Equivalence class DNA_3.0_73490.1 Obsolete
| # | IFE | Standardized name | Molecule | Organism | Source | Rfam | Title | Method | Res. Å | #NTs | Date |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 3JXB|1|A+ 3JXB|1|B (rep) | 5'-D(*CP*AP*TP*TP*TP*AP*AP*GP*AP*CP*GP*TP*CP*TP*TP*AP*AP*AP*TP*A)-3', 5'-D(*TP*AP*TP*TP*TP*AP*AP*GP*AP*CP*GP*TP*CP*TP*TP*AP*AP*AP*TP*G)-3' | Crystal structure of the P22 c2 repressor protein in complex with synthetic operator 9C | X-ray diffraction | 1.67 | 40 | 2010-01-19 | ||||
| 2 | 2R1J|1|A+ 2R1J|1|B | 5'-D(*DCP*DAP*DTP*DTP*DTP*DAP*DAP*DGP*DAP*DTP*DAP*DTP*DCP*DTP*DTP*DAP*DAP*DAP*DTP*DA)-3', 5'-D(*DTP*DAP*DTP*DTP*DTP*DAP*DAP*DGP*DAP*DTP*DAP*DTP*DCP*DTP*DTP*DAP*DAP*DAP*DTP*DG)-3' | Crystal Structure of the P22 c2 Repressor protein in complex with the synthetic operator 9T | X-ray diffraction | 1.53 | 40 | 2008-04-29 | ||||
| 3 | 3JXC|1|A+ 3JXC|1|B | 5'-D(*CP*AP*TP*TP*TP*AP*AP*GP*AP*TP*AP*TP*CP*TP*TP*AP*AP*AP*TP*G)-3' | Crystal structure of the P22 c2 repressor protein in complex with synthetic operator 9T in the presence of Tl+ | X-ray diffraction | 1.9 | 40 | 2010-01-19 | ||||
| 4 | 3JXD|1|A+ 3JXD|1|B | 5'-D(*CP*AP*TP*TP*TP*AP*AP*GP*AP*CP*GP*TP*CP*TP*TP*AP*AP*AP*TP*G)-3' | Crystal structure of the P22 c2 repressor protein in complex with synthetic operator 9C in the presence of Rb+ | X-ray diffraction | 2.1 | 40 | 2010-01-19 | ||||
| 5 | 2HAN|1|C+ 2HAN|1|D | 5'-D(*CP*AP*AP*GP*GP*GP*TP*TP*CP*AP*AP*TP*GP*CP*AP*CP*TP*TP*GP*T)-3', 5'-D(*GP*AP*CP*AP*AP*GP*TP*GP*CP*AP*TP*TP*GP*AP*AP*CP*CP*CP*TP*T)-3' | Structural basis of heterodimeric ecdysteroid receptor interaction with natural response element hsp27 gene promoter | X-ray diffraction | 1.95 | 40 | 2007-05-22 | ||||
| 6 | 3MGV|1|F+ 3MGV|1|H+ 3MGV|1|E+ 3MGV|1|G | DNA (5'-D(*CP*AP*TP*AP*TP*GP*CP*TP*AP*TP*AP*CP*GP*AP*AP*GP*TP*TP*AP*T)-3'), DNA (5'-D(*TP*AP*TP*AP*AP*CP*TP*TP*CP*GP*TP*AP*TP*AP*G)-3') | Cre recombinase-DNA transition state | X-ray diffraction | 2.29 | 70 | 2010-05-26 | ||||
| 7 | 3MGV|1|K+ 3MGV|1|M+ 3MGV|1|I+ 3MGV|1|L | DNA (5'-D(*CP*AP*TP*AP*TP*GP*CP*TP*AP*TP*AP*CP*GP*AP*AP*GP*TP*TP*AP*T)-3'), DNA (5'-D(*TP*AP*TP*AP*AP*CP*TP*TP*CP*GP*TP*AP*TP*AP*G)-3') | Cre recombinase-DNA transition state | X-ray diffraction | 2.29 | 70 | 2010-05-26 | ||||
| 8 | 2VY1|1|W | 5'-D(*TP*TP*AP*CP*GP*GP*AP*CP*CP*AP *CP*TP*GP*GP*TP*CP*CP*TP*TP*CP)-3' | Arabidopsis thaliana | Structure of LEAFY transcription factor from Arabidopsis thaliana in complex with DNA from AP1 promoter | X-ray diffraction | 2.104 | 20 | 2008-09-23 | |||
| 9 | 2VY2|1|W | 5'-D(*AP*TP*TP*TP*AP*AP*TP*CP*CP*AP *AP*TP*GP*GP*TP*TP*AP*CP*AP*A)-3' | Arabidopsis thaliana | Structure of LEAFY transcription factor from Arabidopsis thaliana in complex with DNA from AG-I promoter | X-ray diffraction | 2.3 | 20 | 2008-09-23 | |||
| 10 | 1ZG5|1|C+ 1ZG5|1|D | 5'-D(*CP*GP*TP*AP*CP*CP*CP*CP*TP*AP*TP*AP*GP*GP*GP*GP*TP*AP*CP*G)-3' | NarL complexed to narG-89 promoter palindromic tail-to-tail DNA site | X-ray diffraction | 2.3 | 40 | 2005-11-22 | ||||
| 11 | 1ZG5|1|G+ 1ZG5|1|H | 5'-D(*CP*GP*TP*AP*CP*CP*CP*CP*TP*AP*TP*AP*GP*GP*GP*GP*TP*AP*CP*G)-3' | NarL complexed to narG-89 promoter palindromic tail-to-tail DNA site | X-ray diffraction | 2.3 | 40 | 2005-11-22 | ||||
| 12 | 1PUF|1|D+ 1PUF|1|E | 5'-D(*AP*CP*TP*CP*TP*AP*TP*GP*AP*TP*TP*TP*AP*CP*GP*AP*CP*GP*CP*T)-3', 5'-D(*TP*AP*GP*CP*GP*TP*CP*GP*TP*AP*AP*AP*TP*CP*AP*TP*AP*GP*AP*G)-3' | Crystal Structure of HoxA9 and Pbx1 homeodomains bound to DNA | X-ray diffraction | 1.9 | 40 | 2003-09-02 | ||||
