NR_3.5_88987.8

Members (30)
History
Heat map

#	IFE	Standardized name	Molecule	Organism	Source	Rfam	Title	Method	Res. Å	Date
1	7A0S\|1\|X (rep)	Large subunit ribosomal RNA	RNA (2732-MER)	Deinococcus radiodurans R1	Bacteria	RF02541	50S Deinococcus radiodurans ribosome bounded with mycinamicin I	X-ray diffraction	3.22	2021-08-18
2	4IOA\|1\|X	Large subunit ribosomal RNA	23S ribosomal RNA	Deinococcus radiodurans	Bacteria	RF02541	Crystal structure of compound 4e bound to large ribosomal subunit (50S) from Deinococcus radiodurans	X-ray diffraction	3.2	2013-03-06
3	4IO9\|1\|X	Large subunit ribosomal RNA	23S ribosomal RNA	Deinococcus radiodurans	Bacteria	RF02541	Crystal structure of compound 4d bound to large ribosomal subunit (50S) from Deinococcus radiodurans	X-ray diffraction	3.2	2013-03-06
4	5JVG\|1\|X	Large subunit ribosomal RNA	23S ribosomal RNA	Deinococcus radiodurans	Bacteria	RF02541	The large ribosomal subunit from Deinococcus radiodurans in complex with avilamycin	X-ray diffraction	3.43	2016-11-09
5	5DM6\|1\|X	Large subunit ribosomal RNA	23S ribosomal RNA	Deinococcus radiodurans	Bacteria	RF02541	Crystal structure of the 50S ribosomal subunit from Deinococcus radiodurans	X-ray diffraction	2.9	2015-11-11
6	7A0R\|1\|X	Large subunit ribosomal RNA	RNA (2730-MER)	Deinococcus radiodurans R1	Bacteria	RF02541	50S Deinococcus radiodurans ribosome bounded with mycinamicin I	X-ray diffraction	3.3	2021-08-18
7	3PIO\|1\|X	Large subunit ribosomal RNA	RIBOSOMAL 23S RNA	Deinococcus radiodurans	Bacteria	RF02541	Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunit	X-ray diffraction	3.25	2011-02-23
8	5DM7\|1\|X	Large subunit ribosomal RNA	23S ribosomal RNA	Deinococcus radiodurans	Bacteria	RF02541	Crystal structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with hygromycin A	X-ray diffraction	3	2015-11-11
9	3PIP\|1\|X	Large subunit ribosomal RNA	RIBOSOMAL 23S RNA	Deinococcus radiodurans	Bacteria	RF02541	Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunit	X-ray diffraction	3.45	2011-02-23
10	3DLL\|1\|X	Large subunit ribosomal RNA	rRNA-23S ribosomal RNA	Deinococcus radiodurans	Bacteria	RF02541	The oxazolidinone antibiotics perturb the ribosomal peptidyl-transferase center and effect tRNA positioning	X-ray diffraction	3.5	2008-09-16
11	1OND\|1\|0	Large subunit ribosomal RNA	23S RIBOSOMAL RNA	Deinococcus radiodurans	Bacteria	RF02541	THE CRYSTAL STRUCTURE OF THE 50S LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS COMPLEXED WITH TROLEANDOMYCIN MACROLIDE ANTIBIOTIC	X-ray diffraction	3.4	2003-04-15
12	2AAR\|1\|0	Large subunit ribosomal RNA	23S ribosomal RNA	Deinococcus radiodurans	Bacteria	RF02541	Structure of trigger factor binding domain in biologically homologous complex with eubacterial ribosome.	X-ray diffraction	3.5	2005-08-23
13	1Y69\|1\|0	Large subunit ribosomal RNA	23S ribosomal RNA	Deinococcus radiodurans	Bacteria	RF02541	RRF domain I in complex with the 50S ribosomal subunit from Deinococcus radiodurans	X-ray diffraction	3.33	2005-03-01
14	2ZJR\|1\|X	Large subunit ribosomal RNA	ribosomal 23S RNA	Deinococcus radiodurans	Bacteria	RF02541	Refined native structure of the large ribosomal subunit (50S) from Deinococcus radiodurans	X-ray diffraction	2.91	2008-06-17
15	3CF5\|1\|X	Large subunit ribosomal RNA	RRNA-23S RIBOSOMAL RNA	Deinococcus radiodurans	Bacteria	RF02541	Thiopeptide antibiotic Thiostrepton bound to the large ribosomal subunit of Deinococcus radiodurans	X-ray diffraction	3.3	2008-06-17
