Equivalence class DNA_4.0_23674.1 Current
| # | IFE | Standardized name | Molecule | Organism | Source | Rfam | Title | Method | Res. Å | Date |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 2NTC|1|C+ 2NTC|1|W (rep) | 21-nt PEN element of the SV40 DNA origin | Crystal Structure of sv40 large T antigen origin binding domain with DNA | X-ray diffraction | 2.4 | 2007-02-13 | ||||
| 2 | 2A07|1|A+ 2A07|1|B | 5'-D(*AP*AP*CP*TP*AP*TP*GP*AP*AP*AP*CP*AP*AP*AP*TP*TP*TP*TP*CP*CP*T)-3', 5'-D(*TP*TP*AP*GP*GP*AP*AP*AP*AP*TP*TP*TP*GP*TP*TP*TP*CP*AP*TP*AP*G)-3' | Crystal Structure of Foxp2 bound Specifically to DNA. | X-ray diffraction | 1.9 | 2006-01-31 | ||||
| 3 | 2HOS|1|C+ 2HOS|1|D | 5'-D(*TP*TP*TP*TP*GP*CP*CP*AP*TP*GP*TP*AP*AP*TP*CP*CP*CP*CP*GP*GP*A)-3', 5'-D(*AP*TP*CP*CP*GP*GP*GP*GP*AP*TP*TP*AP*CP*AP*TP*GP*GP*CP*AP*AP*A)-3' | Phage-Selected Homeodomain Bound to Unmodified DNA | X-ray diffraction | 1.9 | 2006-12-12 | ||||
| 4 | 2A07|1|C+ 2A07|1|D | 5'-D(*AP*AP*CP*TP*AP*TP*GP*AP*AP*AP*CP*AP*AP*AP*TP*TP*TP*TP*CP*CP*T)-3', 5'-D(*TP*TP*AP*GP*GP*AP*AP*AP*AP*TP*TP*TP*GP*TP*TP*TP*CP*AP*TP*AP*G)-3' | Crystal Structure of Foxp2 bound Specifically to DNA. | X-ray diffraction | 1.9 | 2006-01-31 | ||||
| 5 | 2HOT|1|C+ 2HOT|1|D | 5'-D(*TP*TP*TP*TP*GP*CP*CP*AP*TP*GP*TP*AP*AP*TP*CP*CP*CP*CP*GP*GP*A)-3', 5'-D(*AP*TP*CP*CP*GP*GP*GP*GP*AP*TP*TP*AP*CP*AP*TP*GP*GP*CP*AP*AP*A)-3' | Phage selected homeodomain bound to modified DNA | X-ray diffraction | 2.19 | 2006-12-12 | ||||
| 6 | 2RBF|1|C+ 2RBF|1|D | DNA (5'-D(*DTP*DT*DTP*DGP*DCP*DGP*DGP*DTP*DTP*DGP*DCP*DAP*DCP*DCP*DTP*DTP*DTP*DCP*DAP*DAP*DA)-3'), DNA (5'-D(*DTP*DTP*DTP*DGP*DAP*DAP*DAP*DGP*DGP*DTP*DGP*DCP*DAP*DAP*DCP*DCP*DGP*DCP*DAP*DAP*DA)-3') | Structure of the ribbon-helix-helix domain of Escherichia coli PutA (PutA52) complexed with operator DNA (O2) | X-ray diffraction | 2.25 | 2008-07-29 | ||||
| 7 | 3G73|1|C+ 3G73|1|D | DNA (5'-D(P*AP*AP*AP*TP*TP*GP*TP*TP*TP*AP*TP*AP*AP*AP*CP*AP*GP*CP*CP*CP*G)-3'), DNA (5'-D(P*TP*TP*CP*GP*GP*GP*CP*TP*GP*TP*TP*TP*AP*TP*AP*AP*AP*CP*AP*AP*T)-3') | Structure of the FOXM1 DNA binding | X-ray diffraction | 2.21 | 2009-03-03 | ||||
| 8 | 3KZ8|1|C | DNA (5'-D(*TP*GP*GP*GP*CP*AP*TP*GP*CP*CP*CP*GP*GP*GP*CP*AP*TP*GP*CP*CP*C)-3') | Diversity in DNA recognition by p53 revealed by crystal structures with Hoogsteen base pairs (p53-DNA complex 3) | X-ray diffraction | 1.91 | 2010-03-31 | ||||
| 9 | 1K61|1|E+ 1K61|1|F | 5'-D(*AP*CP*AP*TP*GP*TP*AP*AP*TP*TP*CP*AP*TP*TP*TP*AP*CP*AP*CP*GP*C)-3', 5'-D(*(5IU)P*GP*CP*GP*TP*GP*TP*AP*AP*AP*TP*GP*AP*AP*TP*TP*AP*CP*AP*TP*G)-3' | MATALPHA2 HOMEODOMAIN BOUND TO DNA | X-ray diffraction | 2.1 | 2002-12-11 | ||||
| 10 | 1ZRF|1|X+ 1ZRF|1|Z+ 1ZRF|1|W+ 1ZRF|1|Y | 5'-D(*CP*TP*AP*GP*AP*TP*CP*GP*CP*AP*TP*TP*TP*TP*TP*CP*GP*AP*AP*AP*T)-3', 5'-D(*AP*TP*TP*TP*CP*GP*AP*AP*AP*AP*AP*TP*GP*CP*GP*AP*T)-3' | 4 crystal structures of CAP-DNA with all base-pair substitutions at position 6, CAP-[6C;17G]ICAP38 DNA | X-ray diffraction | 2.1 | 2006-03-21 | ||||
| 11 | 1AWC|1|D+ 1AWC|1|E | DNA (5'-D(*AP*AP*(BRU)P*GP*AP*CP*CP*GP*GP*AP*AP*GP*TP*AP*(CBR)P*AP*CP*(CBR)P*GP*GP*A)-3'), DNA (5'-D(*TP*TP*CP*CP*GP*GP*(BRU)P*GP*(BRU)P*AP*CP*TP*TP*CP*CP*GP*GP*TP*CP*AP*T)-3') | MOUSE GABP ALPHA/BETA DOMAIN BOUND TO DNA | X-ray diffraction | 2.15 | 1998-03-18 | ||||
| 12 | 2EZV|1|F+ 2EZV|1|G | 5'-D(*TP*GP*GP*CP*CP*AP*AP*CP*AP*AP*GP*GP*CP*CP*T)-3', 5'-D(*AP*GP*GP*CP*CP*TP*TP*GP*TP*TP*GP*GP*CP*CP*A)-3' | Crystal structure of tetrameric restriction endonuclease SfiI bound to cognate DNA. | X-ray diffraction | 2.4 | 2006-01-24 | ||||