| 13 | 1A6Y|1|C+ 1A6Y|1|D | DNA (5'-D(*CP*AP*AP*CP*TP*AP*GP*GP*TP*CP*AP*CP*(5IT)P*AP*GP*GP*TP*CP*AP*G)-3'), DNA (5'-D(*CP*TP*GP*AP*CP*CP*TP*AP*GP*TP*GP*AP*CP*CP*TP*AP*GP*TP*TP*G)-3') | REVERBA ORPHAN NUCLEAR RECEPTOR/DNA COMPLEX | X-ray diffraction | 2.3 | 40 | 1998-10-21 | ||||
| 14 | 1GA5|1|C+ 1GA5|1|D | 5'-D(*CP*AP*AP*CP*TP*AP*GP*GP*TP*CP*AP*CP*TP*AP*GP*GP*TP*CP*AP*G)-3', 5'-D(*CP*TP*GP*AP*CP*CP*TP*AP*GP*TP*GP*AP*CP*CP*TP*AP*GP*TP*(5IT)P*G)-3' | CRYSTAL STRUCTURE OF THE ORPHAN NUCLEAR RECEPTOR REV-ERB(ALPHA) DNA-BINDING DOMAIN BOUND TO ITS COGNATE RESPONSE ELEMENT | X-ray diffraction | 2.4 | 40 | 2001-11-16 | ||||
| 15 | 1GA5|1|G+ 1GA5|1|H | 5'-D(*CP*AP*AP*CP*TP*AP*GP*GP*TP*CP*AP*CP*TP*AP*GP*GP*TP*CP*AP*G)-3', 5'-D(*CP*TP*GP*AP*CP*CP*TP*AP*GP*TP*GP*AP*CP*CP*TP*AP*GP*TP*(5IT)P*G)-3' | CRYSTAL STRUCTURE OF THE ORPHAN NUCLEAR RECEPTOR REV-ERB(ALPHA) DNA-BINDING DOMAIN BOUND TO ITS COGNATE RESPONSE ELEMENT | X-ray diffraction | 2.4 | 40 | 2001-11-16 | ||||
| 16 | 3C2I|1|B+ 3C2I|1|C | DNA (5'-D(*DAP*DTP*DAP*DGP*DAP*DAP*DGP*DAP*DAP*DTP*DTP*DCP*(5CM)P*DGP*DTP*DTP*DCP*DCP*DAP*DG)-3'), DNA (5'-D(*DTP*DCP*DTP*DGP*DGP*DAP*DAP*(5CM)P*DGP*DGP*DAP*DAP*DTP*DTP*DCP*DTP*DTP*DCP*DTP*DA)-3') | The Crystal Structure of Methyl-CpG Binding Domain of Human MeCP2 in Complex with a Methylated DNA Sequence from BDNF | X-ray diffraction | 2.5 | 40 | 2008-05-13 | ||||
| 17 | 1ZG1|1|C+ 1ZG1|1|D | 5'-D(*CP*GP*TP*AP*CP*CP*CP*AP*TP*TP*AP*AP*GP*GP*AP*GP*TP*AP*CP*G)-3', 5'-D(*CP*GP*TP*AP*CP*TP*CP*CP*TP*TP*AP*AP*TP*GP*GP*GP*TP*AP*CP*G)-3' | NarL complexed to nirB promoter non-palindromic tail-to-tail DNA site | X-ray diffraction | 2.3 | 40 | 2005-11-22 | ||||
| 18 | 1ZG1|1|G+ 1ZG1|1|H | 5'-D(*CP*GP*TP*AP*CP*CP*CP*AP*TP*TP*AP*AP*GP*GP*AP*GP*TP*AP*CP*G)-3', 5'-D(*CP*GP*TP*AP*CP*TP*CP*CP*TP*TP*AP*AP*TP*GP*GP*GP*TP*AP*CP*G)-3' | NarL complexed to nirB promoter non-palindromic tail-to-tail DNA site | X-ray diffraction | 2.3 | 40 | 2005-11-22 | ||||
| 19 | 2WTY|1|C+ 2WTY|1|D | DNA (5'-D(*TP*AP*AP*TP*TP*GP*CP*TP*GP*AP*CP*TP*CP*AP *GP*CP*AP*AP*AP*T)-3'), DNA (5'-D(*TP*AP*TP*TP*TP*GP*CP*TP*GP*AP*GP*TP*CP*AP *GP*CP*AP*AP*TP*T)-3') | Crystal structure of the homodimeric MafB in complex with the T-MARE binding site | X-ray diffraction | 2.9 | 39 | 2010-12-08 | ||||
| 20 | 1HLZ|1|C+ 1HLZ|1|D | 5'-D(*CP*AP*AP*CP*TP*AP*GP*GP*TP*CP*AP*CP*TP*AP*GP*GP*TP*CP*AP*G)-3', 5'-D(*CP*TP*GP*AP*CP*CP*TP*AP*GP*TP*GP*AP*CP*CP*TP*AP*GP*TP*TP*G)-3' | CRYSTAL STRUCTURE OF THE ORPHAN NUCLEAR RECEPTOR REV-ERB(ALPHA) DNA-BINDING DOMAIN BOUND TO ITS COGNATE RESPONSE ELEMENT | X-ray diffraction | 2.8 | 40 | 2001-11-16 | ||||
| 21 | 3COQ|1|D+ 3COQ|1|E | DNA (5'-D(*DAP*DCP*DCP*DGP*DGP*DAP*DGP*DGP*DAP*DCP*DAP*DGP*DTP*DCP*DCP*DTP*DCP*DCP*DGP*DG)-3'), DNA (5'-D(*DTP*DCP*DCP*DGP*DGP*DAP*DGP*DGP*DAP*DCP*DTP*DGP*DTP*DCP*DCP*DTP*DCP*DCP*DGP*DG)-3') | synthetic construct | Structural Basis for Dimerization in DNA Recognition by Gal4 | X-ray diffraction | 2.4 | 40 | 2008-07-01 | |||
| 22 | 1LE8|1|C+ 1LE8|1|D | 5'-D(*AP*CP*AP*TP*GP*TP*AP*AP*AP*AP*AP*TP*TP*TP*AP*CP*AP*TP*CP*A)-3', 5'-D(*TP*TP*GP*AP*TP*GP*TP*AP*AP*AP*TP*TP*TP*TP*TP*AP*CP*AP*TP*G)-3' | Crystal Structure of the MATa1/MATalpha2-3A Heterodimer Bound to DNA Complex | X-ray diffraction | 2.3 | 40 | 2002-05-03 | ||||
| 23 | 1FLO|1|F+ 1FLO|1|E | SYMMETRIZED FRT DNA SITES | FLP Recombinase-Holliday Junction Complex I | X-ray diffraction | 2.65 | 0 | 2000-09-04 | ||||
| 24 | 1FLO|1|H+ 1FLO|1|G | SYMMETRIZED FRT DNA SITES | FLP Recombinase-Holliday Junction Complex I | X-ray diffraction | 2.65 | 0 | 2000-09-04 | ||||
