Equivalence class DNA_4.0_90837.2 Current
| # | IFE | Standardized name | Molecule | Organism | Source | Rfam | Title | Method | Res. Å | #NTs | 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 | 69 | 2009-02-17 | ||||
| 2 | 1OWG|1|C+ 1OWG|1|E+ 1OWG|1|D | 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', Phage lambda H' site | Crystal structure of WT IHF complexed with an altered H' site (T44A) | X-ray diffraction | 2.1 | 70 | 2003-07-15 | ||||
| 3 | 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 | 70 | 2004-12-14 | ||||
| 4 | 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 | 70 | 1999-06-14 | ||||
| 5 | 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 | 69 | 2007-06-26 | ||||
| 6 | 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 | 68 | 2007-06-26 | ||||
| 7 | 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 | 70 | 1997-02-12 | ||||
| 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 | 68 | 2007-06-26 | ||||
| 9 | 1OUZ|1|C+ 1OUZ|1|E+ 1OUZ|1|D | 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', Phage lambda H' site | Crystal structure of a mutant IHF (BetaE44A) complexed with a variant H' Site (T44A) | X-ray diffraction | 2.41 | 70 | 2003-07-15 | ||||
| 10 | 2IIE|1|C+ 2IIE|1|E+ 2IIE|1|D | DNA (5'-D(*DGP*DCP*DTP*DTP*DAP*DTP*DCP*DAP*DAP*DTP*DTP*DTP*DGP*DTP*DTP*DGP*DCP*DAP*DCP*DC)-3'), DNA (5'-D(*DGP*DGP*DCP*DCP*DAP*DAP*DAP*DAP*DAP*DAP*DGP*DCP*DAP*DTP*DT)-3'), Phage P H' site | synthetic construct | single chain Integration Host Factor protein (scIHF2) in complex with DNA | X-ray diffraction | 2.41 | 70 | 2007-02-20 | |||
| 11 | 1XNS|1|C+ 1XNS|1|D | loxP DNA | Peptide trapped Holliday junction intermediate in Cre-loxP recombination | X-ray diffraction | 2.8 | 69 | 2004-12-14 | ||||
| 12 | 2IIF|1|C+ 2IIF|1|E+ 2IIF|1|D | DNA (5'-D(*DGP*DCP*DTP*DTP*DAP*DTP*DCP*DAP*DAP*DTP*DTP*DTP*DGP*DTP*DTP*DGP*DCP*DAP*DCP*DC)-3'), DNA (5'-D(*DGP*DGP*DCP*DCP*DAP*DAP*DAP*DAP*DAP*DAP*DGP*DCP*DAP*DTP*DT)-3'), Phage P H' site | synthetic construct | single chain Integration Host Factor mutant protein (scIHF2-K45aE) in complex with DNA | X-ray diffraction | 2.72 | 70 | 2007-02-20 | |||
| 13 | 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 | 35 | 2008-02-19 | |||
| 14 | 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 | 70 | 2008-07-29 | ||||
| 15 | 2IS2|1|C+ 2IS2|1|D | 33-MER | Crystal structure of UvrD-DNA binary complex | X-ray diffraction | 3 | 66 | 2007-01-09 | ||||
| 16 | 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 | 35 | 2008-02-19 | |||
| 17 | 2VW9|1|C | POLY-DT | Single stranded DNA binding protein complex from Helicobacter pylori | X-ray diffraction | 2.3 | 24 | 2009-06-02 | ||||
| 18 | 1OWF|1|C+ 1OWF|1|E+ 1OWF|1|D | 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', Phage lambda H' site | Crystal structure of a mutant IHF (BetaE44A) complexed with the native H' Site | X-ray diffraction | 1.95 | 70 | 2003-07-15 | ||||
| 19 | 3CRX|1|C+ 3CRX|1|F | DNA 35-MER | CRE RECOMBINASE/DNA COMPLEX INTERMEDIATE I | X-ray diffraction | 2.5 | 69 | 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 | 69 | 1999-12-14 | ||||
| 21 | 3CRX|1|D+ 3CRX|1|E | DNA 35-MER | CRE RECOMBINASE/DNA COMPLEX INTERMEDIATE I | X-ray diffraction | 2.5 | 69 | 1999-12-14 | ||||
| 22 | 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 | 66 | 1999-07-07 |
Release history
| Release | 0.6 |
|---|---|
| Date | 2011-03-05 |
