Equivalence class DNA_4.0_10832.1 Current
| # | IFE | Standardized name | Molecule | Organism | Source | Rfam | Title | Method | Res. Å | Date |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 1EGW|1|E+ 1EGW|1|F (rep) | DNA (5'-D(*AP*AP*AP*GP*CP*TP*AP*TP*TP*AP*TP*TP*AP*GP*CP*TP*T)-3'), DNA (5'-D(*TP*AP*AP*GP*CP*TP*AP*AP*TP*AP*AP*TP*AP*GP*CP*TP*T)-3') | CRYSTAL STRUCTURE OF MEF2A CORE BOUND TO DNA | X-ray diffraction | 1.5 | 2000-03-20 | ||||
| 2 | 1EGW|1|G+ 1EGW|1|H | DNA (5'-D(*TP*AP*AP*GP*CP*TP*AP*AP*TP*AP*AP*TP*AP*GP*CP*TP*T)-3'), DNA (5'-D(*AP*AP*AP*GP*CP*TP*AP*TP*TP*AP*TP*TP*AP*GP*CP*TP*T)-3') | CRYSTAL STRUCTURE OF MEF2A CORE BOUND TO DNA | X-ray diffraction | 1.5 | 2000-03-20 | ||||
| 3 | 2AGQ|1|C+ 2AGQ|1|B | 5'-D(*TP*CP*AP*TP*GP*AP*GP*TP*CP*CP*TP*GP*TP*AP*GP*CP*C)-3', 5'-D(*GP*GP*CP*TP*AP*CP*AP*GP*GP*AP*CP*TP*(DOC))-3' | Fidelity of Dpo4: effect of metal ions, nucleotide selection and pyrophosphorolysis | X-ray diffraction | 2.1 | 2005-09-06 | ||||
| 4 | 1S10|1|C+ 1S10|1|B | 5'-D(*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' | Snapshots of replication through an abasic lesion: structural basis for base substitution and frameshift | X-ray diffraction | 2.1 | 2004-03-30 | ||||
| 5 | 1R71|1|E+ 1R71|1|F+ 1R71|1|I+ 1R71|1|J | 5'-D(*AP*(BRU)P*TP*TP*TP*AP*GP*CP*GP*GP*CP*TP*AP*AP*AP*AP*G)-3', 5'-D(*CP*(BRU)P*TP*TP*TP*AP*GP*CP*CP*GP*CP*TP*AP*AP*AP*AP*(BRU))-3' | Crystal Structure of the DNA binding domain of KorB in complex with the operator DNA | X-ray diffraction | 2.2 | 2004-06-01 | ||||
| 6 | 1R71|1|G+ 1R71|1|H+ 1R71|1|K+ 1R71|1|L | 5'-D(*AP*(BRU)P*TP*TP*TP*AP*GP*CP*GP*GP*CP*TP*AP*AP*AP*AP*G)-3', 5'-D(*CP*(BRU)P*TP*TP*TP*AP*GP*CP*CP*GP*CP*TP*AP*AP*AP*AP*(BRU))-3' | Crystal Structure of the DNA binding domain of KorB in complex with the operator DNA | X-ray diffraction | 2.2 | 2004-06-01 | ||||
| 7 | 1S0O|1|D+ 1S0O|1|C | 5'-D(*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*C)-3' | Snapshots of replication through an abasic lesion: structural basis for base substitution and frameshift | X-ray diffraction | 2.1 | 2004-03-30 | ||||
| 8 | 1S0O|1|F+ 1S0O|1|E | 5'-D(*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*C)-3' | Snapshots of replication through an abasic lesion: structural basis for base substitution and frameshift | X-ray diffraction | 2.1 | 2004-03-30 | ||||
| 9 | 2IA6|1|D+ 2IA6|1|C | 5'-D(*TP*CP*AP*TP*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*A)-3' | Bypass of Major Benzopyrene-dG Adduct by Y-Family DNA Polymerase with Unique Structural Gap | X-ray diffraction | 2.5 | 2007-09-11 | ||||
| 10 | 2IA6|1|F+ 2IA6|1|E | 5'-D(*TP*CP*AP*TP*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*A)-3' | Bypass of Major Benzopyrene-dG Adduct by Y-Family DNA Polymerase with Unique Structural Gap | X-ray diffraction | 2.5 | 2007-09-11 | ||||
| 11 | 1N56|1|D+ 1N56|1|C | 5'-D(*TP*CP*AP*TP*(3DR)P*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*AP*A)-3' | synthetic construct | Y-family DNA polymerase Dpo4 in complex with DNA containing abasic lesion | X-ray diffraction | 2.4 | 2004-02-24 | |||