| 13 | 1T2T|1|B+ 1T2T|1|C | 5'-D(*TP*TP*TP*GP*TP*AP*GP*GP*AP*CP*TP*GP*CP*CP*CP*TP*TP*TP*AP*AP*T)-3', 5'-D(*AP*AP*TP*TP*AP*AP*AP*GP*GP*GP*CP*AP*GP*TP*CP*CP*TP*AP*CP*AP*A)-3' | Crystal structure of the DNA-binding domain of intron endonuclease I-TevI with operator site | X-ray diffraction | 2.5 | 2004-09-07 | ||||
| 14 | 3HZI|1|T | 5'-D(*DAP*DCP*DTP*DAP*DTP*DCP*DCP*DCP*DCP*DTP*DTP*DAP*DAP*DGP*DGP*DGP*DGP*DAP*DTP*DAP*DG)-3' | Structure of mdt protein | X-ray diffraction | 2.98 | 2009-07-28 | ||||
| 15 | 3DNV|1|T | DNA (5'-D(*DAP*DCP*DTP*DAP*DTP*DCP*DCP*DCP*DCP*DTP*DTP*DAP*DAP*DGP*DGP*DGP*DGP*DAP*DTP*DAP*DG)-3') | MDT Protein | X-ray diffraction | 2.68 | 2009-01-27 | ||||
| 16 | 1NWQ|1|B+ 1NWQ|1|D | 5'-D(*TP*TP*CP*CP*TP*AP*TP*TP*GP*CP*GP*CP*AP*AP*TP*CP*CP*AP*GP*TP*T)-3', 5'-D(*AP*AP*AP*CP*TP*GP*GP*AP*TP*TP*GP*CP*GP*CP*AP*AP*TP*AP*GP*GP*A)-3' | CRYSTAL STRUCTURE OF C/EBPALPHA-DNA COMPLEX | X-ray diffraction | 2.8 | 2003-05-13 | ||||
| 17 | 2AS5|1|A+ 2AS5|1|B | 5'-D(TP*TP*AP*GP*GP*AP*AP*AP*AP*TP*TP*TP*GP*TP*TP*TP*CP*AP*TP*AP*GP*)-3', 5'-D(AP*AP*CP*TP*AP*TP*GP*AP*AP*AP*CP*AP*AP*AP*TP*TP*TP*TP*CP*CP*TP*)-3' | Structure of the DNA binding domains of NFAT and FOXP2 bound specifically to DNA. | X-ray diffraction | 2.7 | 2006-08-08 | ||||
| 18 | 2AS5|1|C+ 2AS5|1|D | 5'-D(TP*TP*AP*GP*GP*AP*AP*AP*AP*TP*TP*TP*GP*TP*TP*TP*CP*AP*TP*AP*GP*)-3', 5'-D(AP*AP*CP*TP*AP*TP*GP*AP*AP*AP*CP*AP*AP*AP*TP*TP*TP*TP*CP*CP*TP*)-3' | Structure of the DNA binding domains of NFAT and FOXP2 bound specifically to DNA. | X-ray diffraction | 2.7 | 2006-08-08 | ||||
| 19 | 1ZRE|1|X+ 1ZRE|1|Z+ 1ZRE|1|W+ 1ZRE|1|Y | 5'-D(*CP*TP*AP*GP*AP*TP*CP*CP*CP*AP*TP*TP*TP*TP*TP*CP*GP*AP*AP*AP*T)-3', 5'-D(*AP*TP*TP*TP*CP*GP*AP*AP*AP*AP*AP*TP*GP*GP*GP*AP*T)-3' | 4 crystal structures of CAP-DNA with all base-pair substitutions at position 6, CAP-[6G;17C]ICAP38 DNA | X-ray diffraction | 2.8 | 2006-03-21 | ||||
| 20 | 1ZRC|1|X+ 1ZRC|1|Z+ 1ZRC|1|W+ 1ZRC|1|Y | 5'-D(*CP*TP*AP*GP*AP*TP*CP*AP*CP*AP*TP*TP*TP*TP*TP*CP*GP*AP*AP*AP*T)-3', 5'-D(*AP*TP*TP*TP*CP*GP*AP*AP*AP*AP*AP*TP*GP*TP*GP*AP*T)-3' | 4 Crystal structures of CAP-DNA with all base-pair substitutions at position 6, CAP-ICAP38 DNA | X-ray diffraction | 2.8 | 2006-03-21 | ||||
| 21 | 2OYQ|1|E+ 2OYQ|1|F | Template DNA, Primer DNA | Crystal structure of RB69 gp43 in complex with DNA with 5-NIMP opposite an abasic site analog | X-ray diffraction | 2.86 | 2007-10-23 | ||||
| 22 | 2OYQ|1|G+ 2OYQ|1|H | Template DNA, Primer DNA | Crystal structure of RB69 gp43 in complex with DNA with 5-NIMP opposite an abasic site analog | X-ray diffraction | 2.86 | 2007-10-23 | ||||
| 23 | 2OYQ|1|I+ 2OYQ|1|J | Template DNA, Primer DNA | Crystal structure of RB69 gp43 in complex with DNA with 5-NIMP opposite an abasic site analog | X-ray diffraction | 2.86 | 2007-10-23 | ||||
| 24 | 2OYQ|1|K+ 2OYQ|1|L | Template DNA, Primer DNA | Crystal structure of RB69 gp43 in complex with DNA with 5-NIMP opposite an abasic site analog | X-ray diffraction | 2.86 | 2007-10-23 | ||||
| 25 | 2P5G|1|E+ 2P5G|1|F | Template DNA, Primer DNA | Crystal structure of RB69 gp43 in complex with DNA with dAMP opposite an abasic site analog in a 21mer template | X-ray diffraction | 2.8 | 2007-10-23 | ||||
| 26 | 2P5G|1|G+ 2P5G|1|H | Template DNA, Primer DNA | Crystal structure of RB69 gp43 in complex with DNA with dAMP opposite an abasic site analog in a 21mer template | X-ray diffraction | 2.8 | 2007-10-23 | ||||