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 |
|---|
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 | 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 | 2VW9|1|C | Single stranded DNA binding protein complex from Helicobacter pylori | X-RAY DIFFRACTION | 2.3 | 24 | DNA replication/repair,regulatory | ||
| 4 | 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 | 70 | B-form double helix,double helix,structure | β-sheet,DNA-binding transcription factor (TF),IHF-like,regulatory,transcription | |
| 5 | 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 | 70 | B-form double helix,double helix,structure | β-sheet,DNA-binding transcription factor (TF),IHF-like,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 | 70 | B-form double helix,double helix,structure | β-sheet,DNA-binding transcription factor (TF),IHF-like,regulatory,transcription | |
| 7 | 1IHF|1|C+ 1IHF|1|E+ 1IHF|1|D | INTEGRATION HOST FACTOR/DNA COMPLEX | X-RAY DIFFRACTION | 2.5 | 70 | B-form double helix,double helix,structure | regulatory,transcription | |
| 8 | 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 | 70 | B-form double helix,double helix,structure | β-sheet,DNA-binding transcription factor (TF),IHF-like,regulatory,transcription | |
| 9 | 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 | 70 | B-form double helix,double helix,structure | β-sheet,DNA-binding transcription factor (TF),IHF-like,regulatory,transcription | |
| 10 | 2CRX|1|C+ 2CRX|1|D | STRUCTURE OF THE HOLLIDAY JUNCTION INTERMEDIATE IN CRE-LOXP SITE-SPECIFIC RECOMBINATION | X-RAY DIFFRACTION | 2.5 | 69 | Holliday junction,structure | enzyme,recombinase | |
| 11 | 3CRX|1|C+ 3CRX|1|F | CRE RECOMBINASE/DNA COMPLEX INTERMEDIATE I | X-RAY DIFFRACTION | 2.5 | 69 | enzyme,recombinase | ||
| 12 | 1XO0|1|C+ 1XO0|1|D | High resolution structure of the holliday junction intermediate in cre-loxp site-specific recombination | X-RAY DIFFRACTION | 2 | 70 | Holliday junction,structure | enzyme,recombinase | |
| 13 | 1XNS|1|C+ 1XNS|1|D | Peptide trapped Holliday junction intermediate in Cre-loxP recombination | X-RAY DIFFRACTION | 2.8 | 69 | Holliday junction,structure | enzyme,recombinase | |
| 14 | 3C29|1|C+ 3C29|1|D | Cre-loxP Synaptic structure | X-RAY DIFFRACTION | 2.2 | 69 | enzyme,recombinase | ||
| 15 | 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 | 68 | enzyme,recombinase | ||
| 16 | 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 | 69 | enzyme,recombinase | ||
| 17 | 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 | 68 | enzyme,recombinase | ||
| 18 | 4CRX|1|C+ 4CRX|1|D | ASYMMETRIC DNA-BENDING IN THE CRE-LOXP SITE-SPECIFIC RECOMBINATION SYNAPSE | X-RAY DIFFRACTION | 2.2 | 70 | enzyme,recombinase | ||
| 19 | 5CRX|1|C+ 5CRX|1|D | ASYMMETRIC DNA-BENDING IN THE CRE-LOXP SITE-SPECIFIC RECOMBINATION SYNAPSE | X-RAY DIFFRACTION | 2.7 | 66 | enzyme,recombinase | ||
| 20 | 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 | 70 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),lambda repressor-like,regulatory,transcription | |
| 21 | 2IS2|1|C+ 2IS2|1|D | Crystal structure of UvrD-DNA binary complex | X-RAY DIFFRACTION | 3 | 66 | enzyme,helicase,hydrolase | ||
| 22 | 3CRX|1|D+ 3CRX|1|E | CRE RECOMBINASE/DNA COMPLEX INTERMEDIATE I | X-RAY DIFFRACTION | 2.5 | 69 | 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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