Equivalence class DNA_2.0_20780.1 Obsolete
| # | IFE | Standardized name | Molecule | Organism | Source | Rfam | Title | Method | Res. Å | #NTs | Date |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 1MNN|1|B+ 1MNN|1|C (rep) | 5'-D(*AP*GP*TP*TP*TP*TP*TP*GP*TP*GP*TP*CP*GP*C)-3', 5'-D(*TP*GP*CP*GP*AP*CP*AP*CP*AP*AP*AP*AP*AP*C)-3' | Structure of the sporulation specific transcription factor Ndt80 bound to DNA | X-ray diffraction | 1.4 | 28 | 2002-11-20 | ||||
| 2 | 2VBL|1|C+ 2VBL|1|E+ 2VBL|1|S+ 2VBL|1|T | 5'-D(*DA*DA*DA*DA*DG*DG*DC*DA*DG*DAP)-3', 5'-D(*DA*DG*DG*DA*DT*DC*DC*DT*DA*DAP)-3', 5'-D(*DT*DC*DT*DG*DC*DC*DT*DT*DT*DT*DT*DT *DGP*DAP)-3', 5'-D(*DT*DT*DA*DG*DG*DA*DT*DC*DC*DT*DT*DC *DAP*DAP)-3' | Molecular basis of human XPC gene recognition and cleavage by engineered homing endonuclease heterodimers | X-ray diffraction | 1.8 | 48 | 2008-10-28 | ||||
| 3 | 2EVG|1|B+ 2EVG|1|C | 5'-D(*AP*GP*TP*TP*TP*AP*TP*GP*TP*GP*TP*CP*GP*C)-3', 5'-D(*TP*GP*CP*GP*AP*CP*AP*CP*AP*TP*AP*AP*AP*C)-3' | Structure of a Ndt80-DNA complex (MSE mutant mA7T) | X-ray diffraction | 1.55 | 27 | 2006-03-21 | ||||
| 4 | 2EUZ|1|B+ 2EUZ|1|C | 5'-D(*AP*GP*TP*TP*TP*TP*TP*AP*TP*GP*TP*CP*GP*C)-3', 5'-D(*TP*GP*CP*GP*AP*CP*AP*TP*AP*AP*AP*AP*AP*C)-3' | Structure of a Ndt80-DNA complex (MSE mutant mC5T) | X-ray diffraction | 1.56 | 27 | 2006-03-21 | ||||
| 5 | 2EVF|1|B+ 2EVF|1|C | 5'-D(*AP*GP*TP*TP*TP*TP*AP*GP*TP*GP*TP*CP*GP*C)-3', 5'-D(*TP*GP*CP*GP*AP*CP*AP*CP*TP*AP*AP*AP*AP*C)-3' | Structure of a Ndt80-DNA complex (MSE mutant mA6T) | X-ray diffraction | 1.56 | 27 | 2006-03-21 | ||||
| 6 | 2EUX|1|B+ 2EUX|1|C | 5'-D(*AP*GP*TP*TP*TP*TP*TP*GP*CP*GP*TP*CP*GP*C)-3', 5'-D(*TP*GP*CP*GP*AP*CP*GP*CP*AP*AP*AP*AP*AP*C)-3' | Structure of a Ndt80-DNA complex (MSE VARIANT vA4G) | X-ray diffraction | 1.57 | 28 | 2006-03-21 | ||||
| 7 | 2ETW|1|B+ 2ETW|1|C | 5'-D(*AP*GP*TP*TP*TP*TP*TP*GP*TP*GP*TP*GP*GP*C)-3', 5'-D(*TP*GP*CP*CP*AP*CP*AP*CP*AP*AP*AP*AP*AP*C)-3' | Principles of protein-DNA recognition revealed in the structural analysis of Ndt80-MSE DNA complexes | X-ray diffraction | 1.67 | 27 | 2006-03-21 | ||||
| 8 | 2EUW|1|B+ 2EUW|1|C | 5'-D(*AP*GP*TP*TP*TP*TP*TP*GP*AP*GP*TP*CP*GP*C)-3', 5'-D(*TP*GP*CP*GP*AP*CP*TP*CP*AP*AP*AP*AP*AP*C)-3' | Structure of a Ndt80-DNA complex (MSE mutant mA4T) | X-ray diffraction | 1.68 | 27 | 2006-03-21 | ||||
