Equivalence class DNA_4.0_83071.1 Current
| # | IFE | Standardized name | Molecule | Organism | Source | Rfam | Title | Method | Res. Å | Date |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 3C29|1|C+ 3C29|1|D (rep) | LoxP DNA, chain C,, LoxP DNA, chain D,F | Cre-loxP Synaptic structure | X-ray diffraction | 2.2 | 2009-02-17 | ||||
| 2 | 2VJU|1|C | RIGHT END 35-MER | Helicobacter pylori | Crystal structure of the IS608 transposase in complex with the complete Right end 35-mer DNA and manganese | X-ray diffraction | 2.4 | 2008-02-19 | |||
| 3 | 2VJU|1|D | RIGHT END 35-MER | Helicobacter pylori | Crystal structure of the IS608 transposase in complex with the complete Right end 35-mer DNA and manganese | X-ray diffraction | 2.4 | 2008-02-19 | |||
| 4 | 1XO0|1|C+ 1XO0|1|D | loxP | High resolution structure of the holliday junction intermediate in cre-loxp site-specific recombination | X-ray diffraction | 2 | 2004-12-14 | ||||
| 5 | 1OWG|1|C+ 1OWG|1|E+ 1OWG|1|D | Phage lambda H' site, 5'-D(*GP*CP*TP*TP*AP*TP*CP*AP*AP*TP*TP*TP*GP*TP*AP*GP*CP*AP*CP*C)-3', 5'-D(*GP*GP*CP*CP*AP*AP*AP*AP*AP*AP*GP*CP*AP*TP*T)-3' | Crystal structure of WT IHF complexed with an altered H' site (T44A) | X-ray diffraction | 2.1 | 2003-07-15 | ||||
| 6 | 4CRX|1|C+ 4CRX|1|D | DNA (35 NUCLEOTIDE CRE RECOGNITION SITE) | ASYMMETRIC DNA-BENDING IN THE CRE-LOXP SITE-SPECIFIC RECOMBINATION SYNAPSE | X-ray diffraction | 2.2 | 1999-06-14 | ||||
| 7 | 2VW9|1|C | POLY-DT | Single stranded DNA binding protein complex from Helicobacter pylori | X-ray diffraction | 2.3 | 2009-06-02 | ||||
| 8 | 2HOF|1|C+ 2HOF|1|D | LoxP DNA | Crystal structure of the pre-cleavage synaptic complex in the cre-loxp site-specific recombination | X-ray diffraction | 2.4 | 2007-06-26 | ||||
| 9 | 2HOI|1|C+ 2HOI|1|D | LoxP DNA | Crystal structure of the tetrameric pre-cleavage synaptic complex in the cre-loxp site-specific recombination | X-ray diffraction | 2.601 | 2007-06-26 | ||||
| 10 | 2HOI|1|E+ 2HOI|1|F | LoxP DNA | Crystal structure of the tetrameric pre-cleavage synaptic complex in the cre-loxp site-specific recombination | X-ray diffraction | 2.601 | 2007-06-26 | ||||
| 11 | 3CLC|1|E+ 3CLC|1|F | 35-MER | Crystal Structure of the Restriction-Modification Controller Protein C.Esp1396I Tetramer in Complex with its Natural 35 Base-Pair Operator | X-ray diffraction | 2.8 | 2008-07-29 | ||||
| 12 | 1IHF|1|C+ 1IHF|1|E+ 1IHF|1|D | DNA (35-MER), DNA (5'-D(*GP*CP*TP*TP*AP*TP*CP*AP*AP*TP*TP*TP*GP*TP*TP*GP*C P*AP*CP*C)-3'), DNA (5'-D(*GP*GP*CP*CP*AP*AP*AP*AP*AP*AP*GP*CP*AP*TP*T)-3') | INTEGRATION HOST FACTOR/DNA COMPLEX | X-ray diffraction | 2.5 | 1997-02-12 | ||||
| 13 | 1OUZ|1|C+ 1OUZ|1|E+ 1OUZ|1|D | Phage lambda H' site, 5'-D(*GP*CP*TP*TP*AP*TP*CP*AP*AP*TP*TP*TP*GP*TP*AP*GP*CP*AP*CP*C)-3', 5'-D(*GP*GP*CP*CP*AP*AP*AP*AP*AP*AP*GP*CP*AP*TP*T)-3' | Crystal structure of a mutant IHF (BetaE44A) complexed with a variant H' Site (T44A) | X-ray diffraction | 2.41 | 2003-07-15 | ||||
