Equivalence class DNA_2.0_28652.3 Current
| # | IFE | Standardized name | Molecule | Organism | Source | Rfam | Title | Method | Res. Å | Date |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 3BSE|1|A+ 3BSE|1|B (rep) | 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 | 2008-12-23 | ||||
| 2 | 3NCI|1|T+ 3NCI|1|P | DNA (5'-D(*TP*CP*AP*GP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3'), DNA (5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*(DOC))-3') | RB69 DNA Polymerase Ternary Complex with dCTP Opposite dG at 1.8 angstrom resolution | X-ray diffraction | 1.79 | 2011-02-02 | ||||
| 3 | 2W7N|1|E+ 2W7N|1|F+ 2W7N|1|G+ 2W7N|1|H | 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 | 2009-02-17 | |||
| 4 | 1JX4|1|T+ 1JX4|1|P | 5'-D(*T*TP*CP*AP*TP*TP*AP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3', 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*CP*TP*A)-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 | 2001-10-05 | ||||
| 5 | 3NGI|1|T+ 3NGI|1|P | DNA (5'-D(*TP*CP*AP*GP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3'), DNA (5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*(DOC))-3') | RB69 DNA Polymerase (Y567A) Ternary Complex with dTTP Opposite dG | X-ray diffraction | 1.886 | 2011-01-26 | ||||
| 6 | 2OG0|1|C+ 2OG0|1|D | 5'-D(*GP*TP*AP*TP*TP*AP*TP*GP*TP*AP*GP*TP*CP*TP*GP*TP*TP*T)-3', 5'-D(*AP*AP*AP*CP*AP*GP*AP*CP*TP*AP*CP*AP*TP*AP*AP*TP*AP*C)-3' | Crystal Structure of the Lambda Xis-DNA complex | X-ray diffraction | 1.9 | 2007-03-13 | ||||
| 7 | 3NDK|1|T+ 3NDK|1|P | DNA (5'-D(*TP*CP*AP*GP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3'), DNA (5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*(DOC))-3') | RB69 DNA Polymerase (Y567A) Ternary Complex with dCTP Opposite dG | X-ray diffraction | 2 | 2011-01-26 | ||||
| 8 | 1S9F|1|I+ 1S9F|1|E | 5'-D(*T*TP*CP*AP*GP*TP*AP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3', 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*CP*TP*A)-3' | DPO with AT matched | X-ray diffraction | 2 | 2005-02-15 | ||||
| 9 | 1S9F|1|J+ 1S9F|1|F | 5'-D(*T*TP*CP*AP*GP*TP*AP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3', 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*CP*TP*A)-3' | DPO with AT matched | X-ray diffraction | 2 | 2005-02-15 | ||||
| 10 | 1S9F|1|K+ 1S9F|1|G | 5'-D(*T*TP*CP*AP*GP*TP*AP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3', 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*CP*TP*A)-3' | DPO with AT matched | X-ray diffraction | 2 | 2005-02-15 | ||||
| 11 | 1S9F|1|L+ 1S9F|1|H | 5'-D(*T*TP*CP*AP*GP*TP*AP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3', 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*CP*TP*A)-3' | DPO with AT matched | X-ray diffraction | 2 | 2005-02-15 | ||||
| 12 | 2JEJ|1|T+ 2JEJ|1|P | 5'-D(*TP*CP*AP*C BZGP*GP*AP*AP*TP*CP*CP *TP*TP*CP*CP*CP*CP*C)-3', 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP *TP*TP*CP*CP*G)-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 | 2007-03-13 | ||||
| 13 | 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 | 2008-08-19 | |||
| 14 | 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 | 2008-08-19 | |||
| 15 | 3M9N|1|T+ 3M9N|1|P | DNA (5'-D(*TP*CP*TP*GP*GP*CP*TP*TP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3'), DNA (5'-D(*GP*GP*GP*GP*AP*AP*GP*GP*AP*AP*AP*GP*C)-3') | Crystal Structure of Dpo4 in complex with DNA containing the major cisplatin lesion | X-ray diffraction | 1.93 | 2010-06-16 | ||||
| 16 | 2BQ3|1|T+ 2BQ3|1|P | 5'-D(*TP*CP*AP*TP*GNEP*GP*AP*AP*TP*CP*CP *TP*TP*CP*CP*CP*CP*C)-3', 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP *TP*TP*CP*A)-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 | 2005-06-22 | ||||
| 17 | 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 | 2010-10-20 | ||||
| 18 | 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 | 1997-03-12 | ||||
| 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 | 2009-04-21 | ||||
| 20 | 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 | 2003-02-04 | ||||
| 21 | 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 | 2003-02-04 |