| 27 | 2P5G|1|I+ 2P5G|1|J | Template DNA, Primer DNA | Crystal structure of RB69 gp43 in complex with DNA with dAMP opposite an abasic site analog in a 21mer template | X-ray diffraction | 2.8 | 2007-10-23 | ||||
| 28 | 2P5G|1|K+ 2P5G|1|L | Template DNA, Primer DNA | Crystal structure of RB69 gp43 in complex with DNA with dAMP opposite an abasic site analog in a 21mer template | X-ray diffraction | 2.8 | 2007-10-23 | ||||
| 29 | 1ZRD|1|X+ 1ZRD|1|Z+ 1ZRD|1|W+ 1ZRD|1|Y | 5'-D(*CP*TP*AP*GP*AP*TP*CP*TP*CP*AP*TP*TP*TP*TP*TP*CP*GP*AP*AP*AP*T)-3', 5'-D(*AP*TP*TP*TP*CP*GP*AP*AP*AP*AP*AP*TP*GP*AP*GP*AP*T)-3' | 4 crystal structures of CAP-DNA with all base-pair substitutions at position 6, CAP-[6A;17T]ICAP38 DNA | X-ray diffraction | 2.8 | 2006-03-21 | ||||
| 30 | 2DPD|1|D+ 2DPD|1|E | 5'-D(*CP*TP*AP*TP*GP*AP*AP*CP*AP*TP*AP*AP*TP*GP*TP*TP*CP*AP*TP*AP*G)-3', 5'-D(*CP*TP*AP*TP*GP*AP*AP*CP*AP*TP*TP*AP*TP*GP*TP*TP*CP*AP*TP*AP*G)-3' | Crystal structure of the Replication Termination Protein in complex with a pseudosymmetric B-site | X-ray diffraction | 3.17 | 2007-05-15 | ||||
| 31 | 1C0W|1|E+ 1C0W|1|F | DNA (5'-D(P*AP*TP*TP*AP*GP*GP*TP*TP*AP*GP*CP*CP*TP*AP*CP*CP*CP*TP*AP*AP*T)-3'), DNA (5'-D(P*AP*TP*TP*AP*GP*GP*TP*TP*AP*GP*GP*CP*TP*AP*CP*CP*CP*TP*AP*AP*T)-3') | CRYSTAL STRUCTURE OF THE COBALT-ACTIVATED DIPHTHERIA TOXIN REPRESSOR-DNA COMPLEX REVEALS A METAL BINDING SH-LIKE DOMAIN | X-ray diffraction | 3.2 | 2000-07-22 | ||||
| 32 | 2EFW|1|D+ 2EFW|1|E | DNA (5'-D(*DCP*DT*DAP*DTP*DGP*DTP*DAP*DCP*DCP*DAP*DAP*DAP*DTP*DGP*DTP*DTP*DCP*DAP*DGP*DTP*DC)-3'), DNA (5'-D(*DGP*DAP*DCP*DTP*DGP*DAP*DAP*DCP*DAP*DTP*DTP*DTP*DGP*DGP*DTP*DAP*DCP*DAP*DTP*DAP*DG)-3') | Crystal structure of the RTP:nRB complex from Bacillus subtilis | X-ray diffraction | 2.5 | 2008-02-26 | ||||
| 33 | 2EFW|1|I+ 2EFW|1|J | DNA (5'-D(*DCP*DT*DAP*DTP*DGP*DTP*DAP*DCP*DCP*DAP*DAP*DAP*DTP*DGP*DTP*DTP*DCP*DAP*DGP*DTP*DC)-3'), DNA (5'-D(*DGP*DAP*DCP*DTP*DGP*DAP*DAP*DCP*DAP*DTP*DTP*DTP*DGP*DGP*DTP*DAP*DCP*DAP*DTP*DAP*DG)-3') | Crystal structure of the RTP:nRB complex from Bacillus subtilis | X-ray diffraction | 2.5 | 2008-02-26 | ||||
| 34 | 2GM4|1|X+ 2GM4|1|Z+ 2GM4|1|Y | 5'-D(*CP*AP*GP*TP*GP*TP*CP*CP*GP*AP*TP*AP*AP*TP*TP*TP*AP*TP*AP*AP*A)-3', 5'-D(*TP*TP*AP*TP*CP*GP*GP*AP*CP*AP*CP*TP*G)-3' | An activated, tetrameric gamma-delta resolvase: Hin chimaera bound to cleaved DNA | X-ray diffraction | 3.5 | 2006-06-27 | ||||
| 35 | 2HDD|1|C+ 2HDD|1|D | DNA (5'-D(*TP*TP*TP*TP*GP*CP*CP*AP*TP*GP*TP*AP*AP*TP*CP*CP*C P*CP*GP*GP*A)-3'), DNA (5'-D(*AP*TP*CP*CP*GP*GP*GP*GP*AP*TP*TP*AP*CP*AP*TP*GP*G P*CP*AP*AP*A)-3') | ENGRAILED HOMEODOMAIN Q50K VARIANT DNA COMPLEX | X-ray diffraction | 1.9 | 1998-05-27 | ||||
| 36 | 1DU0|1|C+ 1DU0|1|D | DNA (5'-D(*TP*TP*TP*TP*GP*CP*CP*AP*TP*GP*TP*AP*AP*TP*TP*AP*CP*CP*TP*AP*A)-3'), DNA (5'-D(*AP*TP*TP*AP*GP*GP*TP*AP*AP*TP*TP*AP*CP*AP*TP*GP*GP*CP*AP*AP*A)-3') | ENGRAILED HOMEODOMAIN Q50A VARIANT DNA COMPLEX | X-ray diffraction | 2 | 2000-07-31 | ||||
| 37 | 1I3J|1|B+ 1I3J|1|C | 5'-D(*TP*TP*CP*TP*TP*GP*GP*GP*TP*CP*TP*AP*CP*CP*GP*TP*TP*TP*AP*AP*T)-3', 5'-D(*AP*AP*TP*TP*AP*AP*AP*CP*GP*GP*TP*AP*GP*AP*CP*CP*CP*AP*AP*GP*A)-3' | CRYSTAL STRUCTURE OF THE DNA-BINDING DOMAIN OF INTRON ENDONUCLEASE I-TEVI WITH ITS SUBSTRATE | X-ray diffraction | 2.2 | 2001-07-13 | ||||
| 38 | 3HDD|1|C+ 3HDD|1|D | 5'-D(*TP*TP*TP*TP*GP*CP*CP*AP*TP*GP*TP*AP*AP*TP*TP*AP*CP*CP*TP*AP*A)-3', 5'-D(*AP*TP*TP*AP*GP*GP*TP*AP*AP*TP*TP*AP*CP*AP*TP*GP*GP*CP*AP*AP*A)-3' | ENGRAILED HOMEODOMAIN DNA COMPLEX | X-ray diffraction | 2.2 | 1998-11-11 | ||||