| 14 | 2IIE|1|C+ 2IIE|1|E+ 2IIE|1|D | Phage P H' site, DNA (5'-D(*DGP*DGP*DCP*DCP*DAP*DAP*DAP*DAP*DAP*DAP*DGP*DCP*DAP*DTP*DT)-3'), DNA (5'-D(*DGP*DCP*DTP*DTP*DAP*DTP*DCP*DAP*DAP*DTP*DTP*DTP*DGP*DTP*DTP*DGP*DCP*DAP*DCP*DC)-3') | synthetic construct | single chain Integration Host Factor protein (scIHF2) in complex with DNA | X-ray diffraction | 2.41 | 2007-02-20 | |||
| 15 | 1XNS|1|C+ 1XNS|1|D | loxP DNA | Peptide trapped Holliday junction intermediate in Cre-loxP recombination | X-ray diffraction | 2.8 | 2004-12-14 | ||||
| 16 | 2IIF|1|C+ 2IIF|1|E+ 2IIF|1|D | Phage P H' site, DNA (5'-D(*DGP*DGP*DCP*DCP*DAP*DAP*DAP*DAP*DAP*DAP*DGP*DCP*DAP*DTP*DT)-3'), DNA (5'-D(*DGP*DCP*DTP*DTP*DAP*DTP*DCP*DAP*DAP*DTP*DTP*DTP*DGP*DTP*DTP*DGP*DCP*DAP*DCP*DC)-3') | synthetic construct | single chain Integration Host Factor mutant protein (scIHF2-K45aE) in complex with DNA | X-ray diffraction | 2.72 | 2007-02-20 | |||
| 17 | 2IS2|1|C+ 2IS2|1|D | 33-MER | Crystal structure of UvrD-DNA binary complex | X-ray diffraction | 3 | 2007-01-09 | ||||
| 18 | 1OWF|1|C+ 1OWF|1|E+ 1OWF|1|D | Phage lambda H' site, 5'-D(*GP*CP*TP*TP*AP*TP*CP*AP*AP*TP*TP*TP*GP*TP*TP*GP*CP*AP*CP*C)-3', 5'-D(*GP*GP*CP*CP*AP*AP*AP*AP*AP*AP*GP*CP*AP*TP*T)-3' | Crystal structure of a mutant IHF (BetaE44A) complexed with the native H' Site | X-ray diffraction | 1.95 | 2003-07-15 | ||||
| 19 | 3CRX|1|C+ 3CRX|1|D+ 3CRX|1|E+ 3CRX|1|F | DNA 35-MER | CRE RECOMBINASE/DNA COMPLEX INTERMEDIATE I | X-ray diffraction | 2.5 | 1999-12-14 | ||||
| 20 | 2CRX|1|C+ 2CRX|1|D | DNA 35-MER | STRUCTURE OF THE HOLLIDAY JUNCTION INTERMEDIATE IN CRE-LOXP SITE-SPECIFIC RECOMBINATION | X-ray diffraction | 2.5 | 1999-12-14 | ||||
| 21 | 5CRX|1|C+ 5CRX|1|D | DNA (35-MER) | ASYMMETRIC DNA-BENDING IN THE CRE-LOXP SITE-SPECIFIC RECOMBINATION SYNAPSE | X-ray diffraction | 2.7 | 1999-07-07 |
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 | 2VJU|1|C | Crystal structure of the IS608 transposase in complex with the complete Right end 35-mer DNA and manganese | X-RAY DIFFRACTION | 2.4 | 35 | enzyme,recombinase | |
| 2 | 2VJU|1|D | Crystal structure of the IS608 transposase in complex with the complete Right end 35-mer DNA and manganese | X-RAY DIFFRACTION | 2.4 | 35 | enzyme,recombinase | |
| 3 | 1OUZ|1|C+1OUZ|1|E+1OUZ|1|D | Crystal structure of a mutant IHF (BetaE44A) complexed with a variant H' Site (T44A) | X-RAY DIFFRACTION | 2.41 | 35 | B-form double helix,double helix,structure | β-sheet,DNA-binding transcription factor (TF),IHF-like,regulatory,transcription |
| 4 | 1OWG|1|C+1OWG|1|E+1OWG|1|D | Crystal structure of WT IHF complexed with an altered H' site (T44A) | X-RAY DIFFRACTION | 2.1 | 35 | B-form double helix,double helix,structure | β-sheet,DNA-binding transcription factor (TF),IHF-like,regulatory,transcription |
| 5 | 1IHF|1|C+1IHF|1|E+1IHF|1|D | INTEGRATION HOST FACTOR/DNA COMPLEX | X-RAY DIFFRACTION | 2.5 | 35 | B-form double helix,double helix,structure | regulatory,transcription |
| 6 | 1OWF|1|C+1OWF|1|E+1OWF|1|D | Crystal structure of a mutant IHF (BetaE44A) complexed with the native H' Site | X-RAY DIFFRACTION | 1.95 | 35 | B-form double helix,double helix,structure | β-sheet,DNA-binding transcription factor (TF),IHF-like,regulatory,transcription |