| 25 | 1FLO|1|J+ 1FLO|1|I | SYMMETRIZED FRT DNA SITES | FLP Recombinase-Holliday Junction Complex I | X-ray diffraction | 2.65 | 0 | 2000-09-04 | ||||
| 26 | 1FLO|1|L+ 1FLO|1|K | SYMMETRIZED FRT DNA SITES | FLP Recombinase-Holliday Junction Complex I | X-ray diffraction | 2.65 | 0 | 2000-09-04 | ||||
| 27 | 3DFX|1|X+ 3DFX|1|Y | DNA (5'-D(*DAP*DAP*DGP*DGP*DTP*DTP*DAP*DTP*DCP*DTP*DCP*DTP*DGP*DAP*DTP*DTP*DTP*DAP*DTP*DC)-3'), DNA (5'-D(*DTP*DTP*DGP*DAP*DTP*DAP*DAP*DAP*DTP*DCP*DAP*DGP*DAP*DGP*DAP*DTP*DAP*DAP*DCP*DC)-3') | Opposite GATA DNA binding | X-ray diffraction | 2.7 | 40 | 2008-07-29 | ||||
| 28 | 2R5Y|1|C+ 2R5Y|1|D | DNA (5'-D(*DAP*DCP*DTP*DCP*DTP*DAP*DTP*DGP*DAP*DTP*DTP*DTP*DAP*DTP*DGP*DGP*DGP*DCP*DTP*DG)-3'), DNA (5'-D(*DTP*DCP*DAP*DGP*DCP*DCP*DCP*DAP*DTP*DAP*DAP*DAP*DTP*DCP*DAP*DTP*DAP*DGP*DAP*DG)-3') | synthetic construct | Structure of Scr/Exd complex bound to a consensus Hox-Exd site | X-ray diffraction | 2.6 | 40 | 2008-02-05 | |||
| 29 | 2R5Z|1|C+ 2R5Z|1|D | DNA (5'-D(*DAP*DCP*DTP*DCP*DTP*DAP*DAP*DGP*DAP*DTP*DTP*DAP*DAP*DTP*DCP*DGP*DGP*DCP*DTP*DG)-3'), DNA (5'-D(*DTP*DCP*DAP*DGP*DCP*DCP*DGP*DAP*DTP*DTP*DAP*DAP*DTP*DCP*DTP*DTP*DAP*DGP*DAP*DG)-3') | synthetic construct | Structure of Scr/Exd complex bound to a DNA sequence derived from the fkh gene | X-ray diffraction | 2.6 | 40 | 2008-02-05 | |||
| 30 | 1A02|1|A+ 1A02|1|B | DNA (5'-D(*DAP*DAP*DCP*DTP*DAP*DTP*DGP*DAP*DAP*DAP*DCP*DAP*DAP*DAP*DTP*DTP*DTP*DTP*DCP*DC)-3'), DNA (5'-D(*DTP*DTP*DGP*DGP*DAP*DAP*DAP*DAP*DTP*DTP*DTP*DGP*DTP*DTP*DTP*DCP*DAP*DTP*DAP*DG)-3') | STRUCTURE OF THE DNA BINDING DOMAINS OF NFAT, FOS AND JUN BOUND TO DNA | X-ray diffraction | 2.7 | 40 | 1998-05-27 | ||||
| 31 | 2Q2K|1|F | DNA (5'-D(*AP*GP*TP*AP*TP*AP*(5IU)P*AP*CP*(5IU)P*AP*GP*TP*AP*TP*AP*TP*AP*CP*T)-3') | Structure of nucleic-acid binding protein | X-ray diffraction | 3 | 20 | 2008-02-05 | ||||
| 32 | 1L3L|1|E+ 1L3L|1|G | 5'-D(*GP*AP*TP*GP*TP*GP*CP*AP*GP*AP*TP*CP*TP*GP*CP*AP*CP*AP*TP*C)-3' | Crystal structure of a bacterial quorum-sensing transcription factor complexed with pheromone and DNA | X-ray diffraction | 1.66 | 40 | 2002-07-03 | ||||
| 33 | 1L3L|1|F+ 1L3L|1|H | 5'-D(*GP*AP*TP*GP*TP*GP*CP*AP*GP*AP*TP*CP*TP*GP*CP*AP*CP*AP*TP*C)-3' | Crystal structure of a bacterial quorum-sensing transcription factor complexed with pheromone and DNA | X-ray diffraction | 1.66 | 40 | 2002-07-03 | ||||
| 34 | 1LMB|1|1+ 1LMB|1|2 | DNA (5'-D(*AP*AP*TP*AP*CP*CP*AP*CP*TP*GP*GP*CP*GP*GP*TP*GP*A P*TP*AP*T)-3'), DNA (5'-D(*TP*AP*TP*AP*TP*CP*AP*CP*CP*GP*CP*CP*AP*GP*TP*GP*G P*TP*AP*T)-3') | REFINED 1.8 ANGSTROM CRYSTAL STRUCTURE OF THE LAMBDA REPRESSOR-OPERATOR COMPLEX | X-ray diffraction | 1.8 | 40 | 1991-11-05 | ||||
| 35 | 1LLI|1|D+ 1LLI|1|E | DNA (5'-D(*AP*AP*TP*AP*CP*CP*AP*CP*TP*GP*GP*CP*GP*GP*TP*GP*A P*TP*AP*T)-3'), DNA (5'-D(*TP*AP*TP*AP*TP*CP*AP*CP*CP*GP*CP*CP*AP*GP*TP*GP*G P*TP*AP*T)-3') | THE CRYSTAL STRUCTURE OF A MUTANT PROTEIN WITH ALTERED BUT IMPROVED HYDROPHOBIC CORE PACKING | X-ray diffraction | 2.1 | 40 | 1994-08-31 | ||||
| 36 | 1JE8|1|C+ 1JE8|1|D | 5'-D(*CP*GP*TP*AP*CP*CP*CP*AP*TP*TP*AP*AP*TP*GP*GP*GP*TP*AP*CP*G)-3' | Two-Component response regulator NarL/DNA Complex: DNA Bending Found in a High Affinity Site | X-ray diffraction | 2.12 | 40 | 2002-09-27 | ||||
| 37 | 1JE8|1|G+ 1JE8|1|H | 5'-D(*CP*GP*TP*AP*CP*CP*CP*AP*TP*TP*AP*AP*TP*GP*GP*GP*TP*AP*CP*G)-3' | Two-Component response regulator NarL/DNA Complex: DNA Bending Found in a High Affinity Site | X-ray diffraction | 2.12 | 40 | 2002-09-27 | ||||
| 38 | 1JNM|1|C+ 1JNM|1|D | 5'-D(*CP*GP*TP*CP*GP*AP*TP*GP*AP*CP*GP*TP*CP*AP*TP*CP*GP*AP*CP*G)-3' | Crystal Structure of the Jun/CRE Complex | X-ray diffraction | 2.2 | 40 | 2003-06-03 | ||||
| 39 | 1B72|1|D+ 1B72|1|E | DNA (5'-D(*AP*CP*TP*CP*TP*AP*TP*GP*AP*TP*TP*GP*AP*TP*CP*GP*GP*CP*TP*G)-3'), DNA (5'-D(*TP*CP*AP*GP*CP*CP*GP*AP*TP*CP*AP*AP*TP*CP*AP*TP*AP*GP*AP*G)-3') | PBX1, HOMEOBOX PROTEIN HOX-B1/DNA TERNARY COMPLEX | X-ray diffraction | 2.35 | 40 | 1999-02-19 | ||||
| 40 | 2RAM|1|C+ 2RAM|1|D | DNA (5'-D(*CP*GP*GP*CP*TP*GP*GP*AP*AP*AP*TP*(5IU)P*(5IU)P*CP*CP*AP*GP*CP*CP*G)-3') | A NOVEL DNA RECOGNITION MODE BY NF-KB P65 HOMODIMER | X-ray diffraction | 2.4 | 40 | 1998-05-27 | ||||
| 41 | 1RPE|1|A+ 1RPE|1|B | DNA (5'-D(*AP*CP*AP*AP*AP*CP*AP*AP*GP*AP*TP*AP*CP*AP*TP*TP*G P*TP*AP*T)-3'), DNA (5'-D(*TP*AP*TP*AP*CP*AP*AP*TP*GP*TP*AP*TP*CP*TP*TP*GP*T P*TP*TP*G)-3') | THE PHAGE 434 OR2/R1-69 COMPLEX AT 2.5 ANGSTROMS RESOLUTION | X-ray diffraction | 2.5 | 40 | 1994-01-31 | ||||
| 42 | 3CRO|1|A+ 3CRO|1|B | DNA (5'-D(*AP*AP*GP*TP*AP*CP*AP*AP*AP*CP*TP*TP*TP*CP*TP*TP*G P*TP*AP*T)-3'), DNA (5'-D(*TP*AP*TP*AP*CP*AP*AP*GP*AP*AP*AP*GP*TP*TP*TP*GP*T P*AP*CP*T)-3') | THE PHAGE 434 CRO/OR1 COMPLEX AT 2.5 ANGSTROMS RESOLUTION | X-ray diffraction | 2.5 | 40 | 1991-10-15 | ||||
| 43 | 1PER|1|A+ 1PER|1|B | DNA (5'-D(*AP*AP*GP*TP*AP*CP*AP*GP*TP*TP*TP*TP*TP*CP*TP*TP*G P*TP*AP*T)-3'), DNA (5'-D(*TP*AP*TP*AP*CP*AP*AP*GP*AP*AP*AP*AP*AP*CP*TP*GP*T P*AP*CP*T)-3') | THE COMPLEX BETWEEN PHAGE 434 REPRESSION DNA-BINDING DOMAIN AND OPERATOR SITE OR3: STRUCTURAL DIFFERENCES BETWEEN CONSENSUS AND NON-CONSENSUS HALF-SITES | X-ray diffraction | 2.5 | 40 | 1994-01-31 | ||||
| 44 | 1HWT|1|A+ 1HWT|1|B | DNA (5'-D(*GP*CP*GP*CP*TP*AP*TP*TP*AP*TP*CP*GP*CP*TP*AP*TP*TP*AP*GP*C)-3'), DNA (5'-D(*GP*CP*TP*AP*AP*TP*AP*GP*CP*GP*AP*TP*AP*AP*TP*AP*GP*CP*GP*C)-3') | STRUCTURE OF A HAP1/DNA COMPLEX REVEALS DRAMATICALLY ASYMMETRIC DNA BINDING BY A HOMODIMERIC PROTEIN | X-ray diffraction | 2.5 | 40 | 1999-11-10 | ||||
| 45 | 2HAP|1|A+ 2HAP|1|B | DNA (5'-D(*AP*CP*GP*CP*TP*AP*TP*TP*AP*TP*CP*GP*CP*TP*AP*TP*TP*AP*GP*T)-3'), DNA (5'-D(*AP*CP*TP*AP*AP*TP*AP*GP*CP*GP*AP*TP*AP*AP*TP*AP*GP*CP*GP*T)-3') | STRUCTURE OF A HAP1-18/DNA COMPLEX REVEALS THAT PROTEIN/DNA INTERACTIONS CAN HAVE DIRECT ALLOSTERIC EFFECTS ON TRANSCRIPTIONAL ACTIVATION | X-ray diffraction | 2.5 | 40 | 1999-11-10 | ||||
| 46 | 2OR1|1|A+ 2OR1|1|B | DNA (5'-D(*AP*AP*GP*TP*AP*CP*AP*AP*AP*CP*TP*TP*TP*CP*TP*TP*G P*TP*AP*T)-3'), DNA (5'-D(*TP*AP*TP*AP*CP*AP*AP*GP*AP*AP*AP*GP*TP*TP*TP*GP*T P*AP*CP*T)-3') | RECOGNITION OF A DNA OPERATOR BY THE REPRESSOR OF PHAGE 434. A VIEW AT HIGH RESOLUTION | X-ray diffraction | 2.5 | 40 | 1989-09-05 | ||||
| 47 | 1UBD|1|A+ 1UBD|1|B | DNA (5'-D(*AP*GP*GP*GP*TP*CP*TP*CP*CP*AP*TP*TP*TP*TP*GP*AP*A P*GP*CP*G)-3'), DNA (5'-D(*CP*GP*CP*TP*TP*CP*AP*AP*AP*AP*TP*GP*GP*AP*GP*AP*C P*CP*CP*T)-3') | CO-CRYSTAL STRUCTURE OF HUMAN YY1 ZINC FINGER DOMAIN BOUND TO THE ADENO-ASSOCIATED VIRUS P5 INITIATOR ELEMENT | X-ray diffraction | 2.5 | 40 | 1996-12-23 | ||||
| 48 | 1HWT|1|E+ 1HWT|1|F | DNA (5'-D(*GP*CP*GP*CP*TP*AP*TP*TP*AP*TP*CP*GP*CP*TP*AP*TP*TP*AP*GP*C)-3'), DNA (5'-D(*GP*CP*TP*AP*AP*TP*AP*GP*CP*GP*AP*TP*AP*AP*TP*AP*GP*CP*GP*C)-3') | STRUCTURE OF A HAP1/DNA COMPLEX REVEALS DRAMATICALLY ASYMMETRIC DNA BINDING BY A HOMODIMERIC PROTEIN | X-ray diffraction | 2.5 | 40 | 1999-11-10 | ||||
| 49 | 1RAM|1|C+ 1RAM|1|D | DNA (5'-D(*CP*GP*GP*CP*TP*GP*GP*AP*AP*AP*TP*TP*TP*CP*CP*AP*GP*CP*CP*G)-3') | A NOVEL DNA RECOGNITION MODE BY NF-KB P65 HOMODIMER | X-ray diffraction | 2.7 | 40 | 1998-05-27 | ||||
