Equivalence class NR_3.0_98705.3 Obsolete
| # | IFE | Standardized name | Molecule | Organism | Source | Rfam | Title | Method | Res. Å | Date |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 2P7E|1|D+ 2P7E|1|C+ 2P7E|1|P (rep) | 3' substrate strand, octameric fragment, Ribozyme strand II, Ribozyme strand III | Vanadate at the Active Site of a Small Ribozyme Suggests a Role for Water in Transition-State Stabilization | X-ray diffraction | 2.05 | 2007-05-22 | ||||
| 2 | 2NPY|1|D+ 2NPY|1|C+ 2NPY|1|A+ 2NPY|1|B | 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*CP*CP*(U2N)P*GP*UP*CP*CP*AP*CP*CP*G)-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-1 | X-ray diffraction | 2.65 | 2007-08-14 | ||||
| 3 | 1ZFT|1|D+ 1ZFT|1|C+ 1ZFT|1|A+ 1ZFT|1|B | 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*CP*CP*(A2M)P*GP*UP*CP*CP*AP*CP*CP*G)-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 site | X-ray diffraction | 2.33 | 2006-02-14 | ||||
| 4 | 2P7F|1|D+ 2P7F|1|C+ 2P7F|1|A+ 2P7F|1|B | Loop A ribozyme strand, Loop B ribozyme strand, Loop B S-turn strand, substrate strand | The Novel Use of a 2',5'-Phosphodiester Linkage as a Reaction Intermediate at the Active Site of a Small Ribozyme | X-ray diffraction | 2.35 | 2007-05-22 | ||||
| 5 | 1ZFV|1|D+ 1ZFV|1|C+ 1ZFV|1|A+ 1ZFV|1|B | 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*CP*CP*AP*GP*UP*CP*CP*AP*CP*CP*G)-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 site | X-ray diffraction | 2.4 | 2006-02-14 | ||||
| 6 | 2OUE|1|D+ 2OUE|1|C+ 2OUE|1|A+ 2OUE|1|B | Loop A ribozyme strand, Loop B ribozyme strand, Loop B S-turn strand, Substrate strand - Minimal Junctionless Hairpin Ribozyme | Crystal structure of a junctionless all-RNA hairpin ribozyme at 2.05 angstroms resolution | X-ray diffraction | 2.05 | 2007-03-06 | ||||
| 7 | 2P7D|1|D+ 2P7D|1|C+ 2P7D|1|P | 3' substrate strand, octameric fragment, Ribozyme strand II, Ribozyme strand III | A Minimal, 'Hinged' Hairpin Ribozyme Construct Solved with Mimics of the Product Strands at 2.25 Angstroms Resolution | X-ray diffraction | 2.25 | 2007-05-22 | ||||
| 8 | 2D2L|1|D+ 2D2L|1|C+ 2D2L|1|A+ 2D2L|1|B | 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*CP*CP*(A2M)P*GP*UP*CP*CP*AP*CP*CP*G)-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 U39 | X-ray diffraction | 2.5 | 2005-11-01 | ||||
| 9 | 2FGP|1|D+ 2FGP|1|C+ 2FGP|1|A+ 2FGP|1|B | 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*CP*CP*AP*GP*UP*CP*CP*AP*CP*CP*G)-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 8.6 | X-ray diffraction | 2.4 | 2006-02-14 | ||||
| 10 | 1X9C|1|D+ 1X9C|1|C+ 1X9C|1|A+ 1X9C|1|B | 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*CP*CP*(A2M)P*GP*UP*CP*CP*AP*CP*CP*G)-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 U39C | X-ray diffraction | 2.19 | 2005-11-22 | ||||
| 11 | 1ZFX|1|D+ 1ZFX|1|C+ 1ZFX|1|A+ 1ZFX|1|B | 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*CP*CP*AP*GP*UP*CP*CP*AP*CP*CP*G)-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 site | X-ray diffraction | 2.38 | 2006-02-14 | ||||
| 12 | 2BCZ|1|D+ 2BCZ|1|C+ 2BCZ|1|A+ 2BCZ|1|B | 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*CP*CP*(DA)P*GP*UP*CP*CP*AP*CP*CP*G)-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 diffraction | 2.4 | 2006-02-14 | ||||