| 12 | 1N56|1|F+ 1N56|1|E | 5'-D(*TP*CP*AP*TP*(3DR)P*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*AP*A)-3' | synthetic construct | Y-family DNA polymerase Dpo4 in complex with DNA containing abasic lesion | X-ray diffraction | 2.4 | 2004-02-24 | |||
| 13 | 2CAX|1|G+ 2CAX|1|H | 5'-D(*GP*AP*AP*TP*CP*AP*CP*AP*AP*AP *TP*CP*AP*CP*AP*AP*G)-3', 5'-D(*TP*TP*GP*TP*GP*AP*TP*TP*TP*GP *TP*GP*AP*TP*TP*CP*G)-3' | STRUCTURAL BASIS FOR COOPERATIVE BINDING OF RIBBON-HELIX-HELIX REPRESSOR OMEGA TO MUTATED DIRECT DNA HEPTAD REPEATS | X-ray diffraction | 2.9 | 2006-03-15 | ||||
| 14 | 2E1C|1|B+ 2E1C|1|D | DNA (5'-D(*DAP*DGP*DTP*DGP*DAP*DAP*DAP*DAP*DTP*DTP*DTP*DTP*DTP*DCP*DAP*DCP*DA)-3'), DNA (5'-D(*DTP*DGP*DTP*DGP*DAP*DAP*DAP*DAP*DAP*DTP*DTP*DTP*DTP*DCP*DAP*DCP*DT)-3') | Structure of Putative HTH-type transcriptional regulator PH1519/DNA Complex | X-ray diffraction | 2.1 | 2007-12-04 | ||||
| 15 | 2AGO|1|C+ 2AGO|1|B | DNA (5'-D(*TP*TP*TP*TP*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3'), DNA (5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*CP*G)-3') | Fidelity of Dpo4: effect of metal ions, nucleotide selection and pyrophosphorolysis | X-ray diffraction | 2.85 | 2005-09-06 | ||||
| 16 | 2AGP|1|D+ 2AGP|1|C | DNA (5'-D(*TP*TP*TP*TP*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3'), DNA (5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*(DOC)-3') | Fidelity of Dpo4: effect of metal ions, nucleotide selection and pyrophosphorolysis | X-ray diffraction | 2.9 | 2005-09-06 | ||||
| 17 | 2AGP|1|F+ 2AGP|1|E | DNA (5'-D(*TP*TP*TP*TP*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3'), DNA (5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*(DOC)-3') | Fidelity of Dpo4: effect of metal ions, nucleotide selection and pyrophosphorolysis | X-ray diffraction | 2.9 | 2005-09-06 | ||||
| 18 | 1IAW|1|C+ 1IAW|1|D | 5'-D(*TP*GP*CP*CP*AP*CP*GP*CP*CP*GP*GP*CP*GP*TP*GP*GP*C)-3' | CRYSTAL STRUCTURE OF NAEI COMPLEXED WITH 17MER DNA | X-ray diffraction | 2.4 | 2001-08-03 | ||||
| 19 | 3A01|1|C+ 3A01|1|D | 5'-D(*GP*GP*CP*TP*TP*AP*AP*TP*TP*AP*AP*TP*TP*GP*CP*GP*G)-3', 5'-D(*CP*CP*GP*CP*AP*AP*TP*TP*AP*AP*TP*TP*AP*AP*GP*CP*C)-3' | Crystal structure of Aristaless and Clawless homeodomains bound to DNA | X-ray diffraction | 2.7 | 2010-03-09 | ||||
| 20 | 3A01|1|G+ 3A01|1|H | 5'-D(*GP*GP*CP*TP*TP*AP*AP*TP*TP*AP*AP*TP*TP*GP*CP*GP*G)-3', 5'-D(*CP*CP*GP*CP*AP*AP*TP*TP*AP*AP*TP*TP*AP*AP*GP*CP*C)-3' | Crystal structure of Aristaless and Clawless homeodomains bound to DNA | X-ray diffraction | 2.7 | 2010-03-09 | ||||
| 21 | 2I9T|1|C+ 2I9T|1|D | 5'-D(*AP*GP*TP*GP*GP*GP*AP*AP*AP*TP*TP*CP*CP*TP*CP*TP*G)-3', 5'-D(*CP*AP*GP*AP*GP*GP*AP*AP*TP*TP*TP*CP*CP*CP*AP*CP*T)-3' | Structure of NF-kB p65-p50 heterodimer bound to PRDII element of B-interferon promoter | X-ray diffraction | 2.8 | 2007-02-06 | ||||
| 22 | 1SGS|1|A | kB DNA | Crystal structure of a free kB DNA | X-ray diffraction | 1.6 | 2004-03-23 | ||||
