BGSU RNA Site //

Equivalence class NR_all_43554.1 Obsolete

#IFEStandardized nameMoleculeOrganismDomainRfamTitleMethodÅDate
13TD1|1|B+ 3TD1|1|A (rep)RNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*GP*CP*GP*(5BU)P*CP*GP*AP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3')Crystal structure of the bacterial A1408G-mutant and the protozoa cytoplasmic ribosomal decoding site in complex with geneticinX-ray diffraction2.12011-12-07
21YRJ|1|A+ 1YRJ|1|BBacterial 16 S Ribosomal RNA A Site OligonucleotideCrystal Structure of Apramycin bound to a Ribosomal RNA A site oligonucleotideX-ray diffraction2.72005-06-07
32ESI|1|A+ 2ESI|1|B5'-R(*UP*UP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*C)-3'Complex between Kanamycin A and the 16S-Rrna A Site.X-ray diffraction32005-12-20
42F4T|1|B+ 2F4T|1|A5'-R(*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*C)-3', 5'-R(*UP*UP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*C)-3'Asite RNA + designer antibioticX-ray diffraction32006-05-02
52O3V|1|A+ 2O3V|1|BRNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*GP*CP*UP*CP*CP*GP*GP*AP*AP*AP*AP*GP*UP*CP*GP*C)-3')Crystal Structure of the Homo sapiens Cytoplasmic Ribosomal Decoding Site complexed with paromamine derivative NB33X-ray diffraction2.82007-11-06
62O3Y|1|A+ 2O3Y|1|BRNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*GP*CP*UP*CP*CP*GP*GP*AP*AP*AP*AP*GP*UP*CP*GP*C)-3')Crystal Structure of the Homo sapiens Cytoplasmic Ribosomal Decoding Site in Presence of Paromamine Derivative NB30X-ray diffraction2.72007-11-06
72G5K|1|A+ 2G5K|1|B5'-R(*UP*UP*GP*CP*GP*UP*CP*GP*CP*UP*CP*CP*GP*GP*AP*AP*AP*AP*GP*UP*CP*GP*C)-3'Crystal Structure of the Homo sapiens Cytoplasmic Ribosomal Decoding Site complexed with ApramycinX-ray diffraction2.82006-06-20
83BNR|1|A+ 3BNR|1|BA site of human mitochondrial ribosome, chain one, A site of human mitochondrial ribosome, chain twoCrystal Structure of the Homo sapiens Mitochondrial Ribosomal Decoding Site in the presence of nonspecifically bound paromomycin (A1555G mutant, Br-derivative)X-ray diffraction2.12008-06-24
