The structure of the complex of the large ribosomal subunit from D. Radiodurans with the antibiotic lankacidinX-ray diffraction3.522010-09-08
132D3O|1|0Large subunit ribosomal RNA23S RIBOSOMAL RNADeinococcus radioduransBacteriaRF02541Structure of Ribosome Binding Domain of the Trigger Factor on the 50S ribosomal subunit from D. radioduransX-ray diffraction3.352005-12-06
141Y69|1|0Large subunit ribosomal RNA23S ribosomal RNADeinococcus radioduransBacteriaRF02541RRF domain I in complex with the 50S ribosomal subunit from Deinococcus radioduransX-ray diffraction3.332005-03-01
153PIP|1|XLarge subunit ribosomal RNARIBOSOMAL 23S RNADeinococcus radioduransBacteriaRF02541Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunitX-ray diffraction3.452011-02-23
161JZY|1|ALarge subunit ribosomal RNA23S rRNADeinococcus radioduransBacteriaRF02541Structural Basis for the Interaction of Antibiotics with the Peptidyl Transferase Center in EubacteriaX-ray diffraction3.52001-10-26
172OGO|1|0Large subunit ribosomal RNA23S ribosomal RNADeinococcus radioduransBacteriaRF02541The crystal structure of the large ribosomal subunit from Deinococcus radiodurans complexed with the pleuromutilin derivative retapamulin (SB-275833)X-ray diffraction3.662007-05-01
181K01|1|ALarge subunit ribosomal RNA23S rRNADeinococcus radioduransBacteriaRF02541Structural Basis for the Interaction of Antibiotics with the Peptidyl Transferase Center in EubacteriaX-ray diffraction3.52001-10-26
191JZX|1|ALarge subunit ribosomal RNA23S rRNADeinococcus radioduransBacteriaRF02541Structural Basis for the Interaction of Antibiotics with the Peptidyl Transferase Center in EubacteriaX-ray diffraction3.12001-10-26
201JZZ|1|ALarge subunit ribosomal RNA23S rRNADeinococcus radioduransBacteriaRF02541Structural Basis for the Interaction of Antibiotics with the Peptidyl Transferase Center in EubacteriaX-ray diffraction3.82001-10-26
211J5A|1|ALarge subunit ribosomal RNA23S RRNADeinococcus radioduransBacteriaRF02541STRUCTURAL BASIS FOR THE INTERACTION OF ANTIBIOTICS WITH THE PEPTIDYL TRANSFERASE CENTER IN EUBACTERIAX-ray diffraction3.52002-03-08
222O44|1|ALarge subunit ribosomal RNA23S rRNADeinococcus radioduransBacteriaRF02541Structure of 23S rRNA of the large ribosomal subunit from Deinococcus radiodurans in complex with the macrolide josamycinX-ray diffraction3.32007-12-04
232OGN|1|0Large subunit ribosomal RNA23S ribosomal RNADeinococcus radioduransBacteriaRF02541The crystal structure of the large ribosomal subunit from Deinococcus radiodurans complexed with the pleuromutilin derivative SB-280080X-ray diffraction3.562007-05-01
241NWX|1|0Large subunit ribosomal RNA23S RIBOSOMAL RNADeinococcus radioduransBacteriaRF02541COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH ABT-773X-ray diffraction3.52003-03-18
251OND|1|0Large subunit ribosomal RNA23S RIBOSOMAL RNADeinococcus radioduransBacteriaRF02541THE CRYSTAL STRUCTURE OF THE 50S LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS COMPLEXED WITH TROLEANDOMYCIN MACROLIDE ANTIBIOTICX-ray diffraction3.42003-04-15