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 |
|---|
Heat map of mutual geometric discrepancy, in Angstroms per nucleotide. Instances are ordered to put similar structures near each other. The colorbar ranges from 0 to the maximum observed discrepancy, up to 0.5
#S - ordering by similarity (same as in the heat map).| #S | PDB | Title | Method | Resolution | Length | NAKB_NA_annotation | NAKB_protein_annotation |
|---|---|---|---|---|---|---|---|
| 1 | 3DVO|1|E+3DVO|1|F | SgrAI with cognate DNA and calcium bound | X-RAY DIFFRACTION | 1.892 | 18 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease |
| 2 | 3DVO|1|G+3DVO|1|H | SgrAI with cognate DNA and calcium bound | X-RAY DIFFRACTION | 1.892 | 18 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease |
| 3 | 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 | 18 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),Zinc-coordinating,nuclear receptor ZnC4,regulatory,transcription |
| 4 | 3G6P|1|C+3G6P|1|D | GR DNA binding domain:FKBP5 complex, 18bp | X-RAY DIFFRACTION | 1.985 | 18 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),Zinc-coordinating,nuclear receptor ZnC4,regulatory,transcription |
| 5 | 1NLW|1|F+1NLW|1|G | Crystal structure of Mad-Max recognizing DNA | X-RAY DIFFRACTION | 2 | 18 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),basic transcription factor,helix-loop-helix (bHLH),regulatory,transcription |
| 6 | 2OG0|1|C+2OG0|1|D | Crystal Structure of the Lambda Xis-DNA complex | X-RAY DIFFRACTION | 1.9 | 18 | B-form double helix,double helix,structure | enzyme,recombinase |
| 7 | 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 | 18 | B-form double helix,double helix,structure | regulatory,transcription |
| 8 | 1NLW|1|H+1NLW|1|J | Crystal structure of Mad-Max recognizing DNA | X-RAY DIFFRACTION | 2 | 18 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),basic transcription factor,helix-loop-helix (bHLH),regulatory,transcription |
| 9 | 3BSE|1|A+3BSE|1|B | Crystal structure analysis of a 16-base-pair B-DNA | X-RAY DIFFRACTION | 1.6 | 18 | B-form double helix,double helix,structure | |
| 10 | 1S9F|1|K+1S9F|1|G | DPO with AT matched | X-RAY DIFFRACTION | 2 | 18 | B-form double helix,double helix,structure | enzyme,polymerase,transferase |
| 11 | 1S9F|1|J+1S9F|1|F | DPO with AT matched | X-RAY DIFFRACTION | 2 | 18 | B-form double helix,double helix,structure | enzyme,polymerase,transferase |
| 12 | 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 | 18 | B-form double helix,double helix,structure | enzyme,polymerase,transferase |
| 13 | 1S9F|1|I+1S9F|1|E | DPO with AT matched | X-RAY DIFFRACTION | 2 | 18 | B-form double helix,double helix,structure | enzyme,polymerase,transferase |
| 14 | 1S9F|1|L+1S9F|1|H | DPO with AT matched | X-RAY DIFFRACTION | 2 | 18 | B-form double helix,double helix,structure | enzyme,polymerase,transferase |
| 15 | 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 | 18 | enzyme,polymerase,transferase | |
| 16 | 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 | 18 | enzyme,polymerase,transferase | |
| 17 | 3M9N|1|T+3M9N|1|P | Crystal Structure of Dpo4 in complex with DNA containing the major cisplatin lesion | X-RAY DIFFRACTION | 1.93 | 18 | B-form double helix,double helix,structure | enzyme,polymerase,transferase |
| 18 | 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 | 18 | B-form double helix,double helix,structure | enzyme,polymerase,transferase |
| 19 | 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 | 18 | B-form double helix,double helix,structure | enzyme,polymerase,transferase |
| 20 | 3NDK|1|T+3NDK|1|P | RB69 DNA Polymerase (Y567A) Ternary Complex with dCTP Opposite dG | X-RAY DIFFRACTION | 2 | 18 | B-form double helix,double helix,structure | enzyme,polymerase,transferase |
| 21 | 3NGI|1|T+3NGI|1|P | RB69 DNA Polymerase (Y567A) Ternary Complex with dTTP Opposite dG | X-RAY DIFFRACTION | 1.886 | 18 | B-form double helix,double helix,structure | enzyme,polymerase,transferase |
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