Equivalence class DNA_2.0_03402.2 Current
| # | IFE | Standardized name | Molecule | Organism | Source | Rfam | Title | Method | Res. Å | #NTs | Date |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 2W7N|1|E+ 2W7N|1|F+ 2W7N|1|G+ 2W7N|1|H (rep) | 5'-D(*AP*AP*TP*GP*TP*TP*TP*AP*GP*CP *TP*AP*AP*AP*CP*AP*AP*G)-3', 5'-D(*CP*BRUP*BRUP*GP*TP*TP*TP*AP*GP*CP*TP*AP *AP*AP*CP*AP*BRUP*T)-3' | Escherichia coli | Crystal Structure of KorA Bound to Operator DNA: Insight into Repressor Cooperation in RP4 Gene Regulation | X-ray diffraction | 1.85 | 72 | 2009-02-17 | |||
| 2 | 3BSE|1|A+ 3BSE|1|B | DNA (5'-D(*DA*DCP*DAP*DCP*DTP*DAP*DCP*DAP*DAP*DTP*DGP*DTP*DTP*DGP*DCP*DAP*DAP*DT)-3'), DNA (5'-D(*DG*DTP*DAP*DTP*DTP*DGP*DCP*DAP*DAP*DCP*DAP*DTP*DTP*DGP*DTP*DAP*DGP*DT)-3') | Crystal structure analysis of a 16-base-pair B-DNA | X-ray diffraction | 1.6 | 34 | 2008-12-23 | ||||
| 3 | 3NCI|1|T+ 3NCI|1|P | DNA (5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*(DOC))-3'), DNA (5'-D(*TP*CP*AP*GP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3') | RB69 DNA Polymerase Ternary Complex with dCTP Opposite dG at 1.8 angstrom resolution | X-ray diffraction | 1.79 | 31 | 2011-02-02 | ||||
| 4 | 1JX4|1|T+ 1JX4|1|P | 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*CP*TP*A)-3', 5'-D(*T*TP*CP*AP*TP*TP*AP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3' | Crystal Structure of a Y-family DNA Polymerase in a Ternary Complex with DNA Substrates and an Incoming Nucleotide | X-ray diffraction | 1.7 | 30 | 2001-10-05 | ||||
| 5 | 3NGI|1|T+ 3NGI|1|P | DNA (5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*(DOC))-3'), DNA (5'-D(*TP*CP*AP*GP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3') | RB69 DNA Polymerase (Y567A) Ternary Complex with dTTP Opposite dG | X-ray diffraction | 1.886 | 31 | 2011-01-26 | ||||
| 6 | 3NDK|1|T+ 3NDK|1|P | DNA (5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*(DOC))-3'), DNA (5'-D(*TP*CP*AP*GP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3') | RB69 DNA Polymerase (Y567A) Ternary Complex with dCTP Opposite dG | X-ray diffraction | 2 | 31 | 2011-01-26 | ||||
| 7 | 3DVO|1|E+ 3DVO|1|F | DNA (5'-D(*DGP*DAP*DGP*DTP*DCP*DCP*DAP*DCP*DCP*DGP*DGP*DTP*DGP*DGP*DAP*DCP*DTP*DC)-3') | synthetic construct | SgrAI with cognate DNA and calcium bound | X-ray diffraction | 1.892 | 36 | 2008-08-19 | |||
| 8 | 3DVO|1|G+ 3DVO|1|H | DNA (5'-D(*DGP*DAP*DGP*DTP*DCP*DCP*DAP*DCP*DCP*DGP*DGP*DTP*DGP*DGP*DAP*DCP*DTP*DC)-3') | synthetic construct | SgrAI with cognate DNA and calcium bound | X-ray diffraction | 1.892 | 36 | 2008-08-19 | |||
| 9 | 1S9F|1|K+ 1S9F|1|G | 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*CP*TP*A)-3', 5'-D(*T*TP*CP*AP*GP*TP*AP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3' | DPO with AT matched | X-ray diffraction | 2 | 30 | 2005-02-15 | ||||