| 39 | 1TSR|1|E+ 1TSR|1|F | DNA (5'-D(*TP*TP*TP*CP*CP*TP*AP*GP*AP*CP*TP*TP*GP*CP*CP*CP*A P*AP*TP*TP*A)-3'), DNA (5'-D(*AP*TP*AP*AP*TP*TP*GP*GP*GP*CP*AP*AP*GP*TP*CP*TP*A P*GP*GP*AP*A)-3') | P53 CORE DOMAIN IN COMPLEX WITH DNA | X-ray diffraction | 2.2 | 1996-01-29 | ||||
| 40 | 1TUP|1|E+ 1TUP|1|F | DNA (5'-D(*TP*TP*TP*CP*CP*TP*AP*GP*AP*CP*TP*TP*GP*CP*CP*CP*A P*AP*TP*TP*A)-3'), DNA (5'-D(*AP*TP*AP*AP*TP*TP*GP*GP*GP*CP*AP*AP*GP*TP*CP*TP*A P*GP*GP*AP*A)-3') | TUMOR SUPPRESSOR P53 COMPLEXED WITH DNA | X-ray diffraction | 2.2 | 1995-07-11 | ||||
| 41 | 1AM9|1|F+ 1AM9|1|H+ 1AM9|1|E+ 1AM9|1|G | DNA (5'-D(*CP*AP*TP*GP*AP*GP*AP*TP*CP*AP*CP*CP*CP*CP*AP*CP*T P*GP*CP*AP*A)-3'), DNA (5'-D(*TP*TP*GP*CP*AP*GP*TP*GP*GP*GP*GP*TP*GP*AP*TP*CP*T )-3') | HUMAN SREBP-1A BOUND TO LDL RECEPTOR PROMOTER | X-ray diffraction | 2.3 | 1998-07-10 | ||||
| 42 | 1F4K|1|D+ 1F4K|1|E | 5'-D(*CP*TP*AP*TP*GP*AP*AP*CP*AP*TP*AP*AP*TP*GP*TP*TP*CP*AP*TP*AP*G)-3', 5'-D(*CP*TP*AP*TP*GP*AP*AP*CP*AP*TP*TP*AP*TP*GP*TP*TP*CP*AP*TP*AP*G)-3' | CRYSTAL STRUCTURE OF THE REPLICATION TERMINATOR PROTEIN/B-SITE DNA COMPLEX | X-ray diffraction | 2.5 | 2001-06-08 | ||||
| 43 | 1IC8|1|E+ 1IC8|1|F | 5'-D(*CP*TP*TP*GP*GP*TP*TP*AP*AP*TP*AP*AP*TP*TP*CP*AP*CP*CP*AP*GP*A)-3', 5'-D(*TP*CP*TP*GP*GP*TP*GP*AP*AP*TP*TP*AP*TP*TP*AP*AP*CP*CP*AP*AP*G)-3' | HEPATOCYTE NUCLEAR FACTOR 1A BOUND TO DNA : MODY3 GENE PRODUCT | X-ray diffraction | 2.6 | 2002-11-27 | ||||
| 44 | 1APL|1|A+ 1APL|1|B | DNA (5'-D(*AP*CP*AP*TP*GP*TP*AP*AP*TP*TP*CP*AP*TP*TP*TP*AP*C P*AP*CP*GP*C)-3'), DNA (5'-D(*TP*GP*CP*GP*TP*GP*TP*AP*AP*AP*TP*GP*AP*AP*TP*TP*A P*CP*AP*TP*G)-3') | CRYSTAL STRUCTURE OF A MAT-ALPHA2 HOMEODOMAIN-OPERATOR COMPLEX SUGGESTS A GENERAL MODEL FOR HOMEODOMAIN-DNA INTERACTIONS | X-ray diffraction | 2.7 | 1993-10-21 | ||||
| 45 | 1D5Y|1|M+ 1D5Y|1|N | DNA (5'-D(*TP*GP*AP*CP*AP*GP*CP*AP*CP*TP*GP*AP*AP*TP*GP*TP*CP*AP*AP*AP*G)-3'), DNA (5'-D(*AP*CP*TP*TP*TP*GP*AP*CP*AP*TP*TP*CP*AP*GP*TP*GP*CP*TP*GP*TP*C)-3') | CRYSTAL STRUCTURE OF THE E. COLI ROB TRANSCRIPTION FACTOR IN COMPLEX WITH DNA | X-ray diffraction | 2.7 | 2000-04-24 | ||||
| 46 | 1D5Y|1|O+ 1D5Y|1|P | DNA (5'-D(*TP*GP*AP*CP*AP*GP*CP*AP*CP*TP*GP*AP*AP*TP*GP*TP*CP*AP*AP*AP*G)-3'), DNA (5'-D(*AP*CP*TP*TP*TP*GP*AP*CP*AP*TP*TP*CP*AP*GP*TP*GP*CP*TP*GP*TP*C)-3') | CRYSTAL STRUCTURE OF THE E. COLI ROB TRANSCRIPTION FACTOR IN COMPLEX WITH DNA | X-ray diffraction | 2.7 | 2000-04-24 | ||||
| 47 | 1HDD|1|A+ 1HDD|1|B | DNA (5'-D(*TP*TP*TP*TP*GP*CP*CP*AP*TP*GP*TP*AP*AP*TP*TP*AP*C P*CP*TP*AP*A)-3'), DNA (5'-D(*AP*TP*TP*AP*GP*GP*TP*AP*AP*TP*TP*AP*CP*AP*TP*GP*G P*CP*AP*AP*A)-3') | synthetic construct | CRYSTAL STRUCTURE OF AN ENGRAILED HOMEODOMAIN-DNA COMPLEX AT 2.8 ANGSTROMS RESOLUTION: A FRAMEWORK FOR UNDERSTANDING HOMEODOMAIN-DNA INTERACTIONS | X-ray diffraction | 2.8 | 1992-01-15 | |||
| 48 | 1AN4|1|C+ 1AN4|1|D | DNA (5'-D(*CP*AP*CP*CP*CP*GP*GP*TP*CP*AP*CP*GP*TP*GP*GP*CP*C P*TP*AP*CP*A)-3'), DNA (5'-D(*GP*TP*GP*TP*AP*GP*GP*CP*CP*AP*CP*GP*TP*GP*AP*CP*C P*GP*GP*GP*T)-3') | STRUCTURE AND FUNCTION OF THE B/HLH/Z DOMAIN OF USF | X-ray diffraction | 2.9 | 1997-09-17 | ||||
| 49 | 1DH3|1|B+ 1DH3|1|D | DNA (5'-D(*CP*CP*TP*TP*GP*GP*CP*TP*GP*AP*CP*GP*TP*CP*AP*GP*CP*CP*AP*AP*G)-3') | CRYSTAL STRUCTURE OF A CREB BZIP-CRE COMPLEX REVEALS THE BASIS FOR CREB FAIMLY SELECTIVE DIMERIZATION AND DNA BINDING | X-ray diffraction | 3 | 2000-11-27 | ||||
| 50 | 1KSY|1|D+ 1KSY|1|F | E1 Recognition Sequence, Strand 1, E1 Recognition Sequence, Strand 2 | Crystal Structures of Two Intermediates in the Assembly of the Papillomavirus Replication Initiation Complex | X-ray diffraction | 3.05 | 2002-03-15 | ||||