92O3W|1|A+ 2O3W|1|BRNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*GP*CP*UP*CP*CP*GP*GP*AP*AP*AP*AP*GP*UP*CP*GP*C)-3')Crystal Structure of the Homo sapiens Cytoplasmic Ribosomal Decoding Site in presence of paromomycinX-ray diffraction2.82007-11-06
102FQN|1|A+ 2FQN|1|B5'-R(*UP*UP*GP*CP*GP*UP*CP*GP*CP*UP*CP*CP*GP*GP*AP*AP*AP*AP*GP*UP*CP*GP*C)-3'Crystal structure of the Homo sapiens cytoplasmic ribosomal decoding A siteX-ray diffraction2.32006-02-14
113BNQ|1|A+ 3BNQ|1|BA site of human mitochondrial ribosome, A chainCrystal Structure of the Homo sapiens Mitochondrial Ribosomal Decoding Site in the Presence of SrCl2 (A1555G mutant, Br-derivative)X-ray diffraction22008-06-24
124GPY|1|A+ 4GPY|1|BRNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*AP*CP*GP*CP*CP*GP*GP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3')Crystal structure of the bacterial ribosomal decoding site in complex with 6'-hydroxysisomicinX-ray diffraction2.82013-04-03
133BNS|1|A+ 3BNS|1|BA site of human mitochondrial ribosome, chain three, A site of human mitochondrial ribosome, chain twoCrystal Structure of the Homo sapiens Mitochondrial Ribosomal Decoding Site (A1555G mutant, Br-derivative)X-ray diffraction1.92008-06-24
144GPW|1|A+ 4GPW|1|BRNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*GP*CP*GP*CP*CP*GP*GP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3')Crystal structure of the protozoal cytoplasmic ribosomal decoding site in complex with 6'-hydroxysisomicin (P21212 form)X-ray diffraction32013-04-03
154K31|1|B+ 4K31|1|CRNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*GP*UP*UP*CP*CP*GP*GP*AP*AP*AP*AP*GP*UP*CP*GP*C)-3')LeishmaniaEukaryaCrystal structure of apramycin bound to the leishmanial rRNA A-siteX-ray diffraction1.412013-07-31
163TD0|1|B+ 3TD0|1|ARNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*GP*CP*GP*(5BU)P*CP*GP*AP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3')Crystal structure of the bacterial A1408G-mutant and the protozoa cytoplasmic ribosomal decoding siteX-ray diffraction1.62011-12-07
173BNR|1|C+ 3BNR|1|DA site of human mitochondrial ribosome, chain one, A site of human mitochondrial ribosome, chain threeCrystal Structure of the Homo sapiens Mitochondrial Ribosomal Decoding Site in the presence of nonspecifically bound paromomycin (A1555G mutant, Br-derivative)X-ray diffraction2.12008-06-24
