Equivalence class NR_3.0_95119.6 Current
| # | IFE | Standardized name | Molecule | Organism | Source | Rfam | Title | Method | Res. Å | #NTs | Date |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 9ZWW|1|F (rep) | 5'-OH RNA (5'-r(CpCpA)-3') | synthetic construct | Crystal structure of the N4BP2 polynucleotide kinase domain complexed with ATP, Mg, and the trinucleotide substrate CCA. | X-ray diffraction | 1.85 | 3 | 2026-09-23 | |||
| 2 | 9ZWW|1|E | 5'-OH RNA (5'-r(CpCpA)-3') | synthetic construct | Crystal structure of the N4BP2 polynucleotide kinase domain complexed with ATP, Mg, and the trinucleotide substrate CCA. | X-ray diffraction | 1.85 | 3 | 2026-09-23 | |||
| 3 | 9ZWW|1|D | 5'-OH RNA (5'-r(CpCpA)-3') | synthetic construct | Crystal structure of the N4BP2 polynucleotide kinase domain complexed with ATP, Mg, and the trinucleotide substrate CCA. | X-ray diffraction | 1.85 | 3 | 2026-09-23 | |||
| 4 | 9J1M|1|u | tRNA | Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2 | KU13-bond Mycobacterium tuberculosis 70S ribosome | Electron microscopy | 2.33 | 3 | 2025-03-19 | |||
| 5 | 9GUL|1|2 | P-tRNA CCA tail | Homo sapiens | Structure of FLuc-XBP1u+ stalled human 60S ribosome nascent chain complex | Electron microscopy | 2.2 | 3 | 2025-09-24 | |||
| 6 | 7PWO|1|E | P-site tRNA | Giardia lamblia ATCC 50803 | Cryo-EM structure of Giardia lamblia ribosome at 2.75 A resolution | Electron microscopy | 2.75 | 3 | 2022-04-20 | |||
| 7 | 8IP8|1|dl | CCA end of E-tRNA | Triticum aestivum | Wheat 80S ribosome stalled on AUG-Stop boron dependently | Electron microscopy | 2.9 | 3 | 2024-02-21 | |||
| 8 | 8ZTV|1|Z | RNA (5'-R(P*CP*A)-3') | Escherichia coli | 70S ribosome arrested by PepNL with RF2 | Electron microscopy | 2.9 | 2 | 2025-03-19 | |||
| 9 | 1VY7|1|AW | Cytidine-Puromycin | synthetic construct | Crystal structure of the Thermus thermophilus 70S ribosome in the pre-attack state of peptide bond formation containing short substrate-mimic Cytidine-Cytidine-Puromycin in the A site and acylated tRNA in the P site. | X-ray diffraction | 2.8 | 3 | 2014-08-20 | |||
| 10 | 3CD6|1|4 | RNA (5'-R(*CP*CP*(PPU))-3') | Co-cystal of large Ribosomal Subunit mutant G2616A with CC-Puromycin | X-ray diffraction | 2.75 | 3 | 2008-05-20 | ||||
| 11 | 4LNT|1|Z8 | tRNA acceptor end mimic | synthetic construct | Crystal Structure of tRNA Proline (CGG) Bound to Codon CCC-U on the Ribosome | X-ray diffraction | 2.94 | 3 | 2014-08-06 | |||
| 12 | 8ZTU|1|Z | E-tRNA | Escherichia coli | 70S ribosome arrested by PepNL | Electron microscopy | 2.9 | 2 | 2025-03-19 | |||
| 13 | 3CMA|1|6 | RNA (5'-R(*CP*CP*(8AN))-3') | The structure of CCA and CCA-Phe-Cap-Bio bound to the large ribosomal subunit of Haloarcula marismortui | X-ray diffraction | 2.8 | 3 | 2008-09-23 | ||||
| 14 | 4LNT|1|Z6 | tRNA acceptor end mimic | synthetic construct | Crystal Structure of tRNA Proline (CGG) Bound to Codon CCC-U on the Ribosome | X-ray diffraction | 2.94 | 3 | 2014-08-06 | |||
| 15 | 1VY7|1|CW | Cytidine-Puromycin | synthetic construct | Crystal structure of the Thermus thermophilus 70S ribosome in the pre-attack state of peptide bond formation containing short substrate-mimic Cytidine-Cytidine-Puromycin in the A site and acylated tRNA in the P site. | X-ray diffraction | 2.8 | 3 | 2014-08-20 | |||
| 16 | 9I1W|1|9 | E-site tRNA (5'-R(P*CP*CP*A)-3') | Thermochaetoides thermophila DSM 1495 | High resolution structure of the thermophilic 60S ribosomal subunit of Chaetomium thermophilum | Electron microscopy | 2.38 | 3 | 2025-12-17 | |||
| 17 | 7Y38|1|Z | RNA (5'-R(P*CP*CP*A)-3') | in vitro transcription vector pT7-TP(deltai) | Molecular architecture of the chikungunya virus replication complex | Electron microscopy | 2.8 | 3 | 2022-12-14 | |||
| 18 | 3CMA|1|5 | RNA (5'-R(*CP*CP*A)-3') | The structure of CCA and CCA-Phe-Cap-Bio bound to the large ribosomal subunit of Haloarcula marismortui | X-ray diffraction | 2.8 | 3 | 2008-09-23 | ||||
| 19 | 7PWG|1|E | P-site tRNA | Giardia lamblia ATCC 50803 | Cryo-EM structure of large subunit of Giardia lamblia ribosome at 2.7 A resolution | Electron microscopy | 2.75 | 3 | 2022-04-20 | |||
| 20 | 8OIT|1|B7 | E-site tRNA | Homo sapiens | 39S human mitochondrial large ribosomal subunit with mtRF1 and P-site tRNA | Electron microscopy | 2.9 | 3 | 2023-06-14 | |||
| 21 | 1VQO|1|4 | 5'-R(*CP*CP*(PPU))-3' | The structure of CCPMN bound to the large ribosomal subunit haloarcula marismortui | X-ray diffraction | 2.2 | 3 | 2005-11-29 | ||||
| 22 | 1M90|1|5 | CCA | Co-crystal structure of CCA-Phe-caproic acid-biotin and sparsomycin bound to the 50S ribosomal subunit | X-ray diffraction | 2.8 | 3 | 2002-09-06 | ||||
| 23 | 1QVG|1|5 | Oligonucleotide CCA | Structure of CCA oligonucleotide bound to the tRNA binding sites of the large ribosomal subunit of Haloarcula marismortui | X-ray diffraction | 2.9 | 3 | 2003-11-11 | ||||
| 24 | 3CXC|1|4 | 5'-R(*CP*CP*A)-3' | The structure of an enhanced oxazolidinone inhibitor bound to the 50S ribosomal subunit of H. marismortui | X-ray diffraction | 3 | 3 | 2009-04-28 | ||||
| 25 | 1QVG|1|4 | Oligonucleotide CCA | Structure of CCA oligonucleotide bound to the tRNA binding sites of the large ribosomal subunit of Haloarcula marismortui | X-ray diffraction | 2.9 | 3 | 2003-11-11 | ||||
| 26 | 1QVG|1|3 | Oligonucleotide CCA | Structure of CCA oligonucleotide bound to the tRNA binding sites of the large ribosomal subunit of Haloarcula marismortui | X-ray diffraction | 2.9 | 3 | 2003-11-11 | ||||
| 27 | 1Q86|1|5 | CCA-phenylalanine-cariotic-acid-biotin | Crystal structure of CCA-Phe-cap-biotin bound simultaneously at half occupancy to both the A-site and P-site of the the 50S ribosomal Subunit. | X-ray diffraction | 3 | 3 | 2003-10-07 | ||||
| 28 | 3CME|1|6 | RNA (5'-R(*CP*CP*(8AN))-3') | synthetic construct | The Structure of CA and CCA-PHE-CAP-BIO Bound to the Large Ribosomal Subunit of Haloarcula Marismortui | X-ray diffraction | 2.95 | 3 | 2008-09-23 | |||
| 29 | 1Q86|1|6 | CCA-phenylalanine-cariotic-acid-biotin | Crystal structure of CCA-Phe-cap-biotin bound simultaneously at half occupancy to both the A-site and P-site of the the 50S ribosomal Subunit. | X-ray diffraction | 3 | 3 | 2003-10-07 | ||||
| 30 | 3CME|1|5 | RNA (5'-R(*C*CP*A)-3') | synthetic construct | The Structure of CA and CCA-PHE-CAP-BIO Bound to the Large Ribosomal Subunit of Haloarcula Marismortui | X-ray diffraction | 2.95 | 2 | 2008-09-23 |
Release history
| Release | 4.58 |
|---|---|
| Date | 2026-09-23 |
Parents
| This class | Parent classes | Release id | Intersection | Added to this class | Only in parent |
|---|
Children
| This class | Descendant classes | Release id | Intersection | Only in this class | Added to child |
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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 | View | PDB | Title | Method | Resolution | #NTs |
|---|---|---|---|---|---|---|
| 1 | 7Y38|1|Z | Molecular architecture of the chikungunya virus replication complex | ELECTRON MICROSCOPY | 2.8 | 3 | |
| 2 | 9ZWW|1|D | Crystal structure of the N4BP2 polynucleotide kinase domain complexed with ATP, Mg, and the trinucleotide substrate CCA. | X-RAY DIFFRACTION | 1.85 | 3 | |
| 3 | 9ZWW|1|E | Crystal structure of the N4BP2 polynucleotide kinase domain complexed with ATP, Mg, and the trinucleotide substrate CCA. | X-RAY DIFFRACTION | 1.85 | 3 | |
| 4 | 9ZWW|1|F | Crystal structure of the N4BP2 polynucleotide kinase domain complexed with ATP, Mg, and the trinucleotide substrate CCA. | X-RAY DIFFRACTION | 1.85 | 3 | |
| 5 | 1QVG|1|3 | Structure of CCA oligonucleotide bound to the tRNA binding sites of the large ribosomal subunit of Haloarcula marismortui | X-RAY DIFFRACTION | 2.9 | 3 | |
| 6 | 8IP8|1|dl | Wheat 80S ribosome stalled on AUG-Stop boron dependently | ELECTRON MICROSCOPY | 2.9 | 3 | |
| 7 | 9I1W|1|9 | High resolution structure of the thermophilic 60S ribosomal subunit of Chaetomium thermophilum | ELECTRON MICROSCOPY | 2.38 | 3 | |
| 8 | 8OIT|1|B7 | 39S human mitochondrial large ribosomal subunit with mtRF1 and P-site tRNA | ELECTRON MICROSCOPY | 2.9 | 3 | |
| 9 | 9J1M|1|u | KU13-bond Mycobacterium tuberculosis 70S ribosome | ELECTRON MICROSCOPY | 2.33 | 3 | |
| 10 | 9GUL|1|2 | Structure of FLuc-XBP1u+ stalled human 60S ribosome nascent chain complex | ELECTRON MICROSCOPY | 2.2 | 3 | |
| 11 | 1Q86|1|6 | Crystal structure of CCA-Phe-cap-biotin bound simultaneously at half occupancy to both the A-site and P-site of the the 50S ribosomal Subunit. | X-RAY DIFFRACTION | 3 | 3 | |
| 12 | 3CXC|1|4 | The structure of an enhanced oxazolidinone inhibitor bound to the 50S ribosomal subunit of H. marismortui | X-RAY DIFFRACTION | 3 | 3 | |
| 13 | 1QVG|1|4 | Structure of CCA oligonucleotide bound to the tRNA binding sites of the large ribosomal subunit of Haloarcula marismortui | X-RAY DIFFRACTION | 2.9 | 3 | |
| 14 | 1M90|1|5 | Co-crystal structure of CCA-Phe-caproic acid-biotin and sparsomycin bound to the 50S ribosomal subunit | X-RAY DIFFRACTION | 2.8 | 3 | |
| 15 | 3CMA|1|6 | The structure of CCA and CCA-Phe-Cap-Bio bound to the large ribosomal subunit of Haloarcula marismortui | X-RAY DIFFRACTION | 2.8 | 3 | |
| 16 | 3CME|1|6 | The Structure of CA and CCA-PHE-CAP-BIO Bound to the Large Ribosomal Subunit of Haloarcula Marismortui | X-RAY DIFFRACTION | 2.95 | 3 | |
| 17 | 4LNT|1|Z8 | Crystal Structure of tRNA Proline (CGG) Bound to Codon CCC-U on the Ribosome | X-RAY DIFFRACTION | 2.94 | 3 | |
| 18 | 1VY7|1|CW | Crystal structure of the Thermus thermophilus 70S ribosome in the pre-attack state of peptide bond formation containing short substrate-mimic Cytidine-Cytidine-Puromycin in the A site and acylated tRNA in the P site. | X-RAY DIFFRACTION | 2.8 | 3 | |
| 19 | 4LNT|1|Z6 | Crystal Structure of tRNA Proline (CGG) Bound to Codon CCC-U on the Ribosome | X-RAY DIFFRACTION | 2.94 | 3 | |
| 20 | 1QVG|1|5 | Structure of CCA oligonucleotide bound to the tRNA binding sites of the large ribosomal subunit of Haloarcula marismortui | X-RAY DIFFRACTION | 2.9 | 3 | |
| 21 | 1VQO|1|4 | The structure of CCPMN bound to the large ribosomal subunit haloarcula marismortui | X-RAY DIFFRACTION | 2.2 | 3 | |
| 22 | 1Q86|1|5 | Crystal structure of CCA-Phe-cap-biotin bound simultaneously at half occupancy to both the A-site and P-site of the the 50S ribosomal Subunit. | X-RAY DIFFRACTION | 3 | 3 | |
| 23 | 3CMA|1|5 | The structure of CCA and CCA-Phe-Cap-Bio bound to the large ribosomal subunit of Haloarcula marismortui | X-RAY DIFFRACTION | 2.8 | 3 | |
| 24 | 3CD6|1|4 | Co-cystal of large Ribosomal Subunit mutant G2616A with CC-Puromycin | X-RAY DIFFRACTION | 2.75 | 3 | |
| 25 | 1VY7|1|AW | Crystal structure of the Thermus thermophilus 70S ribosome in the pre-attack state of peptide bond formation containing short substrate-mimic Cytidine-Cytidine-Puromycin in the A site and acylated tRNA in the P site. | X-RAY DIFFRACTION | 2.8 | 3 | |
| 26 | 3CME|1|5 | The Structure of CA and CCA-PHE-CAP-BIO Bound to the Large Ribosomal Subunit of Haloarcula Marismortui | X-RAY DIFFRACTION | 2.95 | 2 | |
| 27 | 8ZTU|1|Z | 70S ribosome arrested by PepNL | ELECTRON MICROSCOPY | 2.9 | 2 | |
| 28 | 7PWG|1|E | Cryo-EM structure of large subunit of Giardia lamblia ribosome at 2.7 A resolution | ELECTRON MICROSCOPY | 2.75 | 3 | |
| 29 | 7PWO|1|E | Cryo-EM structure of Giardia lamblia ribosome at 2.75 A resolution | ELECTRON MICROSCOPY | 2.75 | 3 | |
| 30 | 8ZTV|1|Z | 70S ribosome arrested by PepNL with RF2 | ELECTRON MICROSCOPY | 2.9 | 2 |
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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