| 51 | 1KSY|1|E | E1 Recognition Sequence, Strand 1 | Crystal Structures of Two Intermediates in the Assembly of the Papillomavirus Replication Initiation Complex | X-ray diffraction | 3.05 | 2002-03-15 | ||||
| 52 | 2F03|1|E+ 2F03|1|F | DNA (5'-D(*AP*TP*G*TP*GP*GP*CP*CP*AP*AP*CP*AP*AP*GP*GP*CP*CP*TP*AP*TP*T)-3'), DNA (5'-D(*AP*AP*TP*AP*GP*GP*CP*CP*TP*TP*GP*TP*TP*GP*GP*CP*CP*AP*CP*AP*T)-3') | Crystal structure of tetrameric restriction endonuclease SfiI in complex with cognate DNA (partial bound form) | X-ray diffraction | 3.05 | 2007-01-16 | ||||
| 53 | 2F03|1|G+ 2F03|1|H | DNA (5'-D(*AP*TP*G*TP*GP*GP*CP*CP*AP*AP*CP*AP*AP*GP*GP*CP*CP*TP*AP*TP*T)-3'), DNA (5'-D(*AP*AP*TP*AP*GP*GP*CP*CP*TP*TP*GP*TP*TP*GP*GP*CP*CP*AP*CP*AP*T)-3') | Crystal structure of tetrameric restriction endonuclease SfiI in complex with cognate DNA (partial bound form) | X-ray diffraction | 3.05 | 2007-01-16 | ||||
| 54 | 1KSX|1|C+ 1KSX|1|G | E1 Recognition Sequence | Crystal Structures of Two Intermediates in the Assembly of the Papillomavirus Replication Initiation Complex | X-ray diffraction | 3.2 | 2002-03-15 | ||||
| 55 | 1KSX|1|K+ 1KSX|1|O | E1 Recognition Sequence | Crystal Structures of Two Intermediates in the Assembly of the Papillomavirus Replication Initiation Complex | X-ray diffraction | 3.2 | 2002-03-15 |
Release history
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 | 1ZRF|1|X+1ZRF|1|Z+1ZRF|1|W+1ZRF|1|Y | 4 crystal structures of CAP-DNA with all base-pair substitutions at position 6, CAP-[6C;17G]ICAP38 DNA | X-RAY DIFFRACTION | 2.1 | 21 | DNA-binding transcription factor (TF),helix-turn-helix (HTH),regulatory,transcription,winged helix/forkhead | |
| 2 | 1ZRC|1|X+1ZRC|1|Z+1ZRC|1|W+1ZRC|1|Y | 4 Crystal structures of CAP-DNA with all base-pair substitutions at position 6, CAP-ICAP38 DNA | X-RAY DIFFRACTION | 2.8 | 21 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),regulatory,transcription,winged helix/forkhead |
| 3 | 1ZRD|1|X+1ZRD|1|Z+1ZRD|1|W+1ZRD|1|Y | 4 crystal structures of CAP-DNA with all base-pair substitutions at position 6, CAP-[6A;17T]ICAP38 DNA | X-RAY DIFFRACTION | 2.8 | 21 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),regulatory,transcription,winged helix/forkhead |
| 4 | 1ZRE|1|X+1ZRE|1|Z+1ZRE|1|W+1ZRE|1|Y | 4 crystal structures of CAP-DNA with all base-pair substitutions at position 6, CAP-[6G;17C]ICAP38 DNA | X-RAY DIFFRACTION | 2.8 | 21 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),regulatory,transcription,winged helix/forkhead |
| 5 | 2GM4|1|X+2GM4|1|Z+2GM4|1|Y | An activated, tetrameric gamma-delta resolvase: Hin chimaera bound to cleaved DNA | X-RAY DIFFRACTION | 3.5 | 21 | enzyme,recombinase | |
| 6 | 1TSR|1|E+1TSR|1|F | P53 CORE DOMAIN IN COMPLEX WITH DNA | X-RAY DIFFRACTION | 2.2 | 21 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),P53 like,immunoglobulin (Ig) fold,regulatory,transcription |
| 7 | 1TUP|1|E+1TUP|1|F | TUMOR SUPPRESSOR P53 COMPLEXED WITH DNA | X-RAY DIFFRACTION | 2.2 | 21 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),P53 like,immunoglobulin (Ig) fold,regulatory,transcription |
| 8 | 1K61|1|E+1K61|1|F | MATALPHA2 HOMEODOMAIN BOUND TO DNA | X-RAY DIFFRACTION | 2.1 | 21 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),homeodomain,regulatory,transcription |
| 9 | 2NTC|1|C+2NTC|1|W | Crystal Structure of sv40 large T antigen origin binding domain with DNA | X-RAY DIFFRACTION | 2.4 | 21 | B-form double helix,double helix,structure | DNA replication/repair,enzyme,helicase,hydrolase,regulatory |
