Equivalence class DNA_2.5_44558.1 Obsolete
| # | IFE | Standardized name | Molecule | Organism | Source | Rfam | Title | Method | Res. Å | #NTs | Date |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 2I13|1|C+ 2I13|1|D (rep) | 5'-D(*CP*AP*GP*AP*TP*GP*TP*AP*GP*GP*GP*AP*AP*AP*AP*GP*CP*CP*CP*GP*GP*G)-3', 5'-D(*GP*CP*CP*CP*GP*GP*GP*CP*TP*TP*TP*TP*CP*CP*CP*TP*AP*CP*AP*TP*CP*T)-3' | Aart, a six finger zinc finger designed to recognize ANN triplets | X-ray diffraction | 1.96 | 44 | 2006-10-03 | ||||
| 2 | 2I13|1|E+ 2I13|1|F | 5'-D(*CP*AP*GP*AP*TP*GP*TP*AP*GP*GP*GP*AP*AP*AP*AP*GP*CP*CP*CP*GP*GP*G)-3', 5'-D(*GP*CP*CP*CP*GP*GP*GP*CP*TP*TP*TP*TP*CP*CP*CP*TP*AP*CP*AP*TP*CP*T)-3' | Aart, a six finger zinc finger designed to recognize ANN triplets | X-ray diffraction | 1.96 | 44 | 2006-10-03 | ||||
| 3 | 3MLN|1|C+ 3MLN|1|D | DNA (5'-D(*CP*TP*TP*TP*AP*TP*TP*CP*CP*CP*AP*TP*GP*GP*GP*AP*AP*TP*AP*AP*AP*G)-3') | synthetic construct | DNA binding domain of Early B-cell Factor 1 (Ebf1) bound to DNA (crystal form II) | X-ray diffraction | 2.4 | 44 | 2010-12-01 | |||
| 4 | 3M9E|1|C+ 3M9E|1|D | DNA (5'-D(*AP*TP*TP*GP*AP*CP*CP*TP*CP*AP*GP*CP*TP*GP*AP*GP*GP*TP*CP*AP*AP*T)-3') | Thyroid hormone beta DNA binding domain homodimer with inverted palindrome TRE | X-ray diffraction | 2.406 | 44 | 2010-08-18 | ||||
| 5 | 3M9E|1|G+ 3M9E|1|H | DNA (5'-D(*AP*TP*TP*GP*AP*CP*CP*TP*CP*AP*GP*CP*TP*GP*AP*GP*GP*TP*CP*AP*AP*T)-3') | Thyroid hormone beta DNA binding domain homodimer with inverted palindrome TRE | X-ray diffraction | 2.406 | 44 | 2010-08-18 | ||||
| 6 | 3IKT|1|C+ 3IKT|1|D | Rex operator DNA | Crystal structure of a Rex-family repressor/DNA/NAD+ complex from Thermus aquaticus | X-ray diffraction | 2.26 | 44 | 2010-06-09 | ||||
| 7 | 1P47|1|C+ 1P47|1|D | 5'-D(*CP*AP*CP*GP*CP*CP*CP*AP*CP*GP*CP*CP*GP*CP*CP*CP*AP*CP*GP*CP*CP*A)-3', 5'-D(*GP*TP*GP*GP*CP*GP*TP*GP*GP*GP*CP*GP*GP*CP*GP*TP*GP*GP*GP*CP*GP*T)-3' | Crystal Structure of tandem Zif268 molecules complexed to DNA | X-ray diffraction | 2.2 | 44 | 2003-06-24 | ||||
| 8 | 2B9S|1|E+ 2B9S|1|D+ 2B9S|1|C | 5'-D(*AP*AP*AP*AP*AP*GP*AP*CP*TP*T)-3', 5'-D(*AP*AP*AP*AP*AP*TP*TP*TP*TP*TP*CP*TP*AP*AP*GP*TP*CP*TP*TP*TP*TP*T)-3', 5'-D(*AP*GP*AP*AP*AP*AP*AP*TP*TP*TP*TP*T)-3' | Crystal Structure of heterodimeric L. donovani topoisomerase I-vanadate-DNA complex | X-ray diffraction | 2.27 | 44 | 2006-01-17 | ||||
| 9 | 3MX4|1|I+ 3MX4|1|J | DNA (5'-D(P*CP*GP*GP*GP*AP*GP*GP*CP*CP*CP*GP*CP*GP*GP*GP*CP*CP*GP*CP*CP*GP*C)-3'), DNA (5'-D(P*GP*CP*GP*GP*CP*GP*GP*CP*CP*CP*GP*CP*GP*GP*GP*CP*CP*TP*CP*CP*CP*G)-3') | DNA binding and cleavage by the GIY-YIG endonuclease R.Eco29KI inactive variant E142Q | X-ray diffraction | 2.5 | 44 | 2010-09-08 | ||||
| 10 | 3MX4|1|K+ 3MX4|1|L | DNA (5'-D(P*CP*GP*GP*GP*AP*GP*GP*CP*CP*CP*GP*CP*GP*GP*GP*CP*CP*GP*CP*CP*GP*C)-3'), DNA (5'-D(P*GP*CP*GP*GP*CP*GP*GP*CP*CP*CP*GP*CP*GP*GP*GP*CP*CP*TP*CP*CP*CP*G)-3') | DNA binding and cleavage by the GIY-YIG endonuclease R.Eco29KI inactive variant E142Q | X-ray diffraction | 2.5 | 44 | 2010-09-08 | ||||