| 23 | 2BOP|1|B | DNA (5'-D(*CP*CP*GP*AP*CP*CP*GP*AP*CP*GP*TP*CP*GP*GP*TP*CP*G )-3') | CRYSTAL STRUCTURE AT 1.7 ANGSTROMS OF THE BOVINE PAPILLOMAVIRUS-1 E2 DNA-BINDING DOMAIN BOUND TO ITS DNA TARGET | X-ray diffraction | 1.7 | 1994-01-31 | ||||
| 24 | 1W0U|1|C+ 1W0U|1|D | 5'-D(*TP*CP*TP*AP*GP*GP*GP*TP*TP*AP *GP*GP*GP*TP*TP*AP*G)-3', 5'-D(*CP*TP*AP*AP*CP*CP*CP*TP*AP*AP *CP*CP*CP*TP*AP*GP*A)-3' | hTRF2 DNA-binding domain in complex with telomeric DNA. | X-ray diffraction | 1.8 | 2004-12-22 | ||||
| 25 | 1LEI|1|C+ 1LEI|1|D | 5'-D(*CP*TP*CP*AP*GP*GP*GP*AP*AP*AP*GP*TP*AP*CP*AP*GP*A)-3', 5'-D(*TP*CP*TP*GP*5ITP*AP*CP*5ITP*5ITP*5ITP*CP*CP*CP*TP*GP*AP*G)-3' | The kB DNA sequence from the HLV-LTR functions as an allosteric regulator of HIV transcription | X-ray diffraction | 2.7 | 2003-04-15 | ||||
| 26 | 1TQE|1|C+ 1TQE|1|D | MEF2 binding site of nur77 promoter | Mechanism of recruitment of class II histone deacetylases by myocyte enhancer factor-2 | X-ray diffraction | 2.7 | 2004-12-21 | ||||
| 27 | 1TQE|1|E+ 1TQE|1|F | MEF2 binding site of nur77 promoter | Mechanism of recruitment of class II histone deacetylases by myocyte enhancer factor-2 | X-ray diffraction | 2.7 | 2004-12-21 | ||||
| 28 | 1A0A|1|C+ 1A0A|1|D | DNA (5'-D(*CP*TP*CP*AP*CP*AP*CP*GP*TP*GP*GP*GP*AP*CP*TP*AP*G )-3'), DNA (5'-D(*CP*TP*AP*GP*TP*CP*CP*CP*AP*CP*GP*TP*GP*TP*GP*AP*G )-3') | PHOSPHATE SYSTEM POSITIVE REGULATORY PROTEIN PHO4/DNA COMPLEX | X-ray diffraction | 2.8 | 1998-03-18 |
Release history
| Release | 0.19 |
|---|---|
| Date | 2011-05-28 |
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 | 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 |
| 2 | 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 |
| 3 | 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 | |
| 4 | 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 |
| 5 | 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 |
| 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 | 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 |
| 8 | 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 |
| 9 | 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 | |
| 10 | 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 |
| 11 | 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 |
| 12 | 1W0U|1|C+1W0U|1|D | hTRF2 DNA-binding domain in complex with telomeric DNA. | X-RAY DIFFRACTION | 1.8 | 17 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),homeodomain,regulatory,transcription |
| 13 | 1LEI|1|C+1LEI|1|D | The kB DNA sequence from the HLV-LTR functions as an allosteric regulator of HIV transcription | X-RAY DIFFRACTION | 2.7 | 17 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),immunoglobulin (Ig) fold,regulatory,rel homology,transcription |
| 14 | 3A01|1|G+3A01|1|H | Crystal structure of Aristaless and Clawless homeodomains bound to DNA | X-RAY DIFFRACTION | 2.7 | 17 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),homeodomain,regulatory,transcription |
| 15 | 3A01|1|C+3A01|1|D | Crystal structure of Aristaless and Clawless homeodomains bound to DNA | X-RAY DIFFRACTION | 2.7 | 17 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),homeodomain,regulatory,transcription |