183BNS|1|C+ 3BNS|1|DA site of human mitochondrial ribosome, chain threeCrystal Structure of the Homo sapiens Mitochondrial Ribosomal Decoding Site (A1555G mutant, Br-derivative)X-ray diffraction1.92008-06-24
193BNQ|1|C+ 3BNQ|1|DA site of human mitochondrial ribosome, A chain, A site of human mitochondrial ribosome, B chainCrystal Structure of the Homo sapiens Mitochondrial Ribosomal Decoding Site in the Presence of SrCl2 (A1555G mutant, Br-derivative)X-ray diffraction22008-06-24
201LC4|1|A+ 1LC4|1|B5'-R(*UP*UP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*C)-3'Crystal Structure of Tobramycin Bound to the Eubacterial 16S rRNA A SiteX-ray diffraction2.542003-04-08
214P20|1|A+ 4P20|1|B5'-R(*UP*UP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*C)-3'synthetic constructSyntheticCrystal structures of the bacterial ribosomal decoding site complexed with amikacinX-ray diffraction2.72014-05-07
224K32|1|A+ 4K32|1|BRNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*GP*UP*UP*CP*CP*GP*GP*AP*AP*AP*AP*GP*UP*CP*GP*C)-3')LeishmaniaEukaryaCrystal structure of geneticin bound to the leishmanial rRNA A-siteX-ray diffraction2.52013-07-31
232O3X|1|A+ 2O3X|1|BRNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*C)-3')Crystal Structure of the Prokaryotic Ribosomal Decoding Site Complexed with Paromamine Derivative NB30X-ray diffraction2.92007-11-06
243WRU|1|A+ 3WRU|1|BRNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*AP*CP*GP*CP*CP*GP*GP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3')Crystal structure of the bacterial ribosomal decoding site in complex with synthetic aminoglycoside with F-HABA groupX-ray diffraction2.32014-11-05
254GPX|1|A+ 4GPX|1|BRNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*GP*CP*GP*CP*CP*GP*GP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3')Crystal structure of the protozoal cytoplasmic ribosomal decoding site in complex with 6'-hydroxysisomicin (P212121 form)X-ray diffraction2.62013-04-03

Release history

Release2.02.12.22.32.4
Date2014-12-052014-12-122014-12-192014-12-262015-01-02

Parents

This classParent classesRelease idIntersectionAdded to this classOnly in parent

