RNA 3D Hub //

Equivalence class NR_4.0_25764.1 Current

#IFEStandardized nameMoleculeOrganismSourceRfamTitleMethodRes. Å#NTsDate
12P7E|1|D+ 2P7E|1|C (rep)Ribozyme strand II, Ribozyme strand IIIVanadate at the Active Site of a Small Ribozyme Suggests a Role for Water in Transition-State StabilizationX-ray diffraction2.05362007-05-22
22NPY|1|D+ 2NPY|1|C5'-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 diffraction2.65362007-08-14
31ZFT|1|D+ 1ZFT|1|C5'-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 diffraction2.33362006-02-14
42P7F|1|D+ 2P7F|1|CLoop 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 diffraction2.35362007-05-22
51ZFV|1|D+ 1ZFV|1|C5'-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 diffraction2.4362006-02-14
62OUE|1|D+ 2OUE|1|CLoop B ribozyme strand, Loop B S-turn strandCrystal structure of a junctionless all-RNA hairpin ribozyme at 2.05 angstroms resolutionX-ray diffraction2.05362007-03-06
72D2L|1|D+ 2D2L|1|C5'-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 diffraction2.5362005-11-01
82P7D|1|D+ 2P7D|1|CRibozyme strand II, Ribozyme strand IIIA Minimal, 'Hinged' Hairpin Ribozyme Construct Solved with Mimics of the Product Strands at 2.25 Angstroms ResolutionX-ray diffraction2.25362007-05-22
92FGP|1|D+ 2FGP|1|C5'-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 diffraction2.4362006-02-14
101X9C|1|D+ 1X9C|1|C5'-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 diffraction2.19362005-11-22
111ZFX|1|D+ 1ZFX|1|C5'-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 diffraction2.38362006-02-14
122BCZ|1|D+ 2BCZ|1|C5'-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 diffraction2.4362006-02-14
132D2K|1|D+ 2D2K|1|C5'-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 diffraction2.65362005-11-01
142BCY|1|D+ 2BCY|1|C5'-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 diffraction2.7362006-02-14
151X9K|1|D+ 1X9K|1|C5'-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 diffraction3.17362005-11-22
162NPZ|1|D+ 2NPZ|1|C5'-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 diffraction3.35362007-08-14
174G6R|1|D+ 4G6R|1|CLoop B Ribozyme Strand, Loop B S-turn strandMinimal Hairpin Ribozyme in the Transition State with G8I VariationX-ray diffraction2.83362012-08-15
183GS8|1|D+ 3GS8|1|CRNA (5'-R(*UP*CP*GP*UP*GP*GP*UP*AP*CP*AP*UP*UP*AP*CP*CP*UP*GP*CP*C)-3'), RNA (5'-R(P*GP*GP*CP*AP*GP*AP*GP*AP*AP*AP*CP*AP*CP*AP*CP*GP*A)-3')An all-RNA hairpin ribozyme A38N1dA38 variant with a transition-state mimic substrate strandX-ray diffraction2.85362009-04-21
193GS1|1|D+ 3GS1|1|CRNA (5'-R(*UP*CP*GP*UP*GP*GP*UP*AP*CP*AP*UP*UP*AP*CP*CP*UP*GP*CP*C)-3'), RNA (5'-R(P*GP*GP*CP*AP*GP*AP*GP*AP*AP*AP*CP*AP*CP*AP*CP*GP*A)-3')An all-RNA Hairpin Ribozyme with mutation A38N1dAX-ray diffraction2.85362009-05-12

Release history

Release3.3783.3793.3803.3813.3823.3833.3843.3853.3863.3873.3883.3893.3903.391
Date2025-03-132025-03-192025-03-262025-04-022025-04-092025-04-162025-04-232025-04-302025-05-072025-05-142025-05-212025-05-282025-06-042025-06-11

Parents

This classParent classesRelease idIntersectionAdded to this classOnly in parent

Children

This class Descendant classesRelease idIntersectionOnly in this classAdded to child

Instances are ordered to put similar structures near each other. Select one instance to see its 3D structure. Selecting two or more instances will show their superposition, but only chains with identical numbers of observed nucleotides will superpose well. Large structures are slow to display; this tool is not designed for that.

#SViewPDBTitleMethodResolution#NTs
11X9K|1|D+ 1X9K|1|CAn all-RNA Hairpin Ribozyme with mutation U39CX-RAY DIFFRACTION3.1736
22D2L|1|D+ 2D2L|1|CCrystal Structure of a minimal, all-RNA hairpin ribozyme with a propyl linker (C3) at position U39X-RAY DIFFRACTION2.536
31ZFV|1|D+ 1ZFV|1|CThe structure of an all-RNA minimal Hairpin Ribozyme with Mutation G8A at the cleavage siteX-RAY DIFFRACTION2.436
41ZFX|1|D+ 1ZFX|1|CThe Structure of a minimal all-RNA Hairpin Ribozyme with the mutant G8U at the cleavage siteX-RAY DIFFRACTION2.3836
52FGP|1|D+ 2FGP|1|CCrystal structure of a minimal, all RNA hairpin ribozyme with modifications (g8dap, u39c) at ph 8.6X-RAY DIFFRACTION2.436
62BCY|1|D+ 2BCY|1|CCrystal Structure of a minimal, mutant all-RNA hairpin ribozyme (U39C, G8MTU)X-RAY DIFFRACTION2.736
72D2K|1|D+ 2D2K|1|CCrystal Structure of a minimal, native (U39) all-RNA hairpin ribozymeX-RAY DIFFRACTION2.6536
84G6R|1|D+ 4G6R|1|CMinimal Hairpin Ribozyme in the Transition State with G8I VariationX-RAY DIFFRACTION2.8336
91X9C|1|D+ 1X9C|1|CAn all-RNA Hairpin Ribozyme with mutation U39CX-RAY DIFFRACTION2.1936
101ZFT|1|D+ 1ZFT|1|CThe crystal structure of an all-RNA minimal Hairpin Ribozyme with mutant G8I at the cleavage siteX-RAY DIFFRACTION2.3336
112OUE|1|D+ 2OUE|1|CCrystal structure of a junctionless all-RNA hairpin ribozyme at 2.05 angstroms resolutionX-RAY DIFFRACTION2.0536
122BCZ|1|D+ 2BCZ|1|CCrystal Structure of a minimal, mutant all-RNA hairpin ribozyme (U39C, G8I, 2'deoxy A-1)X-RAY DIFFRACTION2.436
133GS1|1|D+ 3GS1|1|CAn all-RNA Hairpin Ribozyme with mutation A38N1dAX-RAY DIFFRACTION2.8536
143GS8|1|D+ 3GS8|1|CAn all-RNA hairpin ribozyme A38N1dA38 variant with a transition-state mimic substrate strandX-RAY DIFFRACTION2.8536
152NPY|1|D+ 2NPY|1|CCrystal Structure of a junctioned hairpin ribozyme incorporating 9atom linker and 2'-deoxy 2'-amino U at A-1X-RAY DIFFRACTION2.6536
162P7D|1|D+ 2P7D|1|CA Minimal, 'Hinged' Hairpin Ribozyme Construct Solved with Mimics of the Product Strands at 2.25 Angstroms ResolutionX-RAY DIFFRACTION2.2536
172P7E|1|D+ 2P7E|1|CVanadate at the Active Site of a Small Ribozyme Suggests a Role for Water in Transition-State StabilizationX-RAY DIFFRACTION2.0536
182P7F|1|D+ 2P7F|1|CThe Novel Use of a 2',5'-Phosphodiester Linkage as a Reaction Intermediate at the Active Site of a Small RibozymeX-RAY DIFFRACTION2.3536
192NPZ|1|D+ 2NPZ|1|CCrystal structure of junctioned hairpin ribozyme incorporating synthetic propyl linkerX-RAY DIFFRACTION3.3536

Heat map of mutual geometric discrepancy, in Angstroms per nucleotide. The ordering in the heat map is the same as in the table. The colorbar ranges from 0 to the maximum observed discrepancy. Click above the diagonal to select a range of structures, below the diagonal to select two structures.


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