| 10 | 1D5Y|1|O+1D5Y|1|P | CRYSTAL STRUCTURE OF THE E. COLI ROB TRANSCRIPTION FACTOR IN COMPLEX WITH DNA | X-RAY DIFFRACTION | 2.7 | 21 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),homeodomain,regulatory,transcription |
| 11 | 1D5Y|1|M+1D5Y|1|N | CRYSTAL STRUCTURE OF THE E. COLI ROB TRANSCRIPTION FACTOR IN COMPLEX WITH DNA | X-RAY DIFFRACTION | 2.7 | 21 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),homeodomain,regulatory,transcription |
| 12 | 1NWQ|1|B+1NWQ|1|D | CRYSTAL STRUCTURE OF C/EBPALPHA-DNA COMPLEX | X-RAY DIFFRACTION | 2.8 | 21 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),basic transcription factor,leucine zipper (bZIP),regulatory,transcription |
| 13 | 1AWC|1|D+1AWC|1|E | MOUSE GABP ALPHA/BETA DOMAIN BOUND TO DNA | X-RAY DIFFRACTION | 2.15 | 21 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),regulatory,transcription,winged helix/forkhead |
| 14 | 1C0W|1|E+1C0W|1|F | CRYSTAL STRUCTURE OF THE COBALT-ACTIVATED DIPHTHERIA TOXIN REPRESSOR-DNA COMPLEX REVEALS A METAL BINDING SH-LIKE DOMAIN | X-RAY DIFFRACTION | 3.2 | 21 | double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),regulatory,transcription,winged helix/forkhead |
| 15 | 3G73|1|C+3G73|1|D | Structure of the FOXM1 DNA binding | X-RAY DIFFRACTION | 2.21 | 21 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),regulatory,transcription,winged helix/forkhead |
| 16 | 2RBF|1|C+2RBF|1|D | Structure of the ribbon-helix-helix domain of Escherichia coli PutA (PutA52) complexed with operator DNA (O2) | X-RAY DIFFRACTION | 2.25 | 21 | B-form double helix,double helix,structure | enzyme,oxidoreductase,regulatory,transcription |
| 17 | 1AM9|1|F+1AM9|1|H+1AM9|1|E+1AM9|1|G | HUMAN SREBP-1A BOUND TO LDL RECEPTOR PROMOTER | X-RAY DIFFRACTION | 2.3 | 21 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),basic transcription factor,helix-loop-helix (bHLH),regulatory,transcription |
| 18 | 1I3J|1|B+1I3J|1|C | CRYSTAL STRUCTURE OF THE DNA-BINDING DOMAIN OF INTRON ENDONUCLEASE I-TEVI WITH ITS SUBSTRATE | X-RAY DIFFRACTION | 2.2 | 21 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease |
| 19 | 1T2T|1|B+1T2T|1|C | Crystal structure of the DNA-binding domain of intron endonuclease I-TevI with operator site | X-RAY DIFFRACTION | 2.5 | 21 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease |
| 20 | 1DH3|1|B+1DH3|1|D | CRYSTAL STRUCTURE OF A CREB BZIP-CRE COMPLEX REVEALS THE BASIS FOR CREB FAIMLY SELECTIVE DIMERIZATION AND DNA BINDING | X-RAY DIFFRACTION | 3 | 21 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),basic transcription factor,leucine zipper (bZIP),regulatory,transcription |
| 21 | 2AS5|1|A+2AS5|1|B | Structure of the DNA binding domains of NFAT and FOXP2 bound specifically to DNA. | X-RAY DIFFRACTION | 2.7 | 21 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),immunoglobulin (Ig) fold,regulatory,rel homology,transcription,winged helix/forkhead |
| 22 | 2AS5|1|C+2AS5|1|D | Structure of the DNA binding domains of NFAT and FOXP2 bound specifically to DNA. | X-RAY DIFFRACTION | 2.7 | 21 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),immunoglobulin (Ig) fold,regulatory,rel homology,transcription,winged helix/forkhead |
| 23 | 2A07|1|A+2A07|1|B | Crystal Structure of Foxp2 bound Specifically to DNA. | X-RAY DIFFRACTION | 1.9 | 21 | DNA-binding transcription factor (TF),helix-turn-helix (HTH),regulatory,transcription,winged helix/forkhead | |