Children

This class Descendant classesRelease idIntersectionOnly in this classAdded to child
NR_all_43554.1NR_1.5_43554.22.5(1) 4K31|1|B+4K31|1|C(24) 1LC4|1|A+1LC4|1|B, 2FQN|1|A+2FQN|1|B, 2O3X|1|A+2O3X|1|B, 3BNR|1|A+3BNR|1|B, 3TD0|1|B+3TD0|1|A, 4GPX|1|A+4GPX|1|B, 2F4T|1|B+2F4T|1|A, 2O3W|1|A+2O3W|1|B, 3BNQ|1|C+3BNQ|1|D, 3BNS|1|C+3BNS|1|D, 4GPW|1|A+4GPW|1|B, 4P20|1|A+4P20|1|B, 2ESI|1|A+2ESI|1|B, 2O3V|1|A+2O3V|1|B, 3BNQ|1|A+3BNQ|1|B, 3BNS|1|A+3BNS|1|B, 3WRU|1|A+3WRU|1|B, 4K32|1|A+4K32|1|B, 1YRJ|1|A+1YRJ|1|B, 2G5K|1|A+2G5K|1|B, 2O3Y|1|A+2O3Y|1|B, 3BNR|1|C+3BNR|1|D, 3TD1|1|B+3TD1|1|A, 4GPY|1|A+4GPY|1|B(0)
NR_all_43554.1NR_2.0_43554.22.5(6) 4K31|1|B+4K31|1|C, 3BNQ|1|C+3BNQ|1|D, 3BNS|1|A+3BNS|1|B, 3BNS|1|C+3BNS|1|D, 3BNQ|1|A+3BNQ|1|B, 3TD0|1|B+3TD0|1|A(19) 4GPW|1|A+4GPW|1|B, 4P20|1|A+4P20|1|B, 2O3Y|1|A+2O3Y|1|B, 4K32|1|A+4K32|1|B, 3WRU|1|A+3WRU|1|B, 2ESI|1|A+2ESI|1|B, 2O3V|1|A+2O3V|1|B, 3BNR|1|A+3BNR|1|B, 2F4T|1|B+2F4T|1|A, 2O3W|1|A+2O3W|1|B, 3BNR|1|C+3BNR|1|D, 1LC4|1|A+1LC4|1|B, 4GPX|1|A+4GPX|1|B, 2FQN|1|A+2FQN|1|B, 2O3X|1|A+2O3X|1|B, 3TD1|1|B+3TD1|1|A, 4GPY|1|A+4GPY|1|B, 1YRJ|1|A+1YRJ|1|B, 2G5K|1|A+2G5K|1|B(0)
NR_all_43554.1NR_2.5_43554.22.5(12) 3WRU|1|A+3WRU|1|B, 3BNR|1|C+3BNR|1|D, 3BNS|1|A+3BNS|1|B, 2FQN|1|A+2FQN|1|B, 3BNS|1|C+3BNS|1|D, 3BNQ|1|A+3BNQ|1|B, 3TD0|1|B+3TD0|1|A, 3BNQ|1|C+3BNQ|1|D, 3TD1|1|B+3TD1|1|A, 3BNR|1|A+3BNR|1|B, 4K31|1|B+4K31|1|C, 4K32|1|A+4K32|1|B(13) 4GPX|1|A+4GPX|1|B, 2O3X|1|A+2O3X|1|B, 4GPY|1|A+4GPY|1|B, 2ESI|1|A+2ESI|1|B, 2O3W|1|A+2O3W|1|B, 2F4T|1|B+2F4T|1|A, 1YRJ|1|A+1YRJ|1|B, 2O3V|1|A+2O3V|1|B, 4GPW|1|A+4GPW|1|B, 1LC4|1|A+1LC4|1|B, 2G5K|1|A+2G5K|1|B, 2O3Y|1|A+2O3Y|1|B, 4P20|1|A+4P20|1|B(0)
NR_all_43554.1NR_20.0_43554.22.5(25) 2F4T|1|B+2F4T|1|A, 2O3W|1|A+2O3W|1|B, 3BNQ|1|C+3BNQ|1|D, 3BNS|1|C+3BNS|1|D, 4GPW|1|A+4GPW|1|B, 4K32|1|A+4K32|1|B, 2ESI|1|A+2ESI|1|B, 2O3V|1|A+2O3V|1|B, 3BNQ|1|A+3BNQ|1|B, 3BNS|1|A+3BNS|1|B, 3WRU|1|A+3WRU|1|B, 4K31|1|B+4K31|1|C, 1YRJ|1|A+1YRJ|1|B, 2G5K|1|A+2G5K|1|B, 2O3Y|1|A+2O3Y|1|B, 3BNR|1|C+3BNR|1|D, 3TD1|1|B+3TD1|1|A, 4GPY|1|A+4GPY|1|B, 1LC4|1|A+1LC4|1|B, 2FQN|1|A+2FQN|1|B, 2O3X|1|A+2O3X|1|B, 3BNR|1|A+3BNR|1|B, 3TD0|1|B+3TD0|1|A, 4GPX|1|A+4GPX|1|B, 4P20|1|A+4P20|1|B(0) (1) 4PDQ|1|A+4PDQ|1|B
