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Equivalence class NR_3.0_92072.1 Obsolete

#IFEStandardized nameMoleculeOrganismSourceRfamTitleMethodRes. ÅDate
12D2K|1|D (rep)5'-R(*UP*CP*CP*CP*(A2M)P*GP*UP*CP*CP*AP*CP*CP*G)-3', 5'-R(*CP*GP*GP*UP*GP*AP*GP*AP*AP*GP*GP*G)-3', 5'-R(*GP*GP*CP*AP*GP*AP*GP*AP*AP*AP*CP*AP*CP*AP*CP*GP*A)-3', 5'-R(*UP*CP*GP*UP*GP*GP*UP*AP*UP*AP*UP*UP*AP*CP*CP*UP*GP*CP*C)-3'Crystal Structure of a minimal, native (U39) all-RNA hairpin ribozymeX-ray diffraction2.652005-11-01
23I2R|1|C5'-R(*UP*CP*GP*UP*GP*GP*UP*AP*CP*AP*UP*UP*AP*CP*CP*UP*GP*CP*C)-3'Crystal structure of the hairpin ribozyme with a 2',5'-linked substrate with N1-deazaadenosine at position A9X-ray diffraction2.82009-11-03
33I2U|1|C5'-R(*UP*CP*GP*UP*GP*GP*UP*AP*CP*AP*UP*UP*AP*CP*CP*UP*GP*CP*C)-3'Crystal structure of the haiprin ribozyme with a 2',5'-linked substrate and N1-deazaadenosine at position A10X-ray diffraction2.82009-11-03
43I2Q|1|C5'-R(*UP*CP*GP*UP*GP*GP*UP*AP*CP*AP*UP*UP*AP*CP*CP*UP*GP*CP*C)-3'Crystal structure of the hairpin ribozyme with 2'OMe substrate strand and N1-deazaadenosine at position A9X-ray diffraction2.92009-11-03
53CQS|1|C19-mer ribozyme strandA 3'-OH, 2',5'-phosphodiester substitution in the hairpin ribozyme active site reveals similarities with protein ribonucleasesX-ray diffraction2.82008-05-20
63CR1|1|CRNA (5'-R(*UP*CP*GP*UP*GP*GP*UP*CP*CP*AP*UP*UP*AP*CP*CP*UP*GP*CP*C)-3')crystal structure of a minimal, mutant, all-RNA hairpin ribozyme (A38C, A-1OMA) grown from MgCl2X-ray diffraction2.252008-08-26
73I2S|1|C5'-R(*UP*CP*GP*UP*GP*GP*UP*AP*CP*AP*UP*UP*AP*CP*CP*UP*GP*CP*C)-3'Crystal structure of the hairpin ribozyme with a 2'OMe substrate and N1-deazaadenosine at position A10X-ray diffraction2.752009-11-03
83GS1|1|DRNA (5'-R(*UP*CP*CP*CP*AP*GP*UP*CP*CP*AP*CP*CP*GP*U)-3'), RNA (5'-R(*CP*GP*GP*UP*GP*AP*GP*AP*AP*GP*GP*G)-3'), RNA (5'-R(P*GP*GP*CP*AP*GP*AP*GP*AP*AP*AP*CP*AP*CP*AP*CP*GP*A)-3'), RNA (5'-R(*UP*CP*GP*UP*GP*GP*UP*AP*CP*AP*UP*UP*AP*CP*CP*UP*GP*CP*C)-3')An all-RNA Hairpin Ribozyme with mutation A38N1dAX-ray diffraction2.852009-05-12