| 24 | 2A07|1|C+2A07|1|D | Crystal Structure of Foxp2 bound Specifically to DNA. | X-RAY DIFFRACTION | 1.9 | 21 | DNA-binding transcription factor (TF),helix-turn-helix (HTH),regulatory,transcription,winged helix/forkhead | |
| 25 | 1DU0|1|C+1DU0|1|D | ENGRAILED HOMEODOMAIN Q50A VARIANT DNA COMPLEX | X-RAY DIFFRACTION | 2 | 21 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),homeodomain,regulatory,transcription |
| 26 | 2HDD|1|C+2HDD|1|D | ENGRAILED HOMEODOMAIN Q50K VARIANT DNA COMPLEX | X-RAY DIFFRACTION | 1.9 | 21 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),homeodomain,regulatory,transcription |
| 27 | 2HOT|1|C+2HOT|1|D | Phage selected homeodomain bound to modified DNA | X-RAY DIFFRACTION | 2.19 | 21 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),homeodomain,regulatory,transcription |
| 28 | 2HOS|1|C+2HOS|1|D | Phage-Selected Homeodomain Bound to Unmodified DNA | X-RAY DIFFRACTION | 1.9 | 21 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),homeodomain,regulatory,transcription |
| 29 | 3HDD|1|C+3HDD|1|D | ENGRAILED HOMEODOMAIN DNA COMPLEX | X-RAY DIFFRACTION | 2.2 | 21 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),homeodomain,regulatory,transcription |
| 30 | 1HDD|1|A+1HDD|1|B | CRYSTAL STRUCTURE OF AN ENGRAILED HOMEODOMAIN-DNA COMPLEX AT 2.8 ANGSTROMS RESOLUTION: A FRAMEWORK FOR UNDERSTANDING HOMEODOMAIN-DNA INTERACTIONS | X-RAY DIFFRACTION | 2.8 | 21 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),homeodomain,regulatory,transcription |
| 31 | 1IC8|1|E+1IC8|1|F | HEPATOCYTE NUCLEAR FACTOR 1A BOUND TO DNA : MODY3 GENE PRODUCT | X-RAY DIFFRACTION | 2.6 | 21 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),homeodomain,regulatory,transcription |
| 32 | 1F4K|1|D+1F4K|1|E | CRYSTAL STRUCTURE OF THE REPLICATION TERMINATOR PROTEIN/B-SITE DNA COMPLEX | X-RAY DIFFRACTION | 2.5 | 21 | B-form double helix,double helix,structure | DNA replication/repair,regulatory |
| 33 | 2DPD|1|D+2DPD|1|E | Crystal structure of the Replication Termination Protein in complex with a pseudosymmetric B-site | X-RAY DIFFRACTION | 3.17 | 21 | B-form double helix,double helix,structure | DNA replication/repair,regulatory |
| 34 | 1APL|1|A+1APL|1|B | CRYSTAL STRUCTURE OF A MAT-ALPHA2 HOMEODOMAIN-OPERATOR COMPLEX SUGGESTS A GENERAL MODEL FOR HOMEODOMAIN-DNA INTERACTIONS | X-RAY DIFFRACTION | 2.7 | 21 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),homeodomain,regulatory,transcription |
| 35 | 2EFW|1|D+2EFW|1|E | Crystal structure of the RTP:nRB complex from Bacillus subtilis | X-RAY DIFFRACTION | 2.5 | 21 | double helix,structure | DNA replication/repair,regulatory |
| 36 | 2EFW|1|I+2EFW|1|J | Crystal structure of the RTP:nRB complex from Bacillus subtilis | X-RAY DIFFRACTION | 2.5 | 21 | double helix,structure | DNA replication/repair,regulatory |
| 37 | 1AN4|1|C+1AN4|1|D | STRUCTURE AND FUNCTION OF THE B/HLH/Z DOMAIN OF USF | X-RAY DIFFRACTION | 2.9 | 21 | double helix,structure | DNA-binding transcription factor (TF),basic transcription factor,helix-loop-helix (bHLH),regulatory,transcription |
| 38 | 1KSY|1|D+1KSY|1|F | Crystal Structures of Two Intermediates in the Assembly of the Papillomavirus Replication Initiation Complex | X-RAY DIFFRACTION | 3.05 | 21 | B-form double helix,double helix,structure | DNA replication/repair,enzyme,helicase,hydrolase,regulatory |
| 39 | 1KSY|1|E | Crystal Structures of Two Intermediates in the Assembly of the Papillomavirus Replication Initiation Complex | X-RAY DIFFRACTION | 3.05 | 21 | B-form double helix,double helix,structure | DNA replication/repair,enzyme,helicase,hydrolase,regulatory |