| 10 | 1S9F|1|L+ 1S9F|1|H | 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*CP*TP*A)-3', 5'-D(*T*TP*CP*AP*GP*TP*AP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3' | DPO with AT matched | X-ray diffraction | 2 | 30 | 2005-02-15 | ||||
| 11 | 1S9F|1|J+ 1S9F|1|F | 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*CP*TP*A)-3', 5'-D(*T*TP*CP*AP*GP*TP*AP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3' | DPO with AT matched | X-ray diffraction | 2 | 30 | 2005-02-15 | ||||
| 12 | 2OG0|1|C+ 2OG0|1|D | 5'-D(*AP*AP*AP*CP*AP*GP*AP*CP*TP*AP*CP*AP*TP*AP*AP*TP*AP*C)-3', 5'-D(*GP*TP*AP*TP*TP*AP*TP*GP*TP*AP*GP*TP*CP*TP*GP*TP*TP*T)-3' | Crystal Structure of the Lambda Xis-DNA complex | X-ray diffraction | 1.9 | 36 | 2007-03-13 | ||||
| 13 | 1S9F|1|I+ 1S9F|1|E | 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*CP*TP*A)-3', 5'-D(*T*TP*CP*AP*GP*TP*AP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3' | DPO with AT matched | X-ray diffraction | 2 | 30 | 2005-02-15 | ||||
| 14 | 2JEJ|1|T+ 2JEJ|1|P | 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP *TP*TP*CP*CP*G)-3', 5'-D(*TP*CP*AP*C BZGP*GP*AP*AP*TP*CP*CP *TP*TP*CP*CP*CP*CP*C)-3' | The Molecular Basis of Selectivity of Nucleoside Triphosphate Incorporation Opposite O6-Benzylguanine by Sulfolobus solfataricus DNA Polymerase IV: Steady-state and Pre-steady-state Kinetics and X- Ray Crystallography of Correct and Incorrect Pairing | X-ray diffraction | 1.86 | 33 | 2007-03-13 | ||||
| 15 | 3M9O|1|T+ 3M9O|1|P | DNA (5'-D(*GP*GP*GP*AP*AP*GP*GP*AP*AP*AP*GP*CP*C)-3'), DNA (5'-D(*TP*CP*TP*GP*GP*CP*TP*TP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3') | Crystal Structure of Dpo4 in complex with DNA containing the major cisplatin lesion | X-ray diffraction | 2 | 31 | 2010-06-16 | ||||
| 16 | 3OSN|1|B+ 3OSN|1|C | 5'-D(*TP*CP*TP*(6OG)P*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*(DOC))-3' | Structural Basis for Proficient Incorporation of dTTP Opposite O6-Methylguanine by Human DNA Polymerase Iota | X-ray diffraction | 1.9 | 15 | 2010-10-20 | ||||
| 17 | 2BQ3|1|T+ 2BQ3|1|P | 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP *TP*TP*CP*A)-3', 5'-D(*TP*CP*AP*TP*GNEP*GP*AP*AP*TP*CP*CP *TP*TP*CP*CP*CP*CP*C)-3' | DNA Adduct Bypass Polymerization by Sulfolobus solfataricus Dpo4. Analysis and Crystal Structures of Multiple Base-Pair Substitution and Frameshift Products with the Adduct 1,N2-Ethenoguanine | X-ray diffraction | 2 | 31 | 2005-06-22 | ||||
| 18 | 3M9N|1|T+ 3M9N|1|P | DNA (5'-D(*GP*GP*GP*GP*AP*AP*GP*GP*AP*AP*AP*GP*C)-3'), DNA (5'-D(*TP*CP*TP*GP*GP*CP*TP*TP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3') | synthetic construct | Crystal Structure of Dpo4 in complex with DNA containing the major cisplatin lesion | X-ray diffraction | 1.93 | 28 | 2010-06-16 | |||
| 19 | 3G6P|1|C+ 3G6P|1|D | DNA (5'-D(*CP*CP*AP*GP*AP*AP*CP*AP*CP*CP*CP*TP*GP*TP*TP*CP*TP*G)-3'), DNA (5'-D(*CP*CP*AP*GP*AP*AP*CP*AP*GP*GP*GP*TP*GP*TP*TP*CP*TP*G)-3') | GR DNA binding domain:FKBP5 complex, 18bp | X-ray diffraction | 1.985 | 36 | 2009-04-21 | ||||
| 20 | 2NLL|1|C+ 2NLL|1|D | DNA (5'-D(*CP*AP*GP*GP*TP*CP*AP*TP*TP*(5IU)P*CP*AP*GP*GP*TP*CP*AP*G)-3'), DNA (5'-D(*CP*TP*GP*AP*CP*CP*TP*GP*AP*AP*AP*TP*GP*AP*CP*CP*T P*G)-3') | RETINOID X RECEPTOR-THYROID HORMONE RECEPTOR DNA-BINDING DOMAIN HETERODIMER BOUND TO THYROID RESPONSE ELEMENT DNA | X-ray diffraction | 1.9 | 36 | 1997-03-12 | ||||
| 21 | 1NLW|1|F+ 1NLW|1|G | 5'-D(*GP*AP*GP*TP*AP*GP*CP*AP*CP*GP*TP*GP*CP*TP*AP*CP*TP*C)-3' | Crystal structure of Mad-Max recognizing DNA | X-ray diffraction | 2 | 36 | 2003-02-04 | ||||
| 22 | 1NLW|1|H+ 1NLW|1|J | 5'-D(*GP*AP*GP*TP*AP*GP*CP*AP*CP*GP*TP*GP*CP*TP*AP*CP*TP*C)-3' | Crystal structure of Mad-Max recognizing DNA | X-ray diffraction | 2 | 36 | 2003-02-04 |
Release history
| Release | 0.6 |
|---|---|
| Date | 2011-03-05 |
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 | #NTs | NAKB NA annotation | NAKB protein annotation |
|---|---|---|---|---|---|---|---|---|
| 1 | 3M9O|1|T+ 3M9O|1|P | Crystal Structure of Dpo4 in complex with DNA containing the major cisplatin lesion | X-RAY DIFFRACTION | 2 | 31 | enzyme,polymerase,transferase | ||
| 2 | 2OG0|1|C+ 2OG0|1|D | Crystal Structure of the Lambda Xis-DNA complex | X-RAY DIFFRACTION | 1.9 | 36 | B-form double helix,double helix,structure | enzyme,recombinase | |
| 3 | 2W7N|1|E+ 2W7N|1|F+ 2W7N|1|G+ 2W7N|1|H | Crystal Structure of KorA Bound to Operator DNA: Insight into Repressor Cooperation in RP4 Gene Regulation | X-RAY DIFFRACTION | 1.85 | 72 | B-form double helix,double helix,structure | regulatory,transcription | |
| 4 | 1NLW|1|H+ 1NLW|1|J | Crystal structure of Mad-Max recognizing DNA | X-RAY DIFFRACTION | 2 | 36 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),basic transcription factor,helix-loop-helix (bHLH),regulatory,transcription | |
| 5 | 1NLW|1|F+ 1NLW|1|G | Crystal structure of Mad-Max recognizing DNA | X-RAY DIFFRACTION | 2 | 36 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),basic transcription factor,helix-loop-helix (bHLH),regulatory,transcription | |
| 6 | 3BSE|1|A+ 3BSE|1|B | Crystal structure analysis of a 16-base-pair B-DNA | X-RAY DIFFRACTION | 1.6 | 34 | B-form double helix,double helix,structure | ||
| 7 | 3G6P|1|C+ 3G6P|1|D | GR DNA binding domain:FKBP5 complex, 18bp | X-RAY DIFFRACTION | 1.985 | 36 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),Zinc-coordinating,nuclear receptor ZnC4,regulatory,transcription | |
| 8 | 2NLL|1|C+ 2NLL|1|D | RETINOID X RECEPTOR-THYROID HORMONE RECEPTOR DNA-BINDING DOMAIN HETERODIMER BOUND TO THYROID RESPONSE ELEMENT DNA | X-RAY DIFFRACTION | 1.9 | 36 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),Zinc-coordinating,nuclear receptor ZnC4,regulatory,transcription | |
| 9 | 3DVO|1|G+ 3DVO|1|H | SgrAI with cognate DNA and calcium bound | X-RAY DIFFRACTION | 1.892 | 36 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease | |
| 10 | 3DVO|1|E+ 3DVO|1|F | SgrAI with cognate DNA and calcium bound | X-RAY DIFFRACTION | 1.892 | 36 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease | |
| 11 | 3OSN|1|B+ 3OSN|1|C | Structural Basis for Proficient Incorporation of dTTP Opposite O6-Methylguanine by Human DNA Polymerase Iota | X-RAY DIFFRACTION | 1.9 | 15 | enzyme,polymerase,transferase | ||
| 12 | 2JEJ|1|T+ 2JEJ|1|P | The Molecular Basis of Selectivity of Nucleoside Triphosphate Incorporation Opposite O6-Benzylguanine by Sulfolobus solfataricus DNA Polymerase IV: Steady-state and Pre-steady-state Kinetics and X- Ray Crystallography of Correct and Incorrect Pairing | X-RAY DIFFRACTION | 1.86 | 33 | enzyme,polymerase,transferase | ||
| 13 | 3M9N|1|T+ 3M9N|1|P | Crystal Structure of Dpo4 in complex with DNA containing the major cisplatin lesion | X-RAY DIFFRACTION | 1.93 | 28 | B-form double helix,double helix,structure | enzyme,polymerase,transferase | |
| 14 | 2BQ3|1|T+ 2BQ3|1|P | DNA Adduct Bypass Polymerization by Sulfolobus solfataricus Dpo4. Analysis and Crystal Structures of Multiple Base-Pair Substitution and Frameshift Products with the Adduct 1,N2-Ethenoguanine | X-RAY DIFFRACTION | 2 | 31 | B-form double helix,double helix,structure | enzyme,polymerase,transferase | |
| 15 | 3NGI|1|T+ 3NGI|1|P | RB69 DNA Polymerase (Y567A) Ternary Complex with dTTP Opposite dG | X-RAY DIFFRACTION | 1.886 | 31 | B-form double helix,double helix,structure | enzyme,polymerase,transferase | |
| 16 | 3NDK|1|T+ 3NDK|1|P | RB69 DNA Polymerase (Y567A) Ternary Complex with dCTP Opposite dG | X-RAY DIFFRACTION | 2 | 31 | B-form double helix,double helix,structure | enzyme,polymerase,transferase | |
| 17 | 3NCI|1|T+ 3NCI|1|P | RB69 DNA Polymerase Ternary Complex with dCTP Opposite dG at 1.8 angstrom resolution | X-RAY DIFFRACTION | 1.79 | 31 | B-form double helix,double helix,structure | enzyme,polymerase,transferase | |
| 18 | 1S9F|1|J+ 1S9F|1|F | DPO with AT matched | X-RAY DIFFRACTION | 2 | 30 | B-form double helix,double helix,structure | enzyme,polymerase,transferase | |
| 19 | 1S9F|1|K+ 1S9F|1|G | DPO with AT matched | X-RAY DIFFRACTION | 2 | 30 | B-form double helix,double helix,structure | enzyme,polymerase,transferase | |
| 20 | 1JX4|1|T+ 1JX4|1|P | Crystal Structure of a Y-family DNA Polymerase in a Ternary Complex with DNA Substrates and an Incoming Nucleotide | X-RAY DIFFRACTION | 1.7 | 30 | B-form double helix,double helix,structure | enzyme,polymerase,transferase | |
| 21 | 1S9F|1|I+ 1S9F|1|E | DPO with AT matched | X-RAY DIFFRACTION | 2 | 30 | B-form double helix,double helix,structure | enzyme,polymerase,transferase | |
| 22 | 1S9F|1|L+ 1S9F|1|H | DPO with AT matched | X-RAY DIFFRACTION | 2 | 30 | 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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