16	2ZJQ\|1\|X	Large subunit ribosomal RNA	ribosomal 23S RNA	Deinococcus radiodurans	Bacteria	RF02541	Interaction of L7 with L11 induced by Microccocin binding to the Deinococcus radiodurans 50S subunit	X-ray diffraction	3.3	2008-06-17
17	2OGM\|1\|0	Large subunit ribosomal RNA	23S ribosomal RNA	Deinococcus radiodurans	Bacteria	RF02541	The crystal structure of the large ribosomal subunit from Deinococcus radiodurans complexed with the pleuromutilin derivative SB-571519	X-ray diffraction	3.5	2007-05-01
18	1JZX\|1\|A	Large subunit ribosomal RNA	23S rRNA	Deinococcus radiodurans	Bacteria	RF02541	Structural Basis for the Interaction of Antibiotics with the Peptidyl Transferase Center in Eubacteria	X-ray diffraction	3.1	2001-10-26
19	1NKW\|1\|0	Large subunit ribosomal RNA	23S ribosomal RNA	Deinococcus radiodurans	Bacteria	RF02541	Crystal Structure Of The Large Ribosomal Subunit From Deinococcus Radiodurans	X-ray diffraction	3.1	2003-02-11
20	1NWY\|1\|0	Large subunit ribosomal RNA	23S RIBOSOMAL RRNA	Deinococcus radiodurans	Bacteria	RF02541	COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH AZITHROMYCIN	X-ray diffraction	3.3	2003-03-18
21	1NJP\|1\|0	Large subunit ribosomal RNA	23S ribosomal RNA	Deinococcus radiodurans	Bacteria	RF02541	The crystal structure of the 50S Large ribosomal subunit from Deinococcus radiodurans complexed with a tRNA acceptor stem mimic (ASM)	X-ray diffraction	3.5	2003-02-11
22	1NWX\|1\|0	Large subunit ribosomal RNA	23S RIBOSOMAL RNA	Deinococcus radiodurans	Bacteria	RF02541	COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH ABT-773	X-ray diffraction	3.5	2003-03-18
23	1J5A\|1\|A	Large subunit ribosomal RNA	23S RRNA	Deinococcus radiodurans	Bacteria	RF02541	STRUCTURAL BASIS FOR THE INTERACTION OF ANTIBIOTICS WITH THE PEPTIDYL TRANSFERASE CENTER IN EUBACTERIA	X-ray diffraction	3.5	2002-03-08
24	1JZY\|1\|A	Large subunit ribosomal RNA	23S rRNA	Deinococcus radiodurans	Bacteria	RF02541	Structural Basis for the Interaction of Antibiotics with the Peptidyl Transferase Center in Eubacteria	X-ray diffraction	3.5	2001-10-26
25	1K01\|1\|A	Large subunit ribosomal RNA	23S rRNA	Deinococcus radiodurans	Bacteria	RF02541	Structural Basis for the Interaction of Antibiotics with the Peptidyl Transferase Center in Eubacteria	X-ray diffraction	3.5	2001-10-26
26	1SM1\|1\|0	Large subunit ribosomal RNA	23S RIBOSOMAL RNA	Deinococcus radiodurans	Bacteria	RF02541	COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH QUINUPRISTIN AND DALFOPRISTIN	X-ray diffraction	3.42	2004-08-03
27	1P9X\|1\|0	Large subunit ribosomal RNA	23S RIBOSOMAL RNA	Deinococcus radiodurans	Bacteria	RF02541	THE CRYSTAL STRUCTURE OF THE 50S LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS COMPLEXED WITH TELITHROMYCIN KETOLIDE ANTIBIOTIC	X-ray diffraction	3.4	2003-08-05
28	2D3O\|1\|0	Large subunit ribosomal RNA	23S RIBOSOMAL RNA	Deinococcus radiodurans	Bacteria	RF02541	Structure of Ribosome Binding Domain of the Trigger Factor on the 50S ribosomal subunit from D. radiodurans	X-ray diffraction	3.35	2005-12-06
29	1XBP\|1\|0	Large subunit ribosomal RNA	23S RIBOSOMAL RNA	Deinococcus radiodurans	Bacteria	RF02541	Inhibition of peptide bond formation by pleuromutilins: The structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with Tiamulin	X-ray diffraction	3.5	2005-03-01
30	2O44\|1\|A	Large subunit ribosomal RNA	23S rRNA	Deinococcus radiodurans	Bacteria	RF02541	Structure of 23S rRNA of the large ribosomal subunit from Deinococcus radiodurans in complex with the macrolide josamycin	X-ray diffraction	3.3	2007-12-04

Release history

Release	3.192	3.193	3.194	3.195	3.196	3.197	3.198
Date	2021-08-18	2021-08-25	2021-09-01	2021-09-08	2021-09-15	2021-09-22	2021-09-29

Parents

This class	Parent classes	Release id	Intersection	Added to this class	Only in parent
NR_3.5_88987.8	NR_3.5_88987.7	3.192	(28) 1NWY\|1\|0, 4IO9\|1\|X, 1NWX\|1\|0, 3PIP\|1\|X, 1NKW\|1\|0, 3PIO\|1\|X, 1NJP\|1\|0, 3DLL\|1\|X, 3CF5\|1\|X, 1K01\|1\|A, 2ZJR\|1\|X, 1JZY\|1\|A, 2ZJQ\|1\|X, 1JZX\|1\|A, 2OGM\|1\|0, 1J5A\|1\|A, 2O44\|1\|A, 2D3O\|1\|0, 2AAR\|1\|0, 1Y69\|1\|0, 1XBP\|1\|0, 5JVG\|1\|X, 1SM1\|1\|0, 5DM7\|1\|X, 1P9X\|1\|0, 5DM6\|1\|X, 1OND\|1\|0, 4IOA\|1\|X	(2) 7A0R\|1\|X, 7A0S\|1\|X	(0)

Children

This class	Descendant classes	Release id	Intersection	Only in this class	Added to child
NR_3.5_88987.8	NR_3.5_88987.9	3.199	(30) 1NWX\|1\|0, 3PIP\|1\|X, 1NKW\|1\|0, 3PIO\|1\|X, 1NJP\|1\|0, 3DLL\|1\|X, 1K01\|1\|A, 3CF5\|1\|X, 1JZY\|1\|A, 2ZJR\|1\|X, 1JZX\|1\|A, 2ZJQ\|1\|X, 1J5A\|1\|A, 2OGM\|1\|0, 2O44\|1\|A, 2D3O\|1\|0, 2AAR\|1\|0, 7A0S\|1\|X, 1Y69\|1\|0, 7A0R\|1\|X, 1XBP\|1\|0, 5JVG\|1\|X, 1SM1\|1\|0, 5DM7\|1\|X, 1P9X\|1\|0, 5DM6\|1\|X, 1OND\|1\|0, 4IOA\|1\|X, 1NWY\|1\|0, 4IO9\|1\|X	(0)	(1) 7A18\|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).

#S	PDB	Title	Method	Resolution	Length
1	2D3O\|1\|0	Structure of Ribosome Binding Domain of the Trigger Factor on the 50S ribosomal subunit from D. radiodurans	X-RAY DIFFRACTION	3.35	2802
2	3DLL\|1\|X	The oxazolidinone antibiotics perturb the ribosomal peptidyl-transferase center and effect tRNA positioning	X-RAY DIFFRACTION	3.5	2686
3	2ZJQ\|1\|X	Interaction of L7 with L11 induced by Microccocin binding to the Deinococcus radiodurans 50S subunit	X-RAY DIFFRACTION	3.3	2686
4	3CF5\|1\|X	Thiopeptide antibiotic Thiostrepton bound to the large ribosomal subunit of Deinococcus radiodurans	X-RAY DIFFRACTION	3.3	2686
5	2ZJR\|1\|X	Refined native structure of the large ribosomal subunit (50S) from Deinococcus radiodurans	X-RAY DIFFRACTION	2.91	2686
6	7A0R\|1\|X	50S Deinococcus radiodurans ribosome bounded with mycinamicin I	X-RAY DIFFRACTION	3.3	2730
7	4IOA\|1\|X	Crystal structure of compound 4e bound to large ribosomal subunit (50S) from Deinococcus radiodurans	X-RAY DIFFRACTION	3.2	2686
8	4IO9\|1\|X	Crystal structure of compound 4d bound to large ribosomal subunit (50S) from Deinococcus radiodurans	X-RAY DIFFRACTION	3.2	2686
9	3PIO\|1\|X	Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunit	X-RAY DIFFRACTION	3.25	2657
10	3PIP\|1\|X	Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunit	X-RAY DIFFRACTION	3.45	2644
11	5DM6\|1\|X	Crystal structure of the 50S ribosomal subunit from Deinococcus radiodurans	X-RAY DIFFRACTION	2.9	2780
12	5DM7\|1\|X	Crystal structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with hygromycin A	X-RAY DIFFRACTION	3	2780
13	7A0S\|1\|X	50S Deinococcus radiodurans ribosome bounded with mycinamicin I	X-RAY DIFFRACTION	3.22	2699
14	5JVG\|1\|X	The large ribosomal subunit from Deinococcus radiodurans in complex with avilamycin	X-RAY DIFFRACTION	3.43	2711
15	2O44\|1\|A	Structure of 23S rRNA of the large ribosomal subunit from Deinococcus radiodurans in complex with the macrolide josamycin	X-RAY DIFFRACTION	3.3	2766
16	2AAR\|1\|0	Structure of trigger factor binding domain in biologically homologous complex with eubacterial ribosome.	X-RAY DIFFRACTION	3.5	2766
17	2OGM\|1\|0	The crystal structure of the large ribosomal subunit from Deinococcus radiodurans complexed with the pleuromutilin derivative SB-571519	X-RAY DIFFRACTION	3.5	2766
18	1P9X\|1\|0	THE CRYSTAL STRUCTURE OF THE 50S LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS COMPLEXED WITH TELITHROMYCIN KETOLIDE ANTIBIOTIC	X-RAY DIFFRACTION	3.4	2738
19	1SM1\|1\|0	COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH QUINUPRISTIN AND DALFOPRISTIN	X-RAY DIFFRACTION	3.42	2766
20	1XBP\|1\|0	Inhibition of peptide bond formation by pleuromutilins: The structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with Tiamulin	X-RAY DIFFRACTION	3.5	2766
21	1OND\|1\|0	THE CRYSTAL STRUCTURE OF THE 50S LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS COMPLEXED WITH TROLEANDOMYCIN MACROLIDE ANTIBIOTIC	X-RAY DIFFRACTION	3.4	2765
22	1NKW\|1\|0	Crystal Structure Of The Large Ribosomal Subunit From Deinococcus Radiodurans	X-RAY DIFFRACTION	3.1	2766
23	1NWX\|1\|0	COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH ABT-773	X-RAY DIFFRACTION	3.5	2766
24	1NWY\|1\|0	COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH AZITHROMYCIN	X-RAY DIFFRACTION	3.3	2766
25	1NJP\|1\|0	The crystal structure of the 50S Large ribosomal subunit from Deinococcus radiodurans complexed with a tRNA acceptor stem mimic (ASM)	X-RAY DIFFRACTION	3.5	2766
26	1J5A\|1\|A	STRUCTURAL BASIS FOR THE INTERACTION OF ANTIBIOTICS WITH THE PEPTIDYL TRANSFERASE CENTER IN EUBACTERIA	X-RAY DIFFRACTION	3.5	2774
27	1JZY\|1\|A	Structural Basis for the Interaction of Antibiotics with the Peptidyl Transferase Center in Eubacteria	X-RAY DIFFRACTION	3.5	2774
28	1JZX\|1\|A	Structural Basis for the Interaction of Antibiotics with the Peptidyl Transferase Center in Eubacteria	X-RAY DIFFRACTION	3.1	2774
29	1K01\|1\|A	Structural Basis for the Interaction of Antibiotics with the Peptidyl Transferase Center in Eubacteria	X-RAY DIFFRACTION	3.5	2774
30	1Y69\|1\|0	RRF domain I in complex with the 50S ribosomal subunit from Deinococcus radiodurans	X-RAY DIFFRACTION	3.33	2766

Equivalence class NR_3.5_88987.8 Obsolete

Release history

Parents

Children