| 7 | 2IIE|1|C+2IIE|1|E+2IIE|1|D | single chain Integration Host Factor protein (scIHF2) in complex with DNA | X-RAY DIFFRACTION | 2.41 | 35 | B-form double helix,double helix,structure | β-sheet,DNA-binding transcription factor (TF),IHF-like,regulatory,transcription |
| 8 | 2IIF|1|C+2IIF|1|E+2IIF|1|D | single chain Integration Host Factor mutant protein (scIHF2-K45aE) in complex with DNA | X-RAY DIFFRACTION | 2.72 | 35 | B-form double helix,double helix,structure | β-sheet,DNA-binding transcription factor (TF),IHF-like,regulatory,transcription |
| 9 | 2HOI|1|E+2HOI|1|F | Crystal structure of the tetrameric pre-cleavage synaptic complex in the cre-loxp site-specific recombination | X-RAY DIFFRACTION | 2.601 | 35 | enzyme,recombinase | |
| 10 | 5CRX|1|C+5CRX|1|D | ASYMMETRIC DNA-BENDING IN THE CRE-LOXP SITE-SPECIFIC RECOMBINATION SYNAPSE | X-RAY DIFFRACTION | 2.7 | 35 | enzyme,recombinase | |
| 11 | 2HOF|1|C+2HOF|1|D | Crystal structure of the pre-cleavage synaptic complex in the cre-loxp site-specific recombination | X-RAY DIFFRACTION | 2.4 | 35 | enzyme,recombinase | |
| 12 | 4CRX|1|C+4CRX|1|D | ASYMMETRIC DNA-BENDING IN THE CRE-LOXP SITE-SPECIFIC RECOMBINATION SYNAPSE | X-RAY DIFFRACTION | 2.2 | 35 | enzyme,recombinase | |
| 13 | 3C29|1|C+3C29|1|D | Cre-loxP Synaptic structure | X-RAY DIFFRACTION | 2.2 | 35 | enzyme,recombinase | |
| 14 | 2HOI|1|C+2HOI|1|D | Crystal structure of the tetrameric pre-cleavage synaptic complex in the cre-loxp site-specific recombination | X-RAY DIFFRACTION | 2.601 | 35 | enzyme,recombinase | |
| 15 | 2IS2|1|C+2IS2|1|D | Crystal structure of UvrD-DNA binary complex | X-RAY DIFFRACTION | 3 | 35 | enzyme,helicase,hydrolase | |
| 16 | 3CLC|1|E+3CLC|1|F | Crystal Structure of the Restriction-Modification Controller Protein C.Esp1396I Tetramer in Complex with its Natural 35 Base-Pair Operator | X-RAY DIFFRACTION | 2.8 | 35 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),lambda repressor-like,regulatory,transcription |
| 17 | 1XNS|1|C+1XNS|1|D | Peptide trapped Holliday junction intermediate in Cre-loxP recombination | X-RAY DIFFRACTION | 2.8 | 35 | Holliday junction,structure | enzyme,recombinase |
| 18 | 1XO0|1|C+1XO0|1|D | High resolution structure of the holliday junction intermediate in cre-loxp site-specific recombination | X-RAY DIFFRACTION | 2 | 35 | Holliday junction,structure | enzyme,recombinase |
| 19 | 3CRX|1|C+3CRX|1|D+3CRX|1|E+3CRX|1|F | CRE RECOMBINASE/DNA COMPLEX INTERMEDIATE I | X-RAY DIFFRACTION | 2.5 | 35 | enzyme,recombinase | |
| 20 | 2CRX|1|C+2CRX|1|D | STRUCTURE OF THE HOLLIDAY JUNCTION INTERMEDIATE IN CRE-LOXP SITE-SPECIFIC RECOMBINATION | X-RAY DIFFRACTION | 2.5 | 35 | Holliday junction,structure | enzyme,recombinase |
| 21 | 2VW9|1|C | Single stranded DNA binding protein complex from Helicobacter pylori | X-RAY DIFFRACTION | 2.3 | 35 | DNA replication/repair,regulatory |
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