| 13 | 2D2K|1|D+ 2D2K|1|C+ 2D2K|1|A+ 2D2K|1|B | 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*CP*CP*(A2M)P*GP*UP*CP*CP*AP*CP*CP*G)-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 ribozyme | X-ray diffraction | 2.65 | 2005-11-01 | ||||
| 14 | 2BCY|1|D+ 2BCY|1|C+ 2BCY|1|A+ 2BCY|1|B | 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*CP*CP*AP*GP*UP*CP*CP*AP*CP*CP*G)-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 diffraction | 2.7 | 2006-02-14 | ||||
| 15 | 4G6R|1|D+ 4G6R|1|C+ 4G6R|1|A+ 4G6R|1|B | Loop A Ribozyme strand, Loop A Substrate strand, Loop B Ribozyme Strand, Loop B S-turn strand | Minimal Hairpin Ribozyme in the Transition State with G8I Variation | X-ray diffraction | 2.83 | 2012-08-15 | ||||
| 16 | 3GS8|1|D+ 3GS8|1|C+ 3GS8|1|A+ 3GS8|1|B | RNA (5'-R(*CP*GP*GP*UP*GP*AP*GP*AP*AP*GP*GP*G)-3'), RNA (5'-R(*UP*CP*CP*CP*AP*GP*UP*CP*CP*AP*CP*CP*GP*U)-3'), RNA (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 strand | X-ray diffraction | 2.85 | 2009-04-21 | ||||
| 17 | 3GS1|1|D+ 3GS1|1|C+ 3GS1|1|A+ 3GS1|1|B | RNA (5'-R(*CP*GP*GP*UP*GP*AP*GP*AP*AP*GP*GP*G)-3'), RNA (5'-R(*UP*CP*CP*CP*AP*GP*UP*CP*CP*AP*CP*CP*GP*U)-3'), RNA (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 A38N1dA | X-ray diffraction | 2.85 | 2009-05-12 | ||||
| 18 | 3CR1|1|C | RNA (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 MgCl2 | X-ray diffraction | 2.25 | 2008-08-26 | ||||
| 19 | 3I2Q|1|C | 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 the hairpin ribozyme with 2'OMe substrate strand and N1-deazaadenosine at position A9 | X-ray diffraction | 2.9 | 2009-11-03 | ||||
| 20 | 3I2S|1|C | 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 the hairpin ribozyme with a 2'OMe substrate and N1-deazaadenosine at position A10 | X-ray diffraction | 2.75 | 2009-11-03 | ||||
| 21 | 3CQS|1|C | 19-mer ribozyme strand | A 3'-OH, 2',5'-phosphodiester substitution in the hairpin ribozyme active site reveals similarities with protein ribonucleases | X-ray diffraction | 2.8 | 2008-05-20 | ||||
| 22 | 3I2U|1|C | 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 the haiprin ribozyme with a 2',5'-linked substrate and N1-deazaadenosine at position A10 | X-ray diffraction | 2.8 | 2009-11-03 | ||||
| 23 | 3I2R|1|C | 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 the hairpin ribozyme with a 2',5'-linked substrate with N1-deazaadenosine at position A9 | X-ray diffraction | 2.8 | 2009-11-03 |
Release history
| Release | 3.51 |
|---|---|
| Date | 2018-12-07 |
Parents
Children
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.
| #S | PDB | Title | Method | Resolution | Length |
|---|---|---|---|---|---|
| 1 | 3GS8|1|D+3GS8|1|C+3GS8|1|A+3GS8|1|B | An all-RNA hairpin ribozyme A38N1dA38 variant with a transition-state mimic substrate strand | X-RAY DIFFRACTION | 2.85 | 19 |
| 2 | 3GS1|1|D+3GS1|1|C+3GS1|1|A+3GS1|1|B | An all-RNA Hairpin Ribozyme with mutation A38N1dA | X-RAY DIFFRACTION | 2.85 | 19 |
| 3 | 2NPY|1|D+2NPY|1|C+2NPY|1|A+2NPY|1|B | Crystal Structure of a junctioned hairpin ribozyme incorporating 9atom linker and 2'-deoxy 2'-amino U at A-1 | X-RAY DIFFRACTION | 2.65 | 19 |
| 4 | 2BCZ|1|D+2BCZ|1|C+2BCZ|1|A+2BCZ|1|B | Crystal Structure of a minimal, mutant all-RNA hairpin ribozyme (U39C, G8I, 2'deoxy A-1) | X-RAY DIFFRACTION | 2.4 | 19 |