261NWY|1|0Large subunit ribosomal RNA23S RIBOSOMAL RRNADeinococcus radioduransBacteriaRF02541COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH AZITHROMYCINX-ray diffraction3.32003-03-18
271NKW|1|0Large subunit ribosomal RNA23S ribosomal RNADeinococcus radioduransBacteriaRF02541Crystal Structure Of The Large Ribosomal Subunit From Deinococcus RadioduransX-ray diffraction3.12003-02-11
283FWO|1|ALarge subunit ribosomal RNA23S RIBOSOMAL RNADeinococcus radioduransBacteriaRF02541The large ribosomal subunit from Deinococcus radiodurans complexed with MethymycinX-ray diffraction3.712010-01-19
291NJO|1|0Large subunit ribosomal RNA23S ribosomal RNA, RNA ACC(Puromycin)Deinococcus radioduransBacteriaRF02541The crystal structure of the 50S Large ribosomal subunit from Deinococcus radiodurans complexed with a short substrate analog ACCPuromycin (ACCP)X-ray diffraction3.72003-02-11
301NJP|1|0Large subunit ribosomal RNA23S ribosomal RNADeinococcus radioduransBacteriaRF02541The crystal structure of the 50S Large ribosomal subunit from Deinococcus radiodurans complexed with a tRNA acceptor stem mimic (ASM)X-ray diffraction3.52003-02-11
311P9X|1|0Large subunit ribosomal RNA23S RIBOSOMAL RNADeinococcus radioduransBacteriaRF02541THE CRYSTAL STRUCTURE OF THE 50S LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS COMPLEXED WITH TELITHROMYCIN KETOLIDE ANTIBIOTICX-ray diffraction3.42003-08-05
321NJM|1|0Large subunit ribosomal RNA23S ribosomal RNADeinococcus radioduransBacteriaRF02541The crystal structure of the 50S Large ribosomal subunit from Deinococcus radiodurans complexed with a tRNA acceptor stem mimic (ASM) and the antibiotic sparsomycinX-ray diffraction3.62003-02-11
331NJN|1|0Large subunit ribosomal RNA23S ribosomal RNADeinococcus radioduransBacteriaRF02541The crystal structure of the 50S Large ribosomal subunit from Deinococcus radiodurans complexed with the antibiotic sparsomycinX-ray diffraction3.72003-02-11
342O43|1|ALarge subunit ribosomal RNA23S rRNADeinococcus radioduransBacteriaRF02541Structure of 23S rRNA of the large ribosomal subunit from Deinococcus radiodurans in complex with the macrolide erythromycylamineX-ray diffraction3.62007-12-04
351SM1|1|0Large subunit ribosomal RNA23S RIBOSOMAL RNADeinococcus radioduransBacteriaRF02541COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH QUINUPRISTIN AND DALFOPRISTINX-ray diffraction3.422004-08-03
361XBP|1|0Large subunit ribosomal RNA23S RIBOSOMAL RNADeinococcus radioduransBacteriaRF02541Inhibition of peptide bond formation by pleuromutilins: The structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with TiamulinX-ray diffraction3.52005-03-01
371Z58|1|2Large subunit ribosomal RNA23S RIBOSOMAL RNADeinococcus radioduransBacteriaRF02541Crystal structure of a complex of the ribosome large subunit with rapamycinX-ray diffraction3.82005-06-28
382O45|1|ALarge subunit ribosomal RNA23S rRNADeinococcus radioduransBacteriaRF02541Structure of the 23S rRNA of the large ribosomal subunit from Deinococcus Radiodurans in complex with the macrolide RU-69874X-ray diffraction3.62007-12-04