93GS8|1|DRNA (5'-R(*UP*CP*CP*CP*AP*GP*UP*CP*CP*AP*CP*CP*GP*U)-3'), RNA (5'-R(*CP*GP*GP*UP*GP*AP*GP*AP*AP*GP*GP*G)-3'), RNA (5'-R(P*GP*GP*CP*AP*GP*AP*GP*AP*AP*AP*CP*AP*CP*AP*CP*GP*A)-3'), RNA (5'-R(*UP*CP*GP*UP*GP*GP*UP*AP*CP*AP*UP*UP*AP*CP*CP*UP*GP*CP*C)-3')An all-RNA hairpin ribozyme A38N1dA38 variant with a transition-state mimic substrate strandX-ray diffraction2.852009-04-21
101ZFX|1|D5'-R(*UP*CP*CP*CP*AP*GP*UP*CP*CP*AP*CP*CP*G)-3', 5'-R(*CP*GP*GP*UP*GP*AP*UP*AP*AP*GP*GP*G)-3', 5'-R(*GP*GP*CP*AP*GP*AP*GP*AP*AP*AP*CP*AP*CP*AP*CP*GP*A)-3', 5'-R(*UP*CP*GP*UP*GP*GP*UP*AP*CP*AP*UP*UP*AP*CP*CP*UP*GP*CP*C)-3'The Structure of a minimal all-RNA Hairpin Ribozyme with the mutant G8U at the cleavage siteX-ray diffraction2.382006-02-14
111X9C|1|D5'-R(*UP*CP*CP*CP*(A2M)P*GP*UP*CP*CP*AP*CP*CP*G)-3', 5'-R(*CP*GP*GP*UP*GP*AP*GP*AP*AP*GP*GP*G)-3', 5'-R(*GP*GP*CP*AP*GP*AP*GP*AP*AP*AP*CP*AP*CP*AP*CP*GP*A)-3', 5'-R(*UP*CP*GP*UP*GP*GP*UP*AP*CP*AP*UP*UP*AP*CP*CP*UP*GP*CP*C)-3'An all-RNA Hairpin Ribozyme with mutation U39CX-ray diffraction2.192005-11-22
121ZFT|1|D5'-R(*UP*CP*CP*CP*(A2M)P*GP*UP*CP*CP*AP*CP*CP*G)-3', 5'-R(*CP*GP*GP*UP*GP*AP*IP*AP*AP*GP*GP*G)-3', 5'-R(*GP*GP*CP*AP*GP*AP*GP*AP*AP*AP*CP*AP*CP*AP*CP*GP*A)-3', 5'-R(*UP*CP*GP*UP*GP*GP*UP*AP*CP*AP*UP*UP*AP*CP*CP*UP*GP*CP*C)-3'The crystal structure of an all-RNA minimal Hairpin Ribozyme with mutant G8I at the cleavage siteX-ray diffraction2.332006-02-14
132BCY|1|D5'-R(*UP*CP*CP*CP*AP*GP*UP*CP*CP*AP*CP*CP*G)-3', 5'-R(*CP*GP*GP*UP*GP*AP*(MTU)P*AP*AP*GP*GP*G)-3', 5'-R(*GP*GP*CP*AP*GP*AP*GP*AP*AP*AP*CP*AP*CP*AP*CP*GP*A)-3', 5'-R(*UP*CP*GP*UP*GP*GP*UP*AP*CP*AP*UP*UP*AP*CP*CP*UP*GP*CP*C)-3'Crystal Structure of a minimal, mutant all-RNA hairpin ribozyme (U39C, G8MTU)X-ray diffraction2.72006-02-14
142NPY|1|D5'-R(*UP*CP*CP*CP*(U2N)P*GP*UP*CP*CP*AP*CP*CP*G)-3', 5'-R(*CP*GP*GP*UP*GP*AP*GP*AP*AP*GP*GP*G)-3', 5'-R(*GP*GP*CP*AP*GP*AP*GP*AP*AP*AP*CP*AP*CP*AP*CP*GP*A)-3', 5'-R(*UP*CP*GP*UP*GP*GP*UP*AP*CP*AP*UP*UP*AP*CP*CP*UP*GP*CP*C)-3'Crystal Structure of a junctioned hairpin ribozyme incorporating 9atom linker and 2'-deoxy 2'-amino U at A-1X-ray diffraction2.652007-08-14
154G6R|1|DLoop A Substrate strand, Loop A Ribozyme strand, Loop B Ribozyme Strand, Loop B S-turn strandMinimal Hairpin Ribozyme in the Transition State with G8I VariationX-ray diffraction2.832012-08-15
