Equivalence class DNA_4.0_52460.1 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(*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 | ||||
| 3 | 1R71|1|E+ 1R71|1|F | 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 | ||||
| 4 | 1R71|1|G+ 1R71|1|H | 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 | ||||
| 5 | 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|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 | 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 | ||||
| 8 | 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 | ||||
| 9 | 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 | ||||
| 10 | 3A01|1|C+ 3A01|1|D | 5'-D(*CP*CP*GP*CP*AP*AP*TP*TP*AP*AP*TP*TP*AP*AP*GP*CP*C)-3', 5'-D(*GP*GP*CP*TP*TP*AP*AP*TP*TP*AP*AP*TP*TP*GP*CP*GP*G)-3' | Crystal structure of Aristaless and Clawless homeodomains bound to DNA | X-ray diffraction | 2.7 | 2010-03-09 | ||||
| 11 | 3A01|1|G+ 3A01|1|H | 5'-D(*CP*CP*GP*CP*AP*AP*TP*TP*AP*AP*TP*TP*AP*AP*GP*CP*C)-3', 5'-D(*GP*GP*CP*TP*TP*AP*AP*TP*TP*AP*AP*TP*TP*GP*CP*GP*G)-3' | Crystal structure of Aristaless and Clawless homeodomains bound to DNA | X-ray diffraction | 2.7 | 2010-03-09 | ||||
| 12 | 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 | ||||
| 13 | 1SGS|1|A | kB DNA | Crystal structure of a free kB DNA | X-ray diffraction | 1.6 | 2004-03-23 | ||||
| 14 | 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 | ||||
| 15 | 1W0U|1|C+ 1W0U|1|D | 5'-D(*CP*TP*AP*AP*CP*CP*CP*TP*AP*AP *CP*CP*CP*TP*AP*GP*A)-3', 5'-D(*TP*CP*TP*AP*GP*GP*GP*TP*TP*AP *GP*GP*GP*TP*TP*AP*G)-3' | hTRF2 DNA-binding domain in complex with telomeric DNA. | X-ray diffraction | 1.8 | 2004-12-22 | ||||
| 16 | 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 | ||||
| 17 | 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 | ||||
| 18 | 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 | ||||
| 19 | 1A0A|1|C+ 1A0A|1|D | DNA (5'-D(*CP*TP*AP*GP*TP*CP*CP*CP*AP*CP*GP*TP*GP*TP*GP*AP*G )-3'), DNA (5'-D(*CP*TP*CP*AP*CP*AP*CP*GP*TP*GP*GP*GP*AP*CP*TP*AP*G )-3') | PHOSPHATE SYSTEM POSITIVE REGULATORY PROTEIN PHO4/DNA COMPLEX | X-ray diffraction | 2.8 | 1998-03-18 |
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 | 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 | |
| 2 | 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 | |
| 3 | 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 | |
| 4 | 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 | |
| 5 | 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 | |
| 6 | 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 | |
| 7 | 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 | ||
| 8 | 1IAW|1|C+ 1IAW|1|D | CRYSTAL STRUCTURE OF NAEI COMPLEXED WITH 17MER DNA | X-RAY DIFFRACTION | 2.4 | 17 | enzyme,hydrolase,nuclease | ||
| 9 | 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 | |
| 10 | 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 | |
| 11 | 1R71|1|E+ 1R71|1|F | 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 | |
| 12 | 1R71|1|G+ 1R71|1|H | 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 | |
| 13 | 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 | |
| 14 | 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 | |
| 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 | 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 | |
| 17 | 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 | |
| 18 | 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 | |
| 19 | 1SGS|1|A | Crystal structure of a free kB DNA | X-RAY DIFFRACTION | 1.6 | 17 | B-form double helix,double helix,structure |
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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