| 50 | 1FOK|1|B+ 1FOK|1|C | DNA (5'-D(*AP*TP*GP*AP*CP*TP*AP*GP*CP*GP*TP*TP*AP*TP*CP*AP*T P*CP*CP*G)-3'), DNA (5'-D(*TP*CP*GP*GP*AP*TP*GP*AP*TP*AP*AP*CP*GP*CP*TP*AP*G P*TP*CP*A)-3') | Planomicrobium okeanokoites | STRUCTURE OF RESTRICTION ENDONUCLEASE FOKI BOUND TO DNA | X-ray diffraction | 2.8 | 40 | 1997-12-03 | |||
| 51 | 1QP9|1|E+ 1QP9|1|F | DNA (5'-D(*AP*CP*GP*CP*TP*AP*TP*TP*AP*TP*CP*GP*CP*TP*AP*TP*TP*AP*GP*T)-3'), DNA (5'-D(*AP*CP*TP*AP*AP*TP*AP*GP*CP*GP*AP*TP*AP*AP*TP*AP*GP*CP*GP*T)-3') | STRUCTURE OF HAP1-PC7 COMPLEXED TO THE UAS OF CYC7 | X-ray diffraction | 2.8 | 40 | 2000-10-09 | ||||
| 52 | 1QP9|1|G+ 1QP9|1|H | DNA (5'-D(*AP*CP*GP*CP*TP*AP*TP*TP*AP*TP*CP*GP*CP*TP*AP*TP*TP*AP*GP*T)-3'), DNA (5'-D(*AP*CP*TP*AP*AP*TP*AP*GP*CP*GP*AP*TP*AP*AP*TP*AP*GP*CP*GP*T)-3') | STRUCTURE OF HAP1-PC7 COMPLEXED TO THE UAS OF CYC7 | X-ray diffraction | 2.8 | 37 | 2000-10-09 | ||||
| 53 | 1YSA|1|A+ 1YSA|1|B | DNA (5'-D(*AP*AP*AP*CP*TP*GP*GP*AP*TP*GP*AP*GP*TP*CP*AP*TP*A P*GP*GP*A)-3'), DNA (5'-D(*TP*TP*CP*CP*TP*AP*TP*GP*AP*CP*TP*CP*AP*TP*CP*CP*A P*GP*TP*T)-3') | THE GCN4 BASIC REGION LEUCINE ZIPPER BINDS DNA AS A DIMER OF UNINTERRUPTED ALPHA HELICES: CRYSTAL STRUCTURE OF THE PROTEIN-DNA COMPLEX | X-ray diffraction | 2.9 | 40 | 1993-10-31 |
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 | 1FLO|1|F+ 1FLO|1|E | FLP Recombinase-Holliday Junction Complex I | X-RAY DIFFRACTION | 2.65 | 0 | Holliday junction,structure | enzyme,recombinase | |
| 2 | 1FLO|1|H+ 1FLO|1|G | FLP Recombinase-Holliday Junction Complex I | X-RAY DIFFRACTION | 2.65 | 0 | Holliday junction,structure | enzyme,recombinase | |
| 3 | 1FLO|1|L+ 1FLO|1|K | FLP Recombinase-Holliday Junction Complex I | X-RAY DIFFRACTION | 2.65 | 0 | Holliday junction,structure | enzyme,recombinase | |
| 4 | 1FLO|1|J+ 1FLO|1|I | FLP Recombinase-Holliday Junction Complex I | X-RAY DIFFRACTION | 2.65 | 0 | Holliday junction,structure | enzyme,recombinase | |
| 5 | 1LE8|1|C+ 1LE8|1|D | Crystal Structure of the MATa1/MATalpha2-3A Heterodimer Bound to DNA Complex | X-RAY DIFFRACTION | 2.3 | 40 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),homeodomain,regulatory,transcription | |
| 6 | 1JE8|1|C+ 1JE8|1|D | Two-Component response regulator NarL/DNA Complex: DNA Bending Found in a High Affinity Site | X-RAY DIFFRACTION | 2.12 | 40 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),regulatory,transcription,winged helix/forkhead | |
| 7 | 1JE8|1|G+ 1JE8|1|H | Two-Component response regulator NarL/DNA Complex: DNA Bending Found in a High Affinity Site | X-RAY DIFFRACTION | 2.12 | 40 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),regulatory,transcription,winged helix/forkhead | |
| 8 | 1ZG5|1|G+ 1ZG5|1|H | NarL complexed to narG-89 promoter palindromic tail-to-tail DNA site | X-RAY DIFFRACTION | 2.3 | 40 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),regulatory,transcription,winged helix/forkhead | |
| 9 | 1ZG5|1|C+ 1ZG5|1|D | NarL complexed to narG-89 promoter palindromic tail-to-tail DNA site | X-RAY DIFFRACTION | 2.3 | 40 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),regulatory,transcription,winged helix/forkhead | |
| 10 | 1ZG1|1|G+ 1ZG1|1|H | NarL complexed to nirB promoter non-palindromic tail-to-tail DNA site | X-RAY DIFFRACTION | 2.3 | 40 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),regulatory,transcription,winged helix/forkhead | |
| 11 | 1ZG1|1|C+ 1ZG1|1|D | NarL complexed to nirB promoter non-palindromic tail-to-tail DNA site | X-RAY DIFFRACTION | 2.3 | 40 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),regulatory,transcription,winged helix/forkhead | |