| 16 | 2I9T|1|C+2I9T|1|D | Structure of NF-kB p65-p50 heterodimer bound to PRDII element of B-interferon promoter | X-RAY DIFFRACTION | 2.8 | 17 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),immunoglobulin (Ig) fold,regulatory,rel homology,transcription |
| 17 | 1R71|1|G+1R71|1|H+1R71|1|K+1R71|1|L | Crystal Structure of the DNA binding domain of KorB in complex with the operator DNA | X-RAY DIFFRACTION | 2.2 | 17 | B-form double helix,double helix,structure | regulatory,transcription |
| 18 | 1R71|1|E+1R71|1|F+1R71|1|I+1R71|1|J | Crystal Structure of the DNA binding domain of KorB in complex with the operator DNA | X-RAY DIFFRACTION | 2.2 | 17 | B-form double helix,double helix,structure | regulatory,transcription |
| 19 | 2CAX|1|G+2CAX|1|H | STRUCTURAL BASIS FOR COOPERATIVE BINDING OF RIBBON-HELIX-HELIX REPRESSOR OMEGA TO MUTATED DIRECT DNA HEPTAD REPEATS | X-RAY DIFFRACTION | 2.9 | 17 | DNA-binding transcription factor (TF),MetR homology,other α-helix,regulatory,transcription | |
| 20 | 1A0A|1|C+1A0A|1|D | PHOSPHATE SYSTEM POSITIVE REGULATORY PROTEIN PHO4/DNA COMPLEX | X-RAY DIFFRACTION | 2.8 | 17 | double helix,structure | DNA-binding transcription factor (TF),basic transcription factor,helix-loop-helix (bHLH),regulatory,transcription |
| 21 | 1IAW|1|C+1IAW|1|D | CRYSTAL STRUCTURE OF NAEI COMPLEXED WITH 17MER DNA | X-RAY DIFFRACTION | 2.4 | 17 | enzyme,hydrolase,nuclease | |
| 22 | 1SGS|1|A | Crystal structure of a free kB DNA | X-RAY DIFFRACTION | 1.6 | 17 | B-form double helix,double helix,structure | |
| 23 | 2E1C|1|B+2E1C|1|D | Structure of Putative HTH-type transcriptional regulator PH1519/DNA Complex | X-RAY DIFFRACTION | 2.1 | 17 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),regulatory,transcription,winged helix/forkhead |
| 24 | 1TQE|1|C+1TQE|1|D | Mechanism of recruitment of class II histone deacetylases by myocyte enhancer factor-2 | X-RAY DIFFRACTION | 2.7 | 17 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),MADS box,enzyme,hydrolase,other α-helix,regulatory,transcription |
| 25 | 1TQE|1|E+1TQE|1|F | Mechanism of recruitment of class II histone deacetylases by myocyte enhancer factor-2 | X-RAY DIFFRACTION | 2.7 | 17 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),MADS box,enzyme,hydrolase,other α-helix,regulatory,transcription |
| 26 | 2BOP|1|B | CRYSTAL STRUCTURE AT 1.7 ANGSTROMS OF THE BOVINE PAPILLOMAVIRUS-1 E2 DNA-BINDING DOMAIN BOUND TO ITS DNA TARGET | X-RAY DIFFRACTION | 1.7 | 17 | B-form double helix,double helix,structure | regulatory,transcription |
| 27 | 1EGW|1|G+1EGW|1|H | CRYSTAL STRUCTURE OF MEF2A CORE BOUND TO DNA | X-RAY DIFFRACTION | 1.5 | 17 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),MADS box,other α-helix,regulatory,transcription |
| 28 | 1EGW|1|E+1EGW|1|F | CRYSTAL STRUCTURE OF MEF2A CORE BOUND TO DNA | X-RAY DIFFRACTION | 1.5 | 17 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),MADS box,other α-helix,regulatory,transcription |
Coloring options: