Equivalence class DNA_3.0_82827.1 Current
| # | IFE | Standardized name | Molecule | Organism | Source | Rfam | Title | Method | Res. Å | 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 | 2010-01-19 | ||||
| 2 | 2R1J|1|A+ 2R1J|1|B | 5'-D(*DTP*DAP*DTP*DTP*DTP*DAP*DAP*DGP*DAP*DTP*DAP*DTP*DCP*DTP*DTP*DAP*DAP*DAP*DTP*DG)-3', 5'-D(*DCP*DAP*DTP*DTP*DTP*DAP*DAP*DGP*DAP*DTP*DAP*DTP*DCP*DTP*DTP*DAP*DAP*DAP*DTP*DA)-3' | Crystal Structure of the P22 c2 Repressor protein in complex with the synthetic operator 9T | X-ray diffraction | 1.53 | 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 | 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 | 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 | 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 | 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 | 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 | 2008-09-23 | |||
| 9 | 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 | 2005-11-22 | ||||
| 10 | 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 | 2005-11-22 | ||||
| 11 | 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 | 2008-09-23 | |||
| 12 | 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 | 2001-11-16 | ||||
| 13 | 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 | 2001-11-16 | ||||
| 14 | 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 | 2003-09-02 | ||||
| 15 | 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 | 1998-10-21 | ||||
| 16 | 1ZG1|1|C+ 1ZG1|1|D | 5'-D(*CP*GP*TP*AP*CP*TP*CP*CP*TP*TP*AP*AP*TP*GP*GP*GP*TP*AP*CP*G)-3', 5'-D(*CP*GP*TP*AP*CP*CP*CP*AP*TP*TP*AP*AP*GP*GP*AP*GP*TP*AP*CP*G)-3' | NarL complexed to nirB promoter non-palindromic tail-to-tail DNA site | X-ray diffraction | 2.3 | 2005-11-22 | ||||
| 17 | 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 | 2005-11-22 | ||||
| 18 | 3C2I|1|B+ 3C2I|1|C | 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'), 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') | 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 | 2008-05-13 | ||||
| 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 | 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 | 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 | 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 | 2002-05-03 | ||||
| 23 | 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 | 2008-02-05 | |||
| 24 | 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 | 2008-02-05 | |||
| 25 | 1A02|1|A+ 1A02|1|B | DNA (5'-D(*DTP*DTP*DGP*DGP*DAP*DAP*DAP*DAP*DTP*DTP*DTP*DGP*DTP*DTP*DTP*DCP*DAP*DTP*DAP*DG)-3'), DNA (5'-D(*DAP*DAP*DCP*DTP*DAP*DTP*DGP*DAP*DAP*DAP*DCP*DAP*DAP*DAP*DTP*DTP*DTP*DTP*DCP*DC)-3') | STRUCTURE OF THE DNA BINDING DOMAINS OF NFAT, FOS AND JUN BOUND TO DNA | X-ray diffraction | 2.7 | 1998-05-27 | ||||
| 26 | 3DFX|1|X+ 3DFX|1|Y | DNA (5'-D(*DTP*DTP*DGP*DAP*DTP*DAP*DAP*DAP*DTP*DCP*DAP*DGP*DAP*DGP*DAP*DTP*DAP*DAP*DCP*DC)-3'), DNA (5'-D(*DAP*DAP*DGP*DGP*DTP*DTP*DAP*DTP*DCP*DTP*DCP*DTP*DGP*DAP*DTP*DTP*DTP*DAP*DTP*DC)-3') | Opposite GATA DNA binding | X-ray diffraction | 2.7 | 2008-07-29 | ||||
| 27 | 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 | 2008-02-05 | ||||
| 28 | 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 | 2002-07-03 | ||||
| 29 | 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 | 2002-07-03 | ||||
| 30 | 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 | 1991-11-05 | ||||
| 31 | 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 | 1994-08-31 | ||||
| 32 | 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 | 2002-09-27 | ||||
| 33 | 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 | 2002-09-27 | ||||
| 34 | 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 | 2003-06-03 | ||||
| 35 | 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 | 1999-02-19 | ||||
| 36 | 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 | 1998-05-27 | ||||
| 37 | 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 | 1994-01-31 | ||||
| 38 | 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 | 1991-10-15 | ||||
| 39 | 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 | 1989-09-05 | ||||
| 40 | 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 | 1994-01-31 | ||||
| 41 | 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 | 1999-11-10 | ||||
| 42 | 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 | 1999-11-10 | ||||
| 43 | 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 | 1996-12-23 | ||||
| 44 | 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 | 1999-11-10 | ||||
| 45 | 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 | 1998-05-27 | ||||
| 46 | 1FOK|1|B+ 1FOK|1|C | 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'), 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') | Planomicrobium okeanokoites | STRUCTURE OF RESTRICTION ENDONUCLEASE FOKI BOUND TO DNA | X-ray diffraction | 2.8 | 1997-12-03 | |||
| 47 | 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 | 2000-10-09 | ||||
| 48 | 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 | 2000-10-09 | ||||
| 49 | 1YSA|1|A+ 1YSA|1|B | 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'), 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') | 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 | 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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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 | 1LE8|1|C+1LE8|1|D | Crystal Structure of the MATa1/MATalpha2-3A Heterodimer Bound to DNA Complex | X-RAY DIFFRACTION | 2.3 | 20 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),homeodomain,regulatory,transcription |
| 2 | 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 | 20 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),regulatory,transcription,winged helix/forkhead |
| 3 | 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 | 20 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),regulatory,transcription,winged helix/forkhead |
| 4 | 1ZG1|1|C+1ZG1|1|D | NarL complexed to nirB promoter non-palindromic tail-to-tail DNA site | X-RAY DIFFRACTION | 2.3 | 20 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),regulatory,transcription,winged helix/forkhead |
| 5 | 1ZG1|1|G+1ZG1|1|H | NarL complexed to nirB promoter non-palindromic tail-to-tail DNA site | X-RAY DIFFRACTION | 2.3 | 20 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),regulatory,transcription,winged helix/forkhead |
| 6 | 1ZG5|1|C+1ZG5|1|D | NarL complexed to narG-89 promoter palindromic tail-to-tail DNA site | X-RAY DIFFRACTION | 2.3 | 20 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),regulatory,transcription,winged helix/forkhead |
| 7 | 1ZG5|1|G+1ZG5|1|H | NarL complexed to narG-89 promoter palindromic tail-to-tail DNA site | X-RAY DIFFRACTION | 2.3 | 20 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),regulatory,transcription,winged helix/forkhead |
| 8 | 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 | 20 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),regulatory,transcription,winged helix/forkhead |
| 9 | 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 | 20 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),regulatory,transcription,winged helix/forkhead |
| 10 | 2Q2K|1|F | Structure of nucleic-acid binding protein | X-RAY DIFFRACTION | 3 | 20 | double helix,structure | centromere,chromatin,structural |
| 11 | 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 | 20 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),lambda repressor-like,regulatory,transcription |
| 12 | 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 | 20 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),lambda repressor-like,regulatory,transcription |
| 13 | 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 | 20 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),lambda repressor-like,regulatory,transcription |
| 14 | 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 | 20 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),lambda repressor-like,regulatory,transcription |
| 15 | 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 | 20 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),lambda repressor-like,regulatory,transcription |
| 16 | 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 | 20 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),lambda repressor-like,regulatory,transcription |
| 17 | 3CRO|1|A+3CRO|1|B | THE PHAGE 434 CRO/OR1 COMPLEX AT 2.5 ANGSTROMS RESOLUTION | X-RAY DIFFRACTION | 2.5 | 20 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),lambda repressor-like,regulatory,transcription |
| 18 | 1RPE|1|A+1RPE|1|B | THE PHAGE 434 OR2/R1-69 COMPLEX AT 2.5 ANGSTROMS RESOLUTION | X-RAY DIFFRACTION | 2.5 | 20 | 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 | 20 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease |
| 20 | 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 | 20 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),lambda repressor-like,regulatory,transcription |
| 21 | 1LMB|1|1+1LMB|1|2 | REFINED 1.8 ANGSTROM CRYSTAL STRUCTURE OF THE LAMBDA REPRESSOR-OPERATOR COMPLEX | X-RAY DIFFRACTION | 1.8 | 20 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),lambda repressor-like,regulatory,transcription |
| 22 | 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 | 20 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),Zinc-coordinating,nuclear receptor ZnC4,regulatory,transcription |
| 23 | 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 | 20 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),Zinc-coordinating,nuclear receptor ZnC4,regulatory,transcription |
