Equivalence class DNA_4.0_41452.1 Current
| # | IFE | Standardized name | Molecule | Organism | Source | Rfam | Title | Method | Res. Å | Date |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 1S10|1|C+ 1S10|1|B (rep) | 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*CP*TP*A)-3', 5'-D(*TP*CP*AP*GP*TP*AP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3' | Snapshots of replication through an abasic lesion: structural basis for base substitution and frameshift | X-ray diffraction | 2.1 | 2004-03-30 | ||||
| 2 | 2AGQ|1|C+ 2AGQ|1|B | 5'-D(*GP*GP*CP*TP*AP*CP*AP*GP*GP*AP*CP*TP*(DOC))-3', 5'-D(*TP*CP*AP*TP*GP*AP*GP*TP*CP*CP*TP*GP*TP*AP*GP*CP*C)-3' | Fidelity of Dpo4: effect of metal ions, nucleotide selection and pyrophosphorolysis | X-ray diffraction | 2.1 | 2005-09-06 | ||||
| 3 | 1S0O|1|D+ 1S0O|1|C | 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*CP*TP*C)-3', 5'-D(*TP*CP*AP*GP*TP*AP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3' | Snapshots of replication through an abasic lesion: structural basis for base substitution and frameshift | X-ray diffraction | 2.1 | 2004-03-30 | ||||
| 4 | 1S0O|1|F+ 1S0O|1|E | 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*CP*TP*C)-3', 5'-D(*TP*CP*AP*GP*TP*AP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3' | Snapshots of replication through an abasic lesion: structural basis for base substitution and frameshift | X-ray diffraction | 2.1 | 2004-03-30 | ||||
| 5 | 2IA6|1|D+ 2IA6|1|C | 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*A)-3', 5'-D(*TP*CP*AP*TP*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3' | Bypass of Major Benzopyrene-dG Adduct by Y-Family DNA Polymerase with Unique Structural Gap | X-ray diffraction | 2.5 | 2007-09-11 | ||||
| 6 | 2IA6|1|F+ 2IA6|1|E | 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*A)-3', 5'-D(*TP*CP*AP*TP*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3' | Bypass of Major Benzopyrene-dG Adduct by Y-Family DNA Polymerase with Unique Structural Gap | X-ray diffraction | 2.5 | 2007-09-11 | ||||
| 7 | 1N56|1|D+ 1N56|1|C | 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*CP*TP*AP*A)-3', 5'-D(*TP*CP*AP*TP*(3DR)P*AP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3' | synthetic construct | Y-family DNA polymerase Dpo4 in complex with DNA containing abasic lesion | X-ray diffraction | 2.4 | 2004-02-24 | |||
| 8 | 1N56|1|F+ 1N56|1|E | 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*CP*TP*AP*A)-3', 5'-D(*TP*CP*AP*TP*(3DR)P*AP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3' | synthetic construct | Y-family DNA polymerase Dpo4 in complex with DNA containing abasic lesion | X-ray diffraction | 2.4 | 2004-02-24 | |||
| 9 | 2AGO|1|C+ 2AGO|1|B | DNA (5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*CP*G)-3'), DNA (5'-D(*TP*TP*TP*TP*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3') | Fidelity of Dpo4: effect of metal ions, nucleotide selection and pyrophosphorolysis | X-ray diffraction | 2.85 | 2005-09-06 | ||||
| 10 | 2AGP|1|D+ 2AGP|1|C | DNA (5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*(DOC)-3'), DNA (5'-D(*TP*TP*TP*TP*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3') | Fidelity of Dpo4: effect of metal ions, nucleotide selection and pyrophosphorolysis | X-ray diffraction | 2.9 | 2005-09-06 | ||||
| 11 | 2AGP|1|F+ 2AGP|1|E | DNA (5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*(DOC)-3'), DNA (5'-D(*TP*TP*TP*TP*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3') | Fidelity of Dpo4: effect of metal ions, nucleotide selection and pyrophosphorolysis | X-ray diffraction | 2.9 | 2005-09-06 |
Parents
| This class | Parent classes | Release id | Intersection | Added to this class | Only in parent |
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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 | Length | NAKB NA annotation | NAKB protein annotation |
|---|---|---|---|---|---|---|---|---|
| 1 | 1S0O|1|D+ 1S0O|1|C | Snapshots of replication through an abasic lesion: structural basis for base substitution and frameshift | X-RAY DIFFRACTION | 2.1 | 17 | B-form double helix,double helix,structure | enzyme,polymerase,transferase | |
| 2 | 2IA6|1|D+ 2IA6|1|C | Bypass of Major Benzopyrene-dG Adduct by Y-Family DNA Polymerase with Unique Structural Gap | X-RAY DIFFRACTION | 2.5 | 17 | B-form double helix,double helix,structure | enzyme,polymerase,transferase | |
| 3 | 1N56|1|D+ 1N56|1|C | Y-family DNA polymerase Dpo4 in complex with DNA containing abasic lesion | X-RAY DIFFRACTION | 2.4 | 17 | enzyme,polymerase,transferase | ||
| 4 | 2AGO|1|C+ 2AGO|1|B | Fidelity of Dpo4: effect of metal ions, nucleotide selection and pyrophosphorolysis | X-RAY DIFFRACTION | 2.85 | 17 | B-form double helix,double helix,structure | enzyme,polymerase,transferase | |
| 5 | 2AGP|1|F+ 2AGP|1|E | Fidelity of Dpo4: effect of metal ions, nucleotide selection and pyrophosphorolysis | X-RAY DIFFRACTION | 2.9 | 17 | B-form double helix,double helix,structure | enzyme,polymerase,transferase | |
| 6 | 2AGP|1|D+ 2AGP|1|C | Fidelity of Dpo4: effect of metal ions, nucleotide selection and pyrophosphorolysis | X-RAY DIFFRACTION | 2.9 | 17 | B-form double helix,double helix,structure | enzyme,polymerase,transferase | |
| 7 | 1S10|1|C+ 1S10|1|B | Snapshots of replication through an abasic lesion: structural basis for base substitution and frameshift | X-RAY DIFFRACTION | 2.1 | 17 | B-form double helix,double helix,structure | enzyme,polymerase,transferase | |
| 8 | 2AGQ|1|C+ 2AGQ|1|B | Fidelity of Dpo4: effect of metal ions, nucleotide selection and pyrophosphorolysis | X-RAY DIFFRACTION | 2.1 | 17 | B-form double helix,double helix,structure | enzyme,polymerase,transferase | |
| 9 | 1N56|1|F+ 1N56|1|E | Y-family DNA polymerase Dpo4 in complex with DNA containing abasic lesion | X-RAY DIFFRACTION | 2.4 | 17 | enzyme,polymerase,transferase | ||
| 10 | 2IA6|1|F+ 2IA6|1|E | Bypass of Major Benzopyrene-dG Adduct by Y-Family DNA Polymerase with Unique Structural Gap | X-RAY DIFFRACTION | 2.5 | 17 | B-form double helix,double helix,structure | enzyme,polymerase,transferase | |
| 11 | 1S0O|1|F+ 1S0O|1|E | Snapshots of replication through an abasic lesion: structural basis for base substitution and frameshift | X-RAY DIFFRACTION | 2.1 | 17 | B-form double helix,double helix,structure | enzyme,polymerase,transferase |
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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