| 11 | 3MX4|1|M+ 3MX4|1|N | DNA (5'-D(P*CP*GP*GP*GP*AP*GP*GP*CP*CP*CP*GP*CP*GP*GP*GP*CP*CP*GP*CP*CP*GP*C)-3'), DNA (5'-D(P*GP*CP*GP*GP*CP*GP*GP*CP*CP*CP*GP*CP*GP*GP*GP*CP*CP*TP*CP*CP*CP*G)-3') | DNA binding and cleavage by the GIY-YIG endonuclease R.Eco29KI inactive variant E142Q | X-ray diffraction | 2.5 | 44 | 2010-09-08 | ||||
| 12 | 3MX4|1|O+ 3MX4|1|P | DNA (5'-D(P*CP*GP*GP*GP*AP*GP*GP*CP*CP*CP*GP*CP*GP*GP*GP*CP*CP*GP*CP*CP*GP*C)-3'), DNA (5'-D(P*GP*CP*GP*GP*CP*GP*GP*CP*CP*CP*GP*CP*GP*GP*GP*CP*CP*TP*CP*CP*CP*G)-3') | DNA binding and cleavage by the GIY-YIG endonuclease R.Eco29KI inactive variant E142Q | X-ray diffraction | 2.5 | 44 | 2010-09-08 | ||||
| 13 | 3IL2|1|C+ 3IL2|1|D | Rex operator DNA | Crystal structure of a Rex-family repressor R90D mutant/DNA complex from Thermus aquaticus | X-ray diffraction | 2.49 | 44 | 2010-06-09 | ||||
| 14 | 3C25|1|C+ 3C25|1|D | DNA (5'-D(*DCP*DGP*DGP*DAP*DGP*DGP*DCP*DGP*DCP*DGP*DGP*DCP*DCP*DGP*DCP*DGP*DCP*DCP*DGP*DCP*DCP*DG)-3'), DNA (5'-D(*DCP*DGP*DGP*DCP*DGP*DGP*DCP*DGP*DCP*DGP*DGP*DCP*DCP*DGP*DCP*DGP*DCP*DCP*DTP*DCP*DCP*DG)-3') | Crystal Structure of NotI Restriction Endonuclease Bound to Cognate DNA | X-ray diffraction | 2.5 | 44 | 2008-02-12 | ||||
| 15 | 1A31|1|C+ 1A31|1|D | DNA (5'-D(*AP*AP*AP*AP*AP*GP*AP*CP*5IUP*5IU*TP*GP*AP*AP*AP*AP*AP*5IUP*5IUP*5IUP*5IUP*T)-3'), DNA (5'-D(*AP*AP*AP*AP*AP*TP*5IUP*5IUP*5IUP*5IUP*CP*AP*AP*AP*GP*TP*CP*TP*TP*TP*TP*T)-3') | HUMAN RECONSTITUTED DNA TOPOISOMERASE I IN COVALENT COMPLEX WITH A 22 BASE PAIR DNA DUPLEX | X-ray diffraction | 2.1 | 44 | 1998-08-28 | ||||
| 16 | 1K4T|1|D+ 1K4T|1|C+ 1K4T|1|B | 5'-D(*(TGP)P*GP*AP*AP*AP*AP*AP*TP*TP*TP*TP*T)-3', 5'-D(*AP*AP*AP*AP*AP*GP*AP*CP*TP*T)-3', 5'-D(*AP*AP*AP*AP*AP*TP*TP*TP*TP*TP*CP*CP*AP*AP*GP*TP*CP*TP*TP*TP*TP*T)-3' | HUMAN DNA TOPOISOMERASE I (70 KDA) IN COMPLEX WITH THE POISON TOPOTECAN AND COVALENT COMPLEX WITH A 22 BASE PAIR DNA DUPLEX | X-ray diffraction | 2.1 | 44 | 2002-12-04 | ||||
| 17 | 1A35|1|C+ 1A35|1|D | DNA (5'-D(*AP*AP*AP*AP*AP*GP*AP*CP*TP*TP*AP*GP*AP*AP*AP*AP*AP*(BRU)P*(BRU)P*TP*TP*T)-3'), DNA (5'-D(*AP*AP*AP*AP*AP*TP*+UP*+UP*+UP*+UP*CP*+UP*AP*AP*GP*TP*CP*TP*TP*TP*+ UP*T)-3') | HUMAN TOPOISOMERASE I/DNA COMPLEX | X-ray diffraction | 2.5 | 44 | 1998-08-28 |
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 | 1K4T|1|D+ 1K4T|1|C+ 1K4T|1|B | HUMAN DNA TOPOISOMERASE I (70 KDA) IN COMPLEX WITH THE POISON TOPOTECAN AND COVALENT COMPLEX WITH A 22 BASE PAIR DNA DUPLEX | X-RAY DIFFRACTION | 2.1 | 44 | B-form double helix,double helix,structure | enzyme,isomerase | |
| 2 | 3MX4|1|O+ 3MX4|1|P | DNA binding and cleavage by the GIY-YIG endonuclease R.Eco29KI inactive variant E142Q | X-RAY DIFFRACTION | 2.5 | 44 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease | |
| 3 | 3MX4|1|K+ 3MX4|1|L | DNA binding and cleavage by the GIY-YIG endonuclease R.Eco29KI inactive variant E142Q | X-RAY DIFFRACTION | 2.5 | 44 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease | |
| 4 | 3MX4|1|M+ 3MX4|1|N | DNA binding and cleavage by the GIY-YIG endonuclease R.Eco29KI inactive variant E142Q | X-RAY DIFFRACTION | 2.5 | 44 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease | |
| 5 | 3MX4|1|I+ 3MX4|1|J | DNA binding and cleavage by the GIY-YIG endonuclease R.Eco29KI inactive variant E142Q | X-RAY DIFFRACTION | 2.5 | 44 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease | |
| 6 | 2B9S|1|E+ 2B9S|1|D+ 2B9S|1|C | Crystal Structure of heterodimeric L. donovani topoisomerase I-vanadate-DNA complex | X-RAY DIFFRACTION | 2.27 | 44 | B-form double helix,double helix,structure | enzyme,isomerase | |
| 7 | 3IKT|1|C+ 3IKT|1|D | Crystal structure of a Rex-family repressor/DNA/NAD+ complex from Thermus aquaticus | X-RAY DIFFRACTION | 2.26 | 44 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),regulatory,transcription,winged helix/forkhead | |
| 8 | 3IL2|1|C+ 3IL2|1|D | Crystal structure of a Rex-family repressor R90D mutant/DNA complex from Thermus aquaticus | X-RAY DIFFRACTION | 2.49 | 44 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),regulatory,transcription,winged helix/forkhead | |
| 9 | 3M9E|1|C+ 3M9E|1|D | Thyroid hormone beta DNA binding domain homodimer with inverted palindrome TRE | X-RAY DIFFRACTION | 2.406 | 44 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),Zinc-coordinating,nuclear receptor ZnC4,regulatory,transcription | |
| 10 | 3M9E|1|G+ 3M9E|1|H | Thyroid hormone beta DNA binding domain homodimer with inverted palindrome TRE | X-RAY DIFFRACTION | 2.406 | 44 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),Zinc-coordinating,nuclear receptor ZnC4,regulatory,transcription | |
| 11 | 1A35|1|C+ 1A35|1|D | HUMAN TOPOISOMERASE I/DNA COMPLEX | X-RAY DIFFRACTION | 2.5 | 44 | B-form double helix,double helix,structure | enzyme,isomerase | |
| 12 | 1A31|1|C+ 1A31|1|D | HUMAN RECONSTITUTED DNA TOPOISOMERASE I IN COVALENT COMPLEX WITH A 22 BASE PAIR DNA DUPLEX | X-RAY DIFFRACTION | 2.1 | 44 | B-form double helix,double helix,structure | enzyme,isomerase | |
| 13 | 1P47|1|C+ 1P47|1|D | Crystal Structure of tandem Zif268 molecules complexed to DNA | X-RAY DIFFRACTION | 2.2 | 44 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),Zinc finger C2H2,Zinc-coordinating,regulatory,transcription | |
| 14 | 2I13|1|C+ 2I13|1|D | Aart, a six finger zinc finger designed to recognize ANN triplets | X-RAY DIFFRACTION | 1.96 | 44 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),Zinc finger C2H2,Zinc-coordinating,regulatory,transcription | |
| 15 | 2I13|1|E+ 2I13|1|F | Aart, a six finger zinc finger designed to recognize ANN triplets | X-RAY DIFFRACTION | 1.96 | 44 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),Zinc finger C2H2,Zinc-coordinating,regulatory,transcription | |
| 16 | 3MLN|1|C+ 3MLN|1|D | DNA binding domain of Early B-cell Factor 1 (Ebf1) bound to DNA (crystal form II) | X-RAY DIFFRACTION | 2.4 | 44 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),P53 like,immunoglobulin (Ig) fold,regulatory,transcription | |
| 17 | 3C25|1|C+ 3C25|1|D | Crystal Structure of NotI Restriction Endonuclease Bound to Cognate DNA | X-RAY DIFFRACTION | 2.5 | 44 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease |
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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