| 12 | 2Q2K|1|F | Structure of nucleic-acid binding protein | X-RAY DIFFRACTION | 3 | 20 | double helix,structure | centromere,chromatin,structural | |
| 13 | 1L3L|1|E+ 1L3L|1|G | Crystal structure of a bacterial quorum-sensing transcription factor complexed with pheromone and DNA | X-RAY DIFFRACTION | 1.66 | 40 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),regulatory,transcription,winged helix/forkhead | |
| 14 | 1L3L|1|F+ 1L3L|1|H | Crystal structure of a bacterial quorum-sensing transcription factor complexed with pheromone and DNA | X-RAY DIFFRACTION | 1.66 | 40 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),regulatory,transcription,winged helix/forkhead | |
| 15 | 3JXB|1|A+ 3JXB|1|B | Crystal structure of the P22 c2 repressor protein in complex with synthetic operator 9C | X-RAY DIFFRACTION | 1.67 | 40 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),lambda repressor-like,regulatory,transcription | |
| 16 | 3JXC|1|A+ 3JXC|1|B | Crystal structure of the P22 c2 repressor protein in complex with synthetic operator 9T in the presence of Tl+ | X-RAY DIFFRACTION | 1.9 | 40 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),lambda repressor-like,regulatory,transcription | |
| 17 | 3JXD|1|A+ 3JXD|1|B | Crystal structure of the P22 c2 repressor protein in complex with synthetic operator 9C in the presence of Rb+ | X-RAY DIFFRACTION | 2.1 | 40 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),lambda repressor-like,regulatory,transcription | |
| 18 | 2R1J|1|A+ 2R1J|1|B | Crystal Structure of the P22 c2 Repressor protein in complex with the synthetic operator 9T | X-RAY DIFFRACTION | 1.53 | 40 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),lambda repressor-like,regulatory,transcription | |
| 19 | 1FOK|1|B+ 1FOK|1|C | STRUCTURE OF RESTRICTION ENDONUCLEASE FOKI BOUND TO DNA | X-RAY DIFFRACTION | 2.8 | 40 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease | |
| 20 | 1PER|1|A+ 1PER|1|B | THE COMPLEX BETWEEN PHAGE 434 REPRESSION DNA-BINDING DOMAIN AND OPERATOR SITE OR3: STRUCTURAL DIFFERENCES BETWEEN CONSENSUS AND NON-CONSENSUS HALF-SITES | X-RAY DIFFRACTION | 2.5 | 40 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),lambda repressor-like,regulatory,transcription | |
| 21 | 2OR1|1|A+ 2OR1|1|B | RECOGNITION OF A DNA OPERATOR BY THE REPRESSOR OF PHAGE 434. A VIEW AT HIGH RESOLUTION | X-RAY DIFFRACTION | 2.5 | 40 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),lambda repressor-like,regulatory,transcription | |
| 22 | 1RPE|1|A+ 1RPE|1|B | THE PHAGE 434 OR2/R1-69 COMPLEX AT 2.5 ANGSTROMS RESOLUTION | X-RAY DIFFRACTION | 2.5 | 40 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),lambda repressor-like,regulatory,transcription | |
| 23 | 3CRO|1|A+ 3CRO|1|B | THE PHAGE 434 CRO/OR1 COMPLEX AT 2.5 ANGSTROMS RESOLUTION | X-RAY DIFFRACTION | 2.5 | 40 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),lambda repressor-like,regulatory,transcription | |
| 24 | 2HAN|1|C+ 2HAN|1|D | Structural basis of heterodimeric ecdysteroid receptor interaction with natural response element hsp27 gene promoter | X-RAY DIFFRACTION | 1.95 | 40 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),Zinc-coordinating,nuclear receptor ZnC4,regulatory,transcription | |
| 25 | 1LLI|1|D+ 1LLI|1|E | THE CRYSTAL STRUCTURE OF A MUTANT PROTEIN WITH ALTERED BUT IMPROVED HYDROPHOBIC CORE PACKING | X-RAY DIFFRACTION | 2.1 | 40 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),lambda repressor-like,regulatory,transcription | |