| 5 | 4G6R|1|D+4G6R|1|C+4G6R|1|A+4G6R|1|B | Minimal Hairpin Ribozyme in the Transition State with G8I Variation | X-RAY DIFFRACTION | 2.83 | 19 |
| 6 | 1ZFX|1|D+1ZFX|1|C+1ZFX|1|A+1ZFX|1|B | The Structure of a minimal all-RNA Hairpin Ribozyme with the mutant G8U at the cleavage site | X-RAY DIFFRACTION | 2.38 | 19 |
| 7 | 1ZFV|1|D+1ZFV|1|C+1ZFV|1|A+1ZFV|1|B | The structure of an all-RNA minimal Hairpin Ribozyme with Mutation G8A at the cleavage site | X-RAY DIFFRACTION | 2.4 | 19 |
| 8 | 2FGP|1|D+2FGP|1|C+2FGP|1|A+2FGP|1|B | Crystal structure of a minimal, all RNA hairpin ribozyme with modifications (g8dap, u39c) at ph 8.6 | X-RAY DIFFRACTION | 2.4 | 19 |
| 9 | 2P7F|1|D+2P7F|1|C+2P7F|1|A+2P7F|1|B | The Novel Use of a 2',5'-Phosphodiester Linkage as a Reaction Intermediate at the Active Site of a Small Ribozyme | X-RAY DIFFRACTION | 2.35 | 19 |
| 10 | 2P7D|1|D+2P7D|1|C+2P7D|1|P | A Minimal, 'Hinged' Hairpin Ribozyme Construct Solved with Mimics of the Product Strands at 2.25 Angstroms Resolution | X-RAY DIFFRACTION | 2.25 | 19 |
| 11 | 2P7E|1|D+2P7E|1|C+2P7E|1|P | Vanadate at the Active Site of a Small Ribozyme Suggests a Role for Water in Transition-State Stabilization | X-RAY DIFFRACTION | 2.05 | 19 |
| 12 | 3I2U|1|C | Crystal structure of the haiprin ribozyme with a 2',5'-linked substrate and N1-deazaadenosine at position A10 | X-RAY DIFFRACTION | 2.8 | 19 |
| 13 | 3I2R|1|C | Crystal structure of the hairpin ribozyme with a 2',5'-linked substrate with N1-deazaadenosine at position A9 | X-RAY DIFFRACTION | 2.8 | 19 |
| 14 | 3CQS|1|C | A 3'-OH, 2',5'-phosphodiester substitution in the hairpin ribozyme active site reveals similarities with protein ribonucleases | X-RAY DIFFRACTION | 2.8 | 19 |
| 15 | 3I2Q|1|C | Crystal structure of the hairpin ribozyme with 2'OMe substrate strand and N1-deazaadenosine at position A9 | X-RAY DIFFRACTION | 2.9 | 19 |
| 16 | 3I2S|1|C | Crystal structure of the hairpin ribozyme with a 2'OMe substrate and N1-deazaadenosine at position A10 | X-RAY DIFFRACTION | 2.75 | 19 |
| 17 | 1ZFT|1|D+1ZFT|1|C+1ZFT|1|A+1ZFT|1|B | The crystal structure of an all-RNA minimal Hairpin Ribozyme with mutant G8I at the cleavage site | X-RAY DIFFRACTION | 2.33 | 19 |
| 18 | 2OUE|1|D+2OUE|1|C+2OUE|1|A+2OUE|1|B | Crystal structure of a junctionless all-RNA hairpin ribozyme at 2.05 angstroms resolution | X-RAY DIFFRACTION | 2.05 | 19 |
| 19 | 1X9C|1|D+1X9C|1|C+1X9C|1|A+1X9C|1|B | An all-RNA Hairpin Ribozyme with mutation U39C | X-RAY DIFFRACTION | 2.19 | 19 |
| 20 | 2BCY|1|D+2BCY|1|C+2BCY|1|A+2BCY|1|B | Crystal Structure of a minimal, mutant all-RNA hairpin ribozyme (U39C, G8MTU) | X-RAY DIFFRACTION | 2.7 | 19 |
| 21 | 2D2L|1|D+2D2L|1|C+2D2L|1|A+2D2L|1|B | Crystal Structure of a minimal, all-RNA hairpin ribozyme with a propyl linker (C3) at position U39 | X-RAY DIFFRACTION | 2.5 | 18 |
| 22 | 2D2K|1|D+2D2K|1|C+2D2K|1|A+2D2K|1|B | Crystal Structure of a minimal, native (U39) all-RNA hairpin ribozyme | X-RAY DIFFRACTION | 2.65 | 22 |
| 23 | 3CR1|1|C | crystal structure of a minimal, mutant, all-RNA hairpin ribozyme (A38C, A-1OMA) grown from MgCl2 | X-RAY DIFFRACTION | 2.25 | 19 |
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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