NR_all_43554.1NR_3.0_43554.22.5(25) 3BNS|1|A+3BNS|1|B, 3WRU|1|A+3WRU|1|B, 4K31|1|B+4K31|1|C, 2ESI|1|A+2ESI|1|B, 2O3V|1|A+2O3V|1|B, 3BNQ|1|A+3BNQ|1|B, 3BNR|1|C+3BNR|1|D, 3TD1|1|B+3TD1|1|A, 4GPY|1|A+4GPY|1|B, 1YRJ|1|A+1YRJ|1|B, 2G5K|1|A+2G5K|1|B, 2O3Y|1|A+2O3Y|1|B, 3TD0|1|B+3TD0|1|A, 4GPX|1|A+4GPX|1|B, 4P20|1|A+4P20|1|B, 1LC4|1|A+1LC4|1|B, 2FQN|1|A+2FQN|1|B, 2O3X|1|A+2O3X|1|B, 3BNR|1|A+3BNR|1|B, 3BNS|1|C+3BNS|1|D, 4GPW|1|A+4GPW|1|B, 4K32|1|A+4K32|1|B, 2F4T|1|B+2F4T|1|A, 2O3W|1|A+2O3W|1|B, 3BNQ|1|C+3BNQ|1|D(0) (1) 4PDQ|1|A+4PDQ|1|B
NR_all_43554.1NR_3.5_43554.22.5(25) 1YRJ|1|A+1YRJ|1|B, 2G5K|1|A+2G5K|1|B, 2O3Y|1|A+2O3Y|1|B, 3BNR|1|C+3BNR|1|D, 3TD1|1|B+3TD1|1|A, 4GPY|1|A+4GPY|1|B, 1LC4|1|A+1LC4|1|B, 2FQN|1|A+2FQN|1|B, 2O3X|1|A+2O3X|1|B, 3BNR|1|A+3BNR|1|B, 3TD0|1|B+3TD0|1|A, 4GPX|1|A+4GPX|1|B, 4P20|1|A+4P20|1|B, 2F4T|1|B+2F4T|1|A, 2O3W|1|A+2O3W|1|B, 3BNQ|1|C+3BNQ|1|D, 3BNS|1|C+3BNS|1|D, 4GPW|1|A+4GPW|1|B, 4K32|1|A+4K32|1|B, 2ESI|1|A+2ESI|1|B, 2O3V|1|A+2O3V|1|B, 3BNQ|1|A+3BNQ|1|B, 3BNS|1|A+3BNS|1|B, 3WRU|1|A+3WRU|1|B, 4K31|1|B+4K31|1|C(0) (1) 4PDQ|1|A+4PDQ|1|B
NR_all_43554.1NR_4.0_43554.22.5(25) 1LC4|1|A+1LC4|1|B, 2FQN|1|A+2FQN|1|B, 2O3X|1|A+2O3X|1|B, 3BNR|1|A+3BNR|1|B, 3TD0|1|B+3TD0|1|A, 4GPX|1|A+4GPX|1|B, 4P20|1|A+4P20|1|B, 2F4T|1|B+2F4T|1|A, 2O3W|1|A+2O3W|1|B, 3BNQ|1|C+3BNQ|1|D, 3BNS|1|C+3BNS|1|D, 4GPW|1|A+4GPW|1|B, 4K32|1|A+4K32|1|B, 2ESI|1|A+2ESI|1|B, 2O3V|1|A+2O3V|1|B, 3BNQ|1|A+3BNQ|1|B, 3BNS|1|A+3BNS|1|B, 3WRU|1|A+3WRU|1|B, 4K31|1|B+4K31|1|C, 1YRJ|1|A+1YRJ|1|B, 2G5K|1|A+2G5K|1|B, 2O3Y|1|A+2O3Y|1|B, 3BNR|1|C+3BNR|1|D, 3TD1|1|B+3TD1|1|A, 4GPY|1|A+4GPY|1|B(0) (1) 4PDQ|1|A+4PDQ|1|B
NR_all_43554.1NR_all_43554.22.5(25) 2F4T|1|B+2F4T|1|A, 2O3W|1|A+2O3W|1|B, 3BNQ|1|C+3BNQ|1|D, 3BNS|1|C+3BNS|1|D, 4GPW|1|A+4GPW|1|B, 4K32|1|A+4K32|1|B, 2ESI|1|A+2ESI|1|B, 2O3V|1|A+2O3V|1|B, 3BNQ|1|A+3BNQ|1|B, 3BNS|1|A+3BNS|1|B, 3WRU|1|A+3WRU|1|B, 4K31|1|B+4K31|1|C, 1YRJ|1|A+1YRJ|1|B, 2G5K|1|A+2G5K|1|B, 2O3Y|1|A+2O3Y|1|B, 3BNR|1|C+3BNR|1|D, 3TD1|1|B+3TD1|1|A, 4GPY|1|A+4GPY|1|B, 1LC4|1|A+1LC4|1|B, 2FQN|1|A+2FQN|1|B, 2O3X|1|A+2O3X|1|B, 3BNR|1|A+3BNR|1|B, 3TD0|1|B+3TD0|1|A, 4GPX|1|A+4GPX|1|B, 4P20|1|A+4P20|1|B(0) (1) 4PDQ|1|A+4PDQ|1|B

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).
#SPDBTitleMethodResolutionLength
12O3V|1|A+2O3V|1|BCrystal Structure of the Homo sapiens Cytoplasmic Ribosomal Decoding Site complexed with paromamine derivative NB33X-RAY DIFFRACTION2.822
22O3Y|1|A+2O3Y|1|BCrystal Structure of the Homo sapiens Cytoplasmic Ribosomal Decoding Site in Presence of Paromamine Derivative NB30X-RAY DIFFRACTION2.722
32FQN|1|A+2FQN|1|BCrystal structure of the Homo sapiens cytoplasmic ribosomal decoding A siteX-RAY DIFFRACTION2.322
42O3W|1|A+2O3W|1|BCrystal Structure of the Homo sapiens Cytoplasmic Ribosomal Decoding Site in presence of paromomycinX-RAY DIFFRACTION2.822
52G5K|1|A+2G5K|1|BCrystal Structure of the Homo sapiens Cytoplasmic Ribosomal Decoding Site complexed with ApramycinX-RAY DIFFRACTION2.822
64K31|1|B+4K31|1|CCrystal structure of apramycin bound to the leishmanial rRNA A-siteX-RAY DIFFRACTION1.4122
74K32|1|A+4K32|1|BCrystal structure of geneticin bound to the leishmanial rRNA A-siteX-RAY DIFFRACTION2.521
84GPW|1|A+4GPW|1|BCrystal structure of the protozoal cytoplasmic ribosomal decoding site in complex with 6'-hydroxysisomicin (P21212 form)X-RAY DIFFRACTION322
94GPX|1|A+4GPX|1|BCrystal structure of the protozoal cytoplasmic ribosomal decoding site in complex with 6'-hydroxysisomicin (P212121 form)X-RAY DIFFRACTION2.621
102O3X|1|A+2O3X|1|BCrystal Structure of the Prokaryotic Ribosomal Decoding Site Complexed with Paromamine Derivative NB30X-RAY DIFFRACTION2.921
111YRJ|1|A+1YRJ|1|BCrystal Structure of Apramycin bound to a Ribosomal RNA A site oligonucleotideX-RAY DIFFRACTION2.723
122F4T|1|B+2F4T|1|AAsite RNA + designer antibioticX-RAY DIFFRACTION323
134GPY|1|A+4GPY|1|BCrystal structure of the bacterial ribosomal decoding site in complex with 6'-hydroxysisomicinX-RAY DIFFRACTION2.822
144P20|1|A+4P20|1|BCrystal structures of the bacterial ribosomal decoding site complexed with amikacinX-RAY DIFFRACTION2.721
151LC4|1|A+1LC4|1|BCrystal Structure of Tobramycin Bound to the Eubacterial 16S rRNA A SiteX-RAY DIFFRACTION2.5421
162ESI|1|A+2ESI|1|BComplex between Kanamycin A and the 16S-Rrna A Site.X-RAY DIFFRACTION323
173WRU|1|A+3WRU|1|BCrystal structure of the bacterial ribosomal decoding site in complex with synthetic aminoglycoside with F-HABA groupX-RAY DIFFRACTION2.321
183TD1|1|B+3TD1|1|ACrystal structure of the bacterial A1408G-mutant and the protozoa cytoplasmic ribosomal decoding site in complex with geneticinX-RAY DIFFRACTION2.122
193TD0|1|B+3TD0|1|ACrystal structure of the bacterial A1408G-mutant and the protozoa cytoplasmic ribosomal decoding siteX-RAY DIFFRACTION1.622
203BNQ|1|A+3BNQ|1|BCrystal Structure of the Homo sapiens Mitochondrial Ribosomal Decoding Site in the Presence of SrCl2 (A1555G mutant, Br-derivative)X-RAY DIFFRACTION222
213BNR|1|A+3BNR|1|BCrystal Structure of the Homo sapiens Mitochondrial Ribosomal Decoding Site in the presence of nonspecifically bound paromomycin (A1555G mutant, Br-derivative)X-RAY DIFFRACTION2.122
223BNS|1|A+3BNS|1|BCrystal Structure of the Homo sapiens Mitochondrial Ribosomal Decoding Site (A1555G mutant, Br-derivative)X-RAY DIFFRACTION1.922
233BNS|1|C+3BNS|1|DCrystal Structure of the Homo sapiens Mitochondrial Ribosomal Decoding Site (A1555G mutant, Br-derivative)X-RAY DIFFRACTION1.922
243BNR|1|C+3BNR|1|DCrystal Structure of the Homo sapiens Mitochondrial Ribosomal Decoding Site in the presence of nonspecifically bound paromomycin (A1555G mutant, Br-derivative)X-RAY DIFFRACTION2.122
253BNQ|1|C+3BNQ|1|DCrystal Structure of the Homo sapiens Mitochondrial Ribosomal Decoding Site in the Presence of SrCl2 (A1555G mutant, Br-derivative)X-RAY DIFFRACTION222