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Equivalence class NR_4.0_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
101X9K|1|D5'-R(*UP*CP*GP*CP*AP*GP*UP*CP*CP*UP*AP*UP*U)-3', 5'-R(*AP*AP*UP*AP*GP*AP*GP*AP*AP*GP*CP*GP*A)-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 diffraction3.172005-11-22
112NPZ|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*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 junctioned hairpin ribozyme incorporating synthetic propyl linkerX-ray diffraction3.352007-08-14
121ZFX|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
131X9C|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
141ZFT|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
152BCY|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
162NPY|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
174G6R|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
181ZFV|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
192P7D|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
202P7E|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
212BCZ|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
222FGP|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
232OUE|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
242P7F|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
252D2L|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

This class Descendant classesRelease idIntersectionOnly in this classAdded to child

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
34G6R|1|DTitle: Minimal Hairpin Ribozyme in the Transition State with G8I VariationX-RAY DIFFRACTION2.8319
43GS1|1|DTitle: An all-RNA Hairpin Ribozyme with mutation A38N1dAX-RAY DIFFRACTION2.8519
51ZFV|1|DTitle: The structure of an all-RNA minimal Hairpin Ribozyme with Mutation G8A at the cleavage siteX-RAY DIFFRACTION2.419
61ZFX|1|DTitle: The Structure of a minimal all-RNA Hairpin Ribozyme with the mutant G8U at the cleavage siteX-RAY DIFFRACTION2.3819
72BCY|1|DTitle: Crystal Structure of a minimal, mutant all-RNA hairpin ribozyme (U39C, G8MTU)X-RAY DIFFRACTION2.719
82BCZ|1|DTitle: Crystal Structure of a minimal, mutant all-RNA hairpin ribozyme (U39C, G8I, 2'deoxy A-1)X-RAY DIFFRACTION2.419
93GS8|1|DTitle: An all-RNA hairpin ribozyme A38N1dA38 variant with a transition-state mimic substrate strandX-RAY DIFFRACTION2.8519
102NPY|1|DTitle: Crystal Structure of a junctioned hairpin ribozyme incorporating 9atom linker and 2'-deoxy 2'-amino U at A-1X-RAY DIFFRACTION2.6519
111ZFT|1|DTitle: The crystal structure of an all-RNA minimal Hairpin Ribozyme with mutant G8I at the cleavage siteX-RAY DIFFRACTION2.3319
122OUE|1|DTitle: Crystal structure of a junctionless all-RNA hairpin ribozyme at 2.05 angstroms resolutionX-RAY DIFFRACTION2.0519
133I2S|1|CTitle: Crystal structure of the hairpin ribozyme with a 2'OMe substrate and N1-deazaadenosine at position A10X-RAY DIFFRACTION2.7519
143I2Q|1|CTitle: Crystal structure of the hairpin ribozyme with 2'OMe substrate strand and N1-deazaadenosine at position A9X-RAY DIFFRACTION2.919
152P7E|1|DTitle: Vanadate at the Active Site of a Small Ribozyme Suggests a Role for Water in Transition-State StabilizationX-RAY DIFFRACTION2.0519
162P7D|1|DTitle: A Minimal, 'Hinged' Hairpin Ribozyme Construct Solved with Mimics of the Product Strands at 2.25 Angstroms ResolutionX-RAY DIFFRACTION2.2519
173I2U|1|CTitle: Crystal structure of the haiprin ribozyme with a 2',5'-linked substrate and N1-deazaadenosine at position A10X-RAY DIFFRACTION2.819
183I2R|1|CTitle: Crystal structure of the hairpin ribozyme with a 2',5'-linked substrate with N1-deazaadenosine at position A9X-RAY DIFFRACTION2.819
192P7F|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
203CQS|1|CTitle: A 3'-OH, 2',5'-phosphodiester substitution in the hairpin ribozyme active site reveals similarities with protein ribonucleasesX-RAY DIFFRACTION2.819
212FGP|1|DTitle: Crystal structure of a minimal, all RNA hairpin ribozyme with modifications (g8dap, u39c) at ph 8.6X-RAY DIFFRACTION2.419
221X9C|1|DTitle: An all-RNA Hairpin Ribozyme with mutation U39CX-RAY DIFFRACTION2.1919
232D2L|1|DTitle: Crystal Structure of a minimal, all-RNA hairpin ribozyme with a propyl linker (C3) at position U39X-RAY DIFFRACTION2.518
241X9K|1|DTitle: An all-RNA Hairpin Ribozyme with mutation U39CX-RAY DIFFRACTION3.1719
252NPZ|1|DTitle: Crystal structure of junctioned hairpin ribozyme incorporating synthetic propyl linkerX-RAY DIFFRACTION3.3519

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