161ZFV|1|D5'-R(*UP*CP*CP*CP*AP*GP*UP*CP*CP*AP*CP*CP*G)-3', 5'-R(*CP*GP*GP*UP*GP*AP*AP*AP*AP*GP*GP*G)-3', 5'-R(*GP*GP*CP*AP*GP*AP*GP*AP*AP*AP*CP*AP*CP*AP*CP*GP*A)-3', 5'-R(*UP*CP*GP*UP*GP*GP*UP*AP*CP*AP*UP*UP*AP*CP*CP*UP*GP*CP*C)-3'The structure of an all-RNA minimal Hairpin Ribozyme with Mutation G8A at the cleavage siteX-ray diffraction2.42006-02-14
172P7D|1|DRibozyme strand II, Ribozyme strand III, 3' substrate strand, octameric fragmentA Minimal, 'Hinged' Hairpin Ribozyme Construct Solved with Mimics of the Product Strands at 2.25 Angstroms ResolutionX-ray diffraction2.252007-05-22
182P7E|1|DRibozyme strand III, Ribozyme strand II, 3' substrate strand, octameric fragmentVanadate at the Active Site of a Small Ribozyme Suggests a Role for Water in Transition-State StabilizationX-ray diffraction2.052007-05-22
192BCZ|1|D5'-R(*UP*CP*CP*CP*(DA)P*GP*UP*CP*CP*AP*CP*CP*G)-3'), 5'-R(*CP*GP*GP*UP*GP*AP*IP*AP*AP*GP*GP*G)-3', 5'-R(*GP*GP*CP*AP*GP*AP*GP*AP*AP*AP*CP*AP*CP*AP*CP*GP*A)-3', 5'-R(*UP*CP*GP*UP*GP*GP*UP*AP*CP*AP*UP*UP*AP*CP*CP*UP*GP*CP*C)-3'Crystal Structure of a minimal, mutant all-RNA hairpin ribozyme (U39C, G8I, 2'deoxy A-1)X-ray diffraction2.42006-02-14
202FGP|1|D5'-R(*UP*CP*CP*CP*AP*GP*UP*CP*CP*AP*CP*CP*G)-3', 5'-R(*CP*GP*GP*UP*GP*AP*(N6G)P*AP*AP*GP*GP*G)-3', 5'-R(*GP*GP*CP*AP*GP*AP*GP*AP*AP*AP*CP*AP*CP*AP*CP*GP*A)-3', 5'-R(*UP*CP*GP*UP*GP*GP*UP*AP*CP*AP*UP*UP*AP*CP*CP*UP*GP*CP*C) -3'Crystal structure of a minimal, all RNA hairpin ribozyme with modifications (g8dap, u39c) at ph 8.6X-ray diffraction2.42006-02-14
212OUE|1|DSubstrate strand - Minimal Junctionless Hairpin Ribozyme, Loop A ribozyme strand, Loop B ribozyme strand, Loop B S-turn strandCrystal structure of a junctionless all-RNA hairpin ribozyme at 2.05 angstroms resolutionX-ray diffraction2.052007-03-06
222P7F|1|Dsubstrate strand, Loop A ribozyme strand, Loop B ribozyme strand, Loop B S-turn strandThe Novel Use of a 2',5'-Phosphodiester Linkage as a Reaction Intermediate at the Active Site of a Small RibozymeX-ray diffraction2.352007-05-22
232D2L|1|D5'-R(*UP*CP*CP*CP*(A2M)P*GP*UP*CP*CP*AP*CP*CP*G)-3', 5'-R(*CP*GP*GP*UP*GP*AP*GP*AP*AP*GP*GP*G)-3', 5'-R(*GP*GP*CP*AP*GP*AP*GP*AP*AP*AP*CP*AP*CP*AP*CP*GP*A)-3', 5'-R(*UP*CP*GP*UP*GP*GP*UP*AP*(P1P)P*AP*UP*UP*AP*CP*CP*UP*GP*CP*C)-3'Crystal Structure of a minimal, all-RNA hairpin ribozyme with a propyl linker (C3) at position U39X-ray diffraction2.52005-11-01