| 26 | 1LMB|1|1+ 1LMB|1|2 | REFINED 1.8 ANGSTROM CRYSTAL STRUCTURE OF THE LAMBDA REPRESSOR-OPERATOR COMPLEX | X-RAY DIFFRACTION | 1.8 | 40 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),lambda repressor-like,regulatory,transcription | |
| 27 | 2WTY|1|C+ 2WTY|1|D | Crystal structure of the homodimeric MafB in complex with the T-MARE binding site | X-RAY DIFFRACTION | 2.9 | 39 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),basic transcription factor,leucine zipper (bZIP),regulatory,transcription | |
| 28 | 3COQ|1|D+ 3COQ|1|E | Structural Basis for Dimerization in DNA Recognition by Gal4 | X-RAY DIFFRACTION | 2.4 | 40 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),Zinc-coordinating,regulatory,transcription | |
| 29 | 3DFX|1|X+ 3DFX|1|Y | Opposite GATA DNA binding | X-RAY DIFFRACTION | 2.7 | 40 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),Zinc-coordinating,nuclear receptor ZnC4,regulatory,transcription | |
| 30 | 1JNM|1|C+ 1JNM|1|D | Crystal Structure of the Jun/CRE Complex | X-RAY DIFFRACTION | 2.2 | 40 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),basic transcription factor,leucine zipper (bZIP),regulatory,transcription | |
| 31 | 1HLZ|1|C+ 1HLZ|1|D | CRYSTAL STRUCTURE OF THE ORPHAN NUCLEAR RECEPTOR REV-ERB(ALPHA) DNA-BINDING DOMAIN BOUND TO ITS COGNATE RESPONSE ELEMENT | X-RAY DIFFRACTION | 2.8 | 40 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),Zinc-coordinating,nuclear receptor ZnC4,regulatory,transcription | |
| 32 | 1GA5|1|G+ 1GA5|1|H | CRYSTAL STRUCTURE OF THE ORPHAN NUCLEAR RECEPTOR REV-ERB(ALPHA) DNA-BINDING DOMAIN BOUND TO ITS COGNATE RESPONSE ELEMENT | X-RAY DIFFRACTION | 2.4 | 40 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),Zinc-coordinating,nuclear receptor ZnC4,regulatory,transcription | |
| 33 | 1GA5|1|C+ 1GA5|1|D | CRYSTAL STRUCTURE OF THE ORPHAN NUCLEAR RECEPTOR REV-ERB(ALPHA) DNA-BINDING DOMAIN BOUND TO ITS COGNATE RESPONSE ELEMENT | X-RAY DIFFRACTION | 2.4 | 40 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),Zinc-coordinating,nuclear receptor ZnC4,regulatory,transcription | |
| 34 | 1A6Y|1|C+ 1A6Y|1|D | REVERBA ORPHAN NUCLEAR RECEPTOR/DNA COMPLEX | X-RAY DIFFRACTION | 2.3 | 40 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),Zinc-coordinating,nuclear receptor ZnC4,regulatory,transcription | |
| 35 | 1UBD|1|A+ 1UBD|1|B | CO-CRYSTAL STRUCTURE OF HUMAN YY1 ZINC FINGER DOMAIN BOUND TO THE ADENO-ASSOCIATED VIRUS P5 INITIATOR ELEMENT | X-RAY DIFFRACTION | 2.5 | 40 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),Zinc finger C2H2,Zinc-coordinating,regulatory,transcription | |
| 36 | 1B72|1|D+ 1B72|1|E | PBX1, HOMEOBOX PROTEIN HOX-B1/DNA TERNARY COMPLEX | X-RAY DIFFRACTION | 2.35 | 40 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),homeodomain,regulatory,transcription | |
| 37 | 3C2I|1|B+ 3C2I|1|C | The Crystal Structure of Methyl-CpG Binding Domain of Human MeCP2 in Complex with a Methylated DNA Sequence from BDNF | X-RAY DIFFRACTION | 2.5 | 40 | B-form double helix,double helix,structure | chromatin,structural | |
| 38 | 1YSA|1|A+ 1YSA|1|B | THE GCN4 BASIC REGION LEUCINE ZIPPER BINDS DNA AS A DIMER OF UNINTERRUPTED ALPHA HELICES: CRYSTAL STRUCTURE OF THE PROTEIN-DNA COMPLEX | X-RAY DIFFRACTION | 2.9 | 40 | DNA-binding transcription factor (TF),basic transcription factor,leucine zipper (bZIP),regulatory,transcription | ||
| 39 | 2VY1|1|W | Structure of LEAFY transcription factor from Arabidopsis thaliana in complex with DNA from AP1 promoter | X-RAY DIFFRACTION | 2.104 | 20 | B-form double helix,double helix,feature,mispair,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),homeodomain,regulatory,transcription | |
