Equivalence class DNA_2.5_70554.3 Current
| # | IFE | Standardized name | Molecule | Organism | Source | Rfam | Title | Method | Res. Å | 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 | 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 | 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 | 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 | 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 | 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 | 2010-06-09 | ||||
| 7 | 3QYN|1|F | 5'-D(*AP*AP*AP*CP*AP*TP*GP*TP*TP*TP*TP*AP*AP*AP*AP*CP*AP*TP*GP*TP*TP*T)-3' | Structure of p63 DNA Binding Domain in Complex with a 22 Base Pair A/T Rich Response Element Containing 2 Base Pair Spacer Between Half Sites | X-ray diffraction | 2.5 | 2011-04-06 | ||||
| 8 | 3QYN|1|E | 5'-D(*AP*AP*AP*CP*AP*TP*GP*TP*TP*TP*TP*AP*AP*AP*AP*CP*AP*TP*GP*TP*TP*T)-3' | Structure of p63 DNA Binding Domain in Complex with a 22 Base Pair A/T Rich Response Element Containing 2 Base Pair Spacer Between Half Sites | X-ray diffraction | 2.5 | 2011-04-06 | ||||
| 9 | 1P47|1|C+ 1P47|1|D | 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', 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' | Crystal Structure of tandem Zif268 molecules complexed to DNA | X-ray diffraction | 2.2 | 2003-06-24 | ||||
| 10 | 2B9S|1|E+ 2B9S|1|D+ 2B9S|1|C | 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', 5'-D(*AP*AP*AP*AP*AP*GP*AP*CP*TP*T)-3' | Crystal Structure of heterodimeric L. donovani topoisomerase I-vanadate-DNA complex | X-ray diffraction | 2.27 | 2006-01-17 | ||||
| 11 | 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 | 2010-06-09 | ||||
| 12 | 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 | 2008-02-12 | ||||
| 13 | 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 | 2010-09-08 | ||||
| 14 | 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 | 2010-09-08 | ||||
| 15 | 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 | 2010-09-08 | ||||
| 16 | 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 | 2010-09-08 | ||||
| 17 | 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 | 1998-08-28 | ||||
| 18 | 1K4T|1|D+ 1K4T|1|C+ 1K4T|1|B | 5'-D(*AP*AP*AP*AP*AP*GP*AP*CP*TP*T)-3', 5'-D(*(TGP)P*GP*AP*AP*AP*AP*AP*TP*TP*TP*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 | 2002-12-04 | ||||
| 19 | 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 | 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 |
|---|
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 | 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 | 22 | B-form double helix,double helix,structure | enzyme,isomerase |
| 2 | 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 | 22 | B-form double helix,double helix,structure | enzyme,isomerase |
| 3 | 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 | 22 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease |
| 4 | 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 | 22 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease |
| 5 | 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 | 22 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease |
| 6 | 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 | 22 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease |
| 7 | 1A35|1|C+1A35|1|D | HUMAN TOPOISOMERASE I/DNA COMPLEX | X-RAY DIFFRACTION | 2.5 | 22 | B-form double helix,double helix,structure | enzyme,isomerase |
| 8 | 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 | 22 | B-form double helix,double helix,structure | enzyme,isomerase |
| 9 | 3M9E|1|G+3M9E|1|H | Thyroid hormone beta DNA binding domain homodimer with inverted palindrome TRE | X-RAY DIFFRACTION | 2.406 | 22 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),Zinc-coordinating,nuclear receptor ZnC4,regulatory,transcription |
| 10 | 3M9E|1|C+3M9E|1|D | Thyroid hormone beta DNA binding domain homodimer with inverted palindrome TRE | X-RAY DIFFRACTION | 2.406 | 22 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),Zinc-coordinating,nuclear receptor ZnC4,regulatory,transcription |
| 11 | 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 | 22 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),regulatory,transcription,winged helix/forkhead |
| 12 | 3IKT|1|C+3IKT|1|D | Crystal structure of a Rex-family repressor/DNA/NAD+ complex from Thermus aquaticus | X-RAY DIFFRACTION | 2.26 | 22 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),regulatory,transcription,winged helix/forkhead |
| 13 | 3QYN|1|F | Structure of p63 DNA Binding Domain in Complex with a 22 Base Pair A/T Rich Response Element Containing 2 Base Pair Spacer Between Half Sites | X-RAY DIFFRACTION | 2.5 | 58 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),P53 like,immunoglobulin (Ig) fold,regulatory,transcription |
| 14 | 3QYN|1|E | Structure of p63 DNA Binding Domain in Complex with a 22 Base Pair A/T Rich Response Element Containing 2 Base Pair Spacer Between Half Sites | X-RAY DIFFRACTION | 2.5 | 52 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),P53 like,immunoglobulin (Ig) fold,regulatory,transcription |
| 15 | 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 | 22 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),P53 like,immunoglobulin (Ig) fold,regulatory,transcription |
| 16 | 2I13|1|E+2I13|1|F | Aart, a six finger zinc finger designed to recognize ANN triplets | X-RAY DIFFRACTION | 1.96 | 22 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),Zinc finger C2H2,Zinc-coordinating,regulatory,transcription |
| 17 | 2I13|1|C+2I13|1|D | Aart, a six finger zinc finger designed to recognize ANN triplets | X-RAY DIFFRACTION | 1.96 | 22 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),Zinc finger C2H2,Zinc-coordinating,regulatory,transcription |
| 18 | 1P47|1|C+1P47|1|D | Crystal Structure of tandem Zif268 molecules complexed to DNA | X-RAY DIFFRACTION | 2.2 | 22 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),Zinc finger C2H2,Zinc-coordinating,regulatory,transcription |
| 19 | 3C25|1|C+3C25|1|D | Crystal Structure of NotI Restriction Endonuclease Bound to Cognate DNA | X-RAY DIFFRACTION | 2.5 | 22 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease |
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