Release history

Release2.0
Date2014-12-05

Parents

This classParent classesRelease idIntersectionAdded to this classOnly in parent

Children

This class Descendant classesRelease idIntersectionOnly in this classAdded to child
NR_all_08124.1NR_20.0_08124.23.0(38) 2ZJP|1|X, 1NKW|1|0, 2ZJQ|1|X, 1NWX|1|0, 2ZJR|1|X, 1NWY|1|0, 3CF5|1|X, 1OND|1|0, 3DLL|1|X, 1P9X|1|0, 3FWO|1|A, 1SM1|1|0, 3JQ4|1|A, 1XBP|1|0, 1Y69|1|0, 1Z58|1|2, 1J5A|1|A, 2AAR|1|0, 1JZX|1|A, 2D3O|1|0, 1JZY|1|A, 2O43|1|A, 1JZZ|1|A, 2O44|1|A, 1K01|1|A, 2O45|1|A, 1NJM|1|0, 2OGM|1|0, 1NJN|1|0, 2OGN|1|0, 1NJO|1|0, 2OGO|1|0, 1NJP|1|0, 3PIO|1|X, 3PIP|1|X, 4IO9|1|X, 4IOA|1|X, 4IOC|1|X(0) (4) 5DM7|1|X, 5DM6|1|X, 4WFN|1|X, 4U67|1|X
NR_all_08124.1NR_3.0_08124.23.0(1) 2ZJR|1|X(37) 2OGM|1|0, 2ZJQ|1|X, 3JQ4|1|A, 4IOA|1|X, 1JZY|1|A, 1NJN|1|0, 1NWX|1|0, 1SM1|1|0, 2AAR|1|0, 2O45|1|A, 2ZJP|1|X, 3FWO|1|A, 4IO9|1|X, 1JZZ|1|A, 1NJO|1|0, 1NWY|1|0, 1XBP|1|0, 2D3O|1|0, 1JZX|1|A, 1NJM|1|0, 1NKW|1|0, 1P9X|1|0, 1Z58|1|2, 2O44|1|A, 2OGO|1|0, 3DLL|1|X, 3PIP|1|X, 1J5A|1|A, 1K01|1|A, 1NJP|1|0, 1OND|1|0, 1Y69|1|0, 2O43|1|A, 2OGN|1|0, 3CF5|1|X, 3PIO|1|X, 4IOC|1|X(2) 5DM6|1|X, 5DM7|1|X
NR_all_08124.1NR_3.5_08124.23.0(25) 1NKW|1|0, 1K01|1|A, 4IOA|1|X, 1NWX|1|0, 3PIP|1|X, 1NJP|1|0, 1JZX|1|A, 1JZY|1|A, 4IO9|1|X, 1XBP|1|0, 1OND|1|0, 1P9X|1|0, 1NWY|1|0, 1SM1|1|0, 2OGM|1|0, 2AAR|1|0, 2D3O|1|0, 1Y69|1|0, 2O44|1|A, 3PIO|1|X, 2ZJR|1|X, 1J5A|1|A, 3CF5|1|X, 2ZJQ|1|X, 3DLL|1|X(13) 2OGN|1|0, 1Z58|1|2, 1NJO|1|0, 3JQ4|1|A, 2OGO|1|0, 1NJN|1|0, 4IOC|1|X, 2O45|1|A, 3FWO|1|A, 1NJM|1|0, 2O43|1|A, 2ZJP|1|X, 1JZZ|1|A(2) 5DM7|1|X, 5DM6|1|X
NR_all_08124.1NR_4.0_08124.23.0(38) 1NWY|1|0, 1OND|1|0, 1P9X|1|0, 1J5A|1|A, 1JZX|1|A, 1JZY|1|A, 1JZZ|1|A, 1K01|1|A, 1NJM|1|0, 1NJN|1|0, 1NJO|1|0, 1NJP|1|0, 1NKW|1|0, 1NWX|1|0, 2ZJQ|1|X, 2ZJR|1|X, 3CF5|1|X, 3DLL|1|X, 3FWO|1|A, 1SM1|1|0, 3JQ4|1|A, 1XBP|1|0, 3PIO|1|X, 1Y69|1|0, 3PIP|1|X, 1Z58|1|2, 4IO9|1|X, 2AAR|1|0, 4IOA|1|X, 2D3O|1|0, 4IOC|1|X, 2O43|1|A, 2O44|1|A, 2O45|1|A, 2OGM|1|0, 2OGN|1|0, 2OGO|1|0, 2ZJP|1|X(0) (4) 4WFN|1|X, 4U67|1|X, 5DM7|1|X, 5DM6|1|X
NR_all_08124.1NR_all_08124.23.0(38) 1NJO|1|0, 1NJP|1|0, 1J5A|1|A, 1JZX|1|A, 1JZY|1|A, 1JZZ|1|A, 1K01|1|A, 1NJM|1|0, 1NJN|1|0, 2OGM|1|0, 2OGN|1|0, 2OGO|1|0, 2ZJP|1|X, 1NKW|1|0, 2ZJQ|1|X, 1NWX|1|0, 2ZJR|1|X, 1NWY|1|0, 3CF5|1|X, 1OND|1|0, 3DLL|1|X, 1P9X|1|0, 3FWO|1|A, 1SM1|1|0, 3JQ4|1|A, 1XBP|1|0, 3PIO|1|X, 1Y69|1|0, 3PIP|1|X, 1Z58|1|2, 4IO9|1|X, 2AAR|1|0, 4IOA|1|X, 2D3O|1|0, 4IOC|1|X, 2O43|1|A, 2O44|1|A, 2O45|1|A(0) (4) 4WFN|1|X, 4U67|1|X, 5DM7|1|X, 5DM6|1|X

Heat map of mutual geometric discrepancy, in Angstroms per nucleotide. Instances are ordered to put similar structures near each other. The colorbar ranges from 0 to the maximum observed discrepancy, up to 0.5

#S - ordering by similarity (same as in the heat map).
#SPDBTitleMethodResolutionLengthNAKB_NA_annotationNAKB_protein_annotation
12D3O|1|0Title: Structure of Ribosome Binding Domain of the Trigger Factor on the 50S ribosomal subunit from D. radioduransX-RAY DIFFRACTION3.352802
23PIP|1|XTitle: Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunitX-RAY DIFFRACTION3.452644
33PIO|1|XTitle: Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunitX-RAY DIFFRACTION3.252657
44IOC|1|XTitle: Crystal structure of compound 4f bound to large ribosomal subunit (50S) from Deinococcus radioduransX-RAY DIFFRACTION3.62686
54IO9|1|XTitle: Crystal structure of compound 4d bound to large ribosomal subunit (50S) from Deinococcus radioduransX-RAY DIFFRACTION3.22686
64IOA|1|XTitle: Crystal structure of compound 4e bound to large ribosomal subunit (50S) from Deinococcus radioduransX-RAY DIFFRACTION3.22686
72ZJR|1|XTitle: Refined native structure of the large ribosomal subunit (50S) from Deinococcus radioduransX-RAY DIFFRACTION2.912686
82ZJP|1|XTitle: Thiopeptide antibiotic Nosiheptide bound to the large ribosomal subunit of Deinococcus radioduransX-RAY DIFFRACTION3.72686
93CF5|1|XTitle: Thiopeptide antibiotic Thiostrepton bound to the large ribosomal subunit of Deinococcus radioduransX-RAY DIFFRACTION3.32686
102ZJQ|1|XTitle: Interaction of L7 with L11 induced by Microccocin binding to the Deinococcus radiodurans 50S subunitX-RAY DIFFRACTION3.32686
113DLL|1|XTitle: The oxazolidinone antibiotics perturb the ribosomal peptidyl-transferase center and effect tRNA positioningX-RAY DIFFRACTION3.52686
123FWO|1|ATitle: The large ribosomal subunit from Deinococcus radiodurans complexed with MethymycinX-RAY DIFFRACTION3.712765
132O44|1|ATitle: Structure of 23S rRNA of the large ribosomal subunit from Deinococcus radiodurans in complex with the macrolide josamycinX-RAY DIFFRACTION3.32766
142O43|1|ATitle: Structure of 23S rRNA of the large ribosomal subunit from Deinococcus radiodurans in complex with the macrolide erythromycylamineX-RAY DIFFRACTION3.62766
152OGN|1|0Title: The crystal structure of the large ribosomal subunit from Deinococcus radiodurans complexed with the pleuromutilin derivative SB-280080X-RAY DIFFRACTION3.562766
162OGM|1|0Title: The crystal structure of the large ribosomal subunit from Deinococcus radiodurans complexed with the pleuromutilin derivative SB-571519X-RAY DIFFRACTION3.52766
172OGO|1|0Title: The crystal structure of the large ribosomal subunit from Deinococcus radiodurans complexed with the pleuromutilin derivative retapamulin (SB-275833)X-RAY DIFFRACTION3.662765
182AAR|1|0Title: Structure of trigger factor binding domain in biologically homologous complex with eubacterial ribosome.X-RAY DIFFRACTION3.52766