| 24 | 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 | 20 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),Zinc-coordinating,nuclear receptor ZnC4,regulatory,transcription |
| 25 | 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 | 20 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),Zinc-coordinating,nuclear receptor ZnC4,regulatory,transcription |
| 26 | 1A6Y|1|C+1A6Y|1|D | REVERBA ORPHAN NUCLEAR RECEPTOR/DNA COMPLEX | X-RAY DIFFRACTION | 2.3 | 20 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),Zinc-coordinating,nuclear receptor ZnC4,regulatory,transcription |
| 27 | 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 | 20 | DNA-binding transcription factor (TF),basic transcription factor,leucine zipper (bZIP),regulatory,transcription | |
| 28 | 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 | 20 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),Zinc finger C2H2,Zinc-coordinating,regulatory,transcription |
| 29 | 1B72|1|D+1B72|1|E | PBX1, HOMEOBOX PROTEIN HOX-B1/DNA TERNARY COMPLEX | X-RAY DIFFRACTION | 2.35 | 20 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),homeodomain,regulatory,transcription |
| 30 | 3COQ|1|D+3COQ|1|E | Structural Basis for Dimerization in DNA Recognition by Gal4 | X-RAY DIFFRACTION | 2.4 | 20 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),Zinc-coordinating,regulatory,transcription |
| 31 | 3DFX|1|X+3DFX|1|Y | Opposite GATA DNA binding | X-RAY DIFFRACTION | 2.7 | 20 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),Zinc-coordinating,nuclear receptor ZnC4,regulatory,transcription |
| 32 | 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 | 20 | 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 |
| 33 | 1PUF|1|D+1PUF|1|E | Crystal Structure of HoxA9 and Pbx1 homeodomains bound to DNA | X-RAY DIFFRACTION | 1.9 | 20 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),homeodomain,regulatory,transcription |
| 34 | 2R5Y|1|C+2R5Y|1|D | Structure of Scr/Exd complex bound to a consensus Hox-Exd site | X-RAY DIFFRACTION | 2.6 | 20 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),homeodomain,regulatory,transcription |
| 35 | 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 | 20 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),homeodomain,regulatory,transcription |
| 36 | 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 |
| 37 | 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 |
| 38 | 2RAM|1|C+2RAM|1|D | A NOVEL DNA RECOGNITION MODE BY NF-KB P65 HOMODIMER | X-RAY DIFFRACTION | 2.4 | 20 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),immunoglobulin (Ig) fold,regulatory,rel homology,transcription |
| 39 | 1JNM|1|C+1JNM|1|D | Crystal Structure of the Jun/CRE Complex | X-RAY DIFFRACTION | 2.2 | 20 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),basic transcription factor,leucine zipper (bZIP),regulatory,transcription |
| 40 | 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 | 20 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),basic transcription factor,leucine zipper (bZIP),regulatory,transcription |
| 41 | 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 | 20 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),Zinc-coordinating,regulatory,transcription |
| 42 | 1QP9|1|G+1QP9|1|H | STRUCTURE OF HAP1-PC7 COMPLEXED TO THE UAS OF CYC7 | X-RAY DIFFRACTION | 2.8 | 20 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),Zinc-coordinating,regulatory,transcription |
| 43 | 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 | 20 | double helix,structure | DNA-binding transcription factor (TF),Zinc-coordinating,regulatory,transcription |
| 44 | 1QP9|1|E+1QP9|1|F | STRUCTURE OF HAP1-PC7 COMPLEXED TO THE UAS OF CYC7 | X-RAY DIFFRACTION | 2.8 | 20 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),Zinc-coordinating,regulatory,transcription |
| 45 | 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 | 20 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),Zinc-coordinating,regulatory,transcription |
| 46 | 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 | 20 | B-form double helix,double helix,structure | chromatin,structural |
| 47 | 1RAM|1|C+1RAM|1|D | A NOVEL DNA RECOGNITION MODE BY NF-KB P65 HOMODIMER | X-RAY DIFFRACTION | 2.7 | 20 | double helix,structure | DNA-binding transcription factor (TF),immunoglobulin (Ig) fold,regulatory,rel homology,transcription |
| 48 | 3MGV|1|K+3MGV|1|M+3MGV|1|I+3MGV|1|L | Cre recombinase-DNA transition state | X-RAY DIFFRACTION | 2.29 | 20 | enzyme,recombinase | |
| 49 | 3MGV|1|F+3MGV|1|H+3MGV|1|E+3MGV|1|G | Cre recombinase-DNA transition state | X-RAY DIFFRACTION | 2.29 | 20 | enzyme,recombinase |
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