| 40 | 1KSX|1|K+1KSX|1|O | Crystal Structures of Two Intermediates in the Assembly of the Papillomavirus Replication Initiation Complex | X-RAY DIFFRACTION | 3.2 | 21 | DNA replication/repair,enzyme,helicase,hydrolase,regulatory | |
| 41 | 1KSX|1|C+1KSX|1|G | Crystal Structures of Two Intermediates in the Assembly of the Papillomavirus Replication Initiation Complex | X-RAY DIFFRACTION | 3.2 | 21 | DNA replication/repair,enzyme,helicase,hydrolase,regulatory | |
| 42 | 3KZ8|1|C | Diversity in DNA recognition by p53 revealed by crystal structures with Hoogsteen base pairs (p53-DNA complex 3) | X-RAY DIFFRACTION | 1.91 | 21 | DNA-binding transcription factor (TF),P53 like,immunoglobulin (Ig) fold,regulatory,transcription | |
| 43 | 2OYQ|1|G+2OYQ|1|H | Crystal structure of RB69 gp43 in complex with DNA with 5-NIMP opposite an abasic site analog | X-RAY DIFFRACTION | 2.86 | 21 | double helix,structure | enzyme,polymerase,transferase |
| 44 | 2P5G|1|G+2P5G|1|H | Crystal structure of RB69 gp43 in complex with DNA with dAMP opposite an abasic site analog in a 21mer template | X-RAY DIFFRACTION | 2.8 | 21 | B-form double helix,double helix,structure | enzyme,polymerase,transferase |
| 45 | 2EZV|1|F+2EZV|1|G | Crystal structure of tetrameric restriction endonuclease SfiI bound to cognate DNA. | X-RAY DIFFRACTION | 2.4 | 21 | enzyme,hydrolase,nuclease | |
| 46 | 2P5G|1|K+2P5G|1|L | Crystal structure of RB69 gp43 in complex with DNA with dAMP opposite an abasic site analog in a 21mer template | X-RAY DIFFRACTION | 2.8 | 21 | B-form double helix,double helix,structure | enzyme,polymerase,transferase |
| 47 | 2OYQ|1|K+2OYQ|1|L | Crystal structure of RB69 gp43 in complex with DNA with 5-NIMP opposite an abasic site analog | X-RAY DIFFRACTION | 2.86 | 21 | double helix,structure | enzyme,polymerase,transferase |
| 48 | 2OYQ|1|I+2OYQ|1|J | Crystal structure of RB69 gp43 in complex with DNA with 5-NIMP opposite an abasic site analog | X-RAY DIFFRACTION | 2.86 | 21 | double helix,structure | enzyme,polymerase,transferase |
| 49 | 2P5G|1|I+2P5G|1|J | Crystal structure of RB69 gp43 in complex with DNA with dAMP opposite an abasic site analog in a 21mer template | X-RAY DIFFRACTION | 2.8 | 21 | B-form double helix,double helix,structure | enzyme,polymerase,transferase |
| 50 | 2P5G|1|E+2P5G|1|F | Crystal structure of RB69 gp43 in complex with DNA with dAMP opposite an abasic site analog in a 21mer template | X-RAY DIFFRACTION | 2.8 | 21 | B-form double helix,double helix,structure | enzyme,polymerase,transferase |
| 51 | 2OYQ|1|E+2OYQ|1|F | Crystal structure of RB69 gp43 in complex with DNA with 5-NIMP opposite an abasic site analog | X-RAY DIFFRACTION | 2.86 | 21 | double helix,structure | enzyme,polymerase,transferase |
| 52 | 2F03|1|E+2F03|1|F | Crystal structure of tetrameric restriction endonuclease SfiI in complex with cognate DNA (partial bound form) | X-RAY DIFFRACTION | 3.05 | 21 | enzyme,hydrolase,nuclease | |
| 53 | 3HZI|1|T | Structure of mdt protein | X-RAY DIFFRACTION | 2.98 | 21 | double helix,structure | enzyme,kinase,regulatory,transcription,transferase |
| 54 | 3DNV|1|T | MDT Protein | X-RAY DIFFRACTION | 2.68 | 21 | double helix,structure | enzyme,kinase,regulatory,transcription,transferase |
| 55 | 2F03|1|G+2F03|1|H | Crystal structure of tetrameric restriction endonuclease SfiI in complex with cognate DNA (partial bound form) | X-RAY DIFFRACTION | 3.05 | 21 | enzyme,hydrolase,nuclease |
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