193JQ4|1|ATitle: The structure of the complex of the large ribosomal subunit from D. Radiodurans with the antibiotic lankacidinX-RAY DIFFRACTION3.522765
201P9X|1|0Title: THE CRYSTAL STRUCTURE OF THE 50S LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS COMPLEXED WITH TELITHROMYCIN KETOLIDE ANTIBIOTICX-RAY DIFFRACTION3.42738
211SM1|1|0Title: COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH QUINUPRISTIN AND DALFOPRISTINX-RAY DIFFRACTION3.422766
221XBP|1|0Title: Inhibition of peptide bond formation by pleuromutilins: The structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with TiamulinX-RAY DIFFRACTION3.52766
231OND|1|0Title: THE CRYSTAL STRUCTURE OF THE 50S LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS COMPLEXED WITH TROLEANDOMYCIN MACROLIDE ANTIBIOTICX-RAY DIFFRACTION3.42765
241NKW|1|0Title: Crystal Structure Of The Large Ribosomal Subunit From Deinococcus RadioduransX-RAY DIFFRACTION3.12766
251NWX|1|0Title: COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH ABT-773X-RAY DIFFRACTION3.52766
261NWY|1|0Title: COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH AZITHROMYCINX-RAY DIFFRACTION3.32766
271NJP|1|0Title: The crystal structure of the 50S Large ribosomal subunit from Deinococcus radiodurans complexed with a tRNA acceptor stem mimic (ASM)X-RAY DIFFRACTION3.52766
281NJO|1|0Title: The crystal structure of the 50S Large ribosomal subunit from Deinococcus radiodurans complexed with a short substrate analog ACCPuromycin (ACCP)X-RAY DIFFRACTION3.72766
291NJN|1|0Title: The crystal structure of the 50S Large ribosomal subunit from Deinococcus radiodurans complexed with the antibiotic sparsomycinX-RAY DIFFRACTION3.72766
301NJM|1|0Title: The crystal structure of the 50S Large ribosomal subunit from Deinococcus radiodurans complexed with a tRNA acceptor stem mimic (ASM) and the antibiotic sparsomycinX-RAY DIFFRACTION3.62766
311K01|1|ATitle: Structural Basis for the Interaction of Antibiotics with the Peptidyl Transferase Center in EubacteriaX-RAY DIFFRACTION3.52774
321JZX|1|ATitle: Structural Basis for the Interaction of Antibiotics with the Peptidyl Transferase Center in EubacteriaX-RAY DIFFRACTION3.12774
331JZY|1|ATitle: Structural Basis for the Interaction of Antibiotics with the Peptidyl Transferase Center in EubacteriaX-RAY DIFFRACTION3.52774
341JZZ|1|ATitle: Structural Basis for the Interaction of Antibiotics with the Peptidyl Transferase Center in EubacteriaX-RAY DIFFRACTION3.82774
351J5A|1|ATitle: STRUCTURAL BASIS FOR THE INTERACTION OF ANTIBIOTICS WITH THE PEPTIDYL TRANSFERASE CENTER IN EUBACTERIAX-RAY DIFFRACTION3.52774
361Y69|1|0Title: RRF domain I in complex with the 50S ribosomal subunit from Deinococcus radioduransX-RAY DIFFRACTION3.332766
371Z58|1|2Title: Crystal structure of a complex of the ribosome large subunit with rapamycinX-RAY DIFFRACTION3.82766
382O45|1|ATitle: Structure of the 23S rRNA of the large ribosomal subunit from Deinococcus Radiodurans in complex with the macrolide RU-69874X-RAY DIFFRACTION3.62766

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