| 9 | 2VBN|1|C+ 2VBN|1|E+ 2VBN|1|S+ 2VBN|1|T | 5'-D(*AP*AP*AP*AP*GP*GP*CP*AP*GP*AP)-3', 5'-D(*AP*GP*GP*AP*TP*CP*CP*TP*AP*AP)-3', 5'-D(*TP*CP*TP*GP*CP*CP*TP*TP*TP*TP *TP*TP*GP*AP)-3', 5'-D(*TP*TP*AP*GP*GP*AP*TP*CP*CP*TP *TP*CP*AP*AP)-3' | Molecular basis of human XPC gene recognition and cleavage by engineered homing endonuclease heterodimers | X-ray diffraction | 1.9 | 48 | 2008-10-28 | ||||
| 10 | 2HHS|1|C+ 2HHS|1|B | 5'-D(*CP*AP*TP*(6OG)P*CP*GP*AP*GP*TP*CP*AP*GP*G)-3', 5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*GP*CP*AP*TP*GP*A)-3' | O6-methyl:C pair in the polymerase-10 basepair position | X-ray diffraction | 1.8 | 27 | 2006-12-12 | ||||
| 11 | 2EVJ|1|B+ 2EVJ|1|C | 5'-D(*AP*GP*TP*GP*TP*TP*TP*GP*TP*GP*TP*CP*GP*C)-3', 5'-D(*TP*GP*CP*GP*AP*CP*AP*CP*AP*AP*AP*CP*AP*C)-3' | Structure of an Ndt80-DNA complex (MSE mutant mA9C) | X-ray diffraction | 1.89 | 27 | 2006-03-21 | ||||
| 12 | 2EVI|1|B+ 2EVI|1|C | 5'-D(*AP*GP*TP*TP*AP*TP*TP*GP*TP*GP*TP*CP*GP*C)-3', 5'-D(*TP*GP*CP*GP*AP*CP*AP*CP*AP*AP*TP*AP*AP*C)-3' | Structure of a Ndt80-DNA complex (MSE mutant mA8T) | X-ray diffraction | 1.8 | 27 | 2006-03-21 | ||||
| 13 | 2EVH|1|B+ 2EVH|1|C | 5'-D(*AP*GP*TP*TP*TP*CP*TP*GP*TP*GP*TP*CP*GP*C)-3', 5'-D(*TP*GP*CP*GP*AP*CP*AP*CP*AP*GP*AP*AP*AP*C)-3' | Structure of a Ndt80-DNA complex (MSE mutant mA7G) | X-ray diffraction | 1.989 | 27 | 2006-03-21 | ||||
| 14 | 1N3F|1|C+ 1N3F|1|E+ 1N3F|1|D+ 1N3F|1|F | 5'-D(*CP*GP*AP*AP*AP*CP*TP*GP*TP*CP*TP*CP*GP*A)-3', 5'-D(P*GP*AP*CP*AP*GP*TP*TP*TP*CP*G-3') | Crystal structure of I-CreI bound to a palindromic DNA sequence II (palindrome of right side of wildtype DNA target sequence) | X-ray diffraction | 2 | 48 | 2003-06-03 | ||||
| 15 | 1N3F|1|I+ 1N3F|1|K+ 1N3F|1|J+ 1N3F|1|L | 5'-D(*CP*GP*AP*AP*AP*CP*TP*GP*TP*CP*TP*CP*GP*A)-3', 5'-D(P*GP*AP*CP*AP*GP*TP*TP*TP*CP*G-3') | Crystal structure of I-CreI bound to a palindromic DNA sequence II (palindrome of right side of wildtype DNA target sequence) | X-ray diffraction | 2 | 48 | 2003-06-03 | ||||
| 16 | 2EUV|1|B+ 2EUV|1|C | 5'-D(*AP*GP*TP*AP*TP*TP*TP*GP*TP*GP*TP*TP*GP*C)-3', 5'-D(*TP*GP*CP*AP*AP*CP*AP*CP*AP*AP*AP*TP*AP*C)-3' | Principles of protein-DNA recognition revealed in the structural analysis of Ndt80-MSE DNA complexes | X-ray diffraction | 1.94 | 25 | 2006-03-21 | ||||
| 17 | 1UA1|1|C+ 1UA1|1|B | DNA primer strand, DNA template strand with aminofluorene adduct | Structure of aminofluorene adduct paired opposite cytosine at the polymerase active site. | X-ray diffraction | 2 | 23 | 2004-09-28 | ||||