| 40 | 2VY2|1|W | Structure of LEAFY transcription factor from Arabidopsis thaliana in complex with DNA from AG-I promoter | X-RAY DIFFRACTION | 2.3 | 20 | B-form double helix,double helix,feature,mispair,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),homeodomain,regulatory,transcription | |
| 41 | 2R5Y|1|C+ 2R5Y|1|D | Structure of Scr/Exd complex bound to a consensus Hox-Exd site | X-RAY DIFFRACTION | 2.6 | 40 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),homeodomain,regulatory,transcription | |
| 42 | 2R5Z|1|C+ 2R5Z|1|D | Structure of Scr/Exd complex bound to a DNA sequence derived from the fkh gene | X-RAY DIFFRACTION | 2.6 | 40 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),homeodomain,regulatory,transcription | |
| 43 | 2RAM|1|C+ 2RAM|1|D | A NOVEL DNA RECOGNITION MODE BY NF-KB P65 HOMODIMER | X-RAY DIFFRACTION | 2.4 | 40 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),immunoglobulin (Ig) fold,regulatory,rel homology,transcription | |
| 44 | 1RAM|1|C+ 1RAM|1|D | A NOVEL DNA RECOGNITION MODE BY NF-KB P65 HOMODIMER | X-RAY DIFFRACTION | 2.7 | 40 | double helix,structure | DNA-binding transcription factor (TF),immunoglobulin (Ig) fold,regulatory,rel homology,transcription | |
| 45 | 1A02|1|A+ 1A02|1|B | STRUCTURE OF THE DNA BINDING DOMAINS OF NFAT, FOS AND JUN BOUND TO DNA | X-RAY DIFFRACTION | 2.7 | 40 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),basic transcription factor,immunoglobulin (Ig) fold,leucine zipper (bZIP),regulatory,rel homology,transcription | |
| 46 | 1PUF|1|D+ 1PUF|1|E | Crystal Structure of HoxA9 and Pbx1 homeodomains bound to DNA | X-RAY DIFFRACTION | 1.9 | 40 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),homeodomain,regulatory,transcription | |
| 47 | 1HWT|1|A+ 1HWT|1|B | STRUCTURE OF A HAP1/DNA COMPLEX REVEALS DRAMATICALLY ASYMMETRIC DNA BINDING BY A HOMODIMERIC PROTEIN | X-RAY DIFFRACTION | 2.5 | 40 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),Zinc-coordinating,regulatory,transcription | |
| 48 | 1HWT|1|E+ 1HWT|1|F | STRUCTURE OF A HAP1/DNA COMPLEX REVEALS DRAMATICALLY ASYMMETRIC DNA BINDING BY A HOMODIMERIC PROTEIN | X-RAY DIFFRACTION | 2.5 | 40 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),Zinc-coordinating,regulatory,transcription | |
| 49 | 1QP9|1|G+ 1QP9|1|H | STRUCTURE OF HAP1-PC7 COMPLEXED TO THE UAS OF CYC7 | X-RAY DIFFRACTION | 2.8 | 37 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),Zinc-coordinating,regulatory,transcription | |
| 50 | 1QP9|1|E+ 1QP9|1|F | STRUCTURE OF HAP1-PC7 COMPLEXED TO THE UAS OF CYC7 | X-RAY DIFFRACTION | 2.8 | 40 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),Zinc-coordinating,regulatory,transcription | |
| 51 | 2HAP|1|A+ 2HAP|1|B | STRUCTURE OF A HAP1-18/DNA COMPLEX REVEALS THAT PROTEIN/DNA INTERACTIONS CAN HAVE DIRECT ALLOSTERIC EFFECTS ON TRANSCRIPTIONAL ACTIVATION | X-RAY DIFFRACTION | 2.5 | 40 | double helix,structure | DNA-binding transcription factor (TF),Zinc-coordinating,regulatory,transcription | |
| 52 | 3MGV|1|F+ 3MGV|1|H+ 3MGV|1|E+ 3MGV|1|G | Cre recombinase-DNA transition state | X-RAY DIFFRACTION | 2.29 | 70 | enzyme,recombinase | ||
| 53 | 3MGV|1|K+ 3MGV|1|M+ 3MGV|1|I+ 3MGV|1|L | Cre recombinase-DNA transition state | X-RAY DIFFRACTION | 2.29 | 70 | enzyme,recombinase |
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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