Release history

Release2.0
Date2014-12-05

Parents

This classParent classesRelease idIntersectionAdded to this classOnly in parent

Children

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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
13CR1|1|CTitle: crystal structure of a minimal, mutant, all-RNA hairpin ribozyme (A38C, A-1OMA) grown from MgCl2X-RAY DIFFRACTION2.2519
22D2K|1|DTitle: Crystal Structure of a minimal, native (U39) all-RNA hairpin ribozymeX-RAY DIFFRACTION2.6522
32FGP|1|DTitle: Crystal structure of a minimal, all RNA hairpin ribozyme with modifications (g8dap, u39c) at ph 8.6X-RAY DIFFRACTION2.419
41X9C|1|DTitle: An all-RNA Hairpin Ribozyme with mutation U39CX-RAY DIFFRACTION2.1919
52OUE|1|DTitle: Crystal structure of a junctionless all-RNA hairpin ribozyme at 2.05 angstroms resolutionX-RAY DIFFRACTION2.0519
61ZFT|1|DTitle: The crystal structure of an all-RNA minimal Hairpin Ribozyme with mutant G8I at the cleavage siteX-RAY DIFFRACTION2.3319
72BCZ|1|DTitle: Crystal Structure of a minimal, mutant all-RNA hairpin ribozyme (U39C, G8I, 2'deoxy A-1)X-RAY DIFFRACTION2.419
81ZFX|1|DTitle: The Structure of a minimal all-RNA Hairpin Ribozyme with the mutant G8U at the cleavage siteX-RAY DIFFRACTION2.3819
91ZFV|1|DTitle: The structure of an all-RNA minimal Hairpin Ribozyme with Mutation G8A at the cleavage siteX-RAY DIFFRACTION2.419
103GS1|1|DTitle: An all-RNA Hairpin Ribozyme with mutation A38N1dAX-RAY DIFFRACTION2.8519
112BCY|1|DTitle: Crystal Structure of a minimal, mutant all-RNA hairpin ribozyme (U39C, G8MTU)X-RAY DIFFRACTION2.719
123I2S|1|CTitle: Crystal structure of the hairpin ribozyme with a 2'OMe substrate and N1-deazaadenosine at position A10X-RAY DIFFRACTION2.7519
133I2Q|1|CTitle: Crystal structure of the hairpin ribozyme with 2'OMe substrate strand and N1-deazaadenosine at position A9X-RAY DIFFRACTION2.919
143CQS|1|CTitle: A 3'-OH, 2',5'-phosphodiester substitution in the hairpin ribozyme active site reveals similarities with protein ribonucleasesX-RAY DIFFRACTION2.819
153I2R|1|CTitle: Crystal structure of the hairpin ribozyme with a 2',5'-linked substrate with N1-deazaadenosine at position A9X-RAY DIFFRACTION2.819
163I2U|1|CTitle: Crystal structure of the haiprin ribozyme with a 2',5'-linked substrate and N1-deazaadenosine at position A10X-RAY DIFFRACTION2.819
172P7D|1|DTitle: A Minimal, 'Hinged' Hairpin Ribozyme Construct Solved with Mimics of the Product Strands at 2.25 Angstroms ResolutionX-RAY DIFFRACTION2.2519
182P7F|1|DTitle: The Novel Use of a 2',5'-Phosphodiester Linkage as a Reaction Intermediate at the Active Site of a Small RibozymeX-RAY DIFFRACTION2.3519
192P7E|1|DTitle: Vanadate at the Active Site of a Small Ribozyme Suggests a Role for Water in Transition-State StabilizationX-RAY DIFFRACTION2.0519
202NPY|1|DTitle: Crystal Structure of a junctioned hairpin ribozyme incorporating 9atom linker and 2'-deoxy 2'-amino U at A-1X-RAY DIFFRACTION2.6519
213GS8|1|DTitle: An all-RNA hairpin ribozyme A38N1dA38 variant with a transition-state mimic substrate strandX-RAY DIFFRACTION2.8519
224G6R|1|DTitle: Minimal Hairpin Ribozyme in the Transition State with G8I VariationX-RAY DIFFRACTION2.8319
232D2L|1|DTitle: Crystal Structure of a minimal, all-RNA hairpin ribozyme with a propyl linker (C3) at position U39X-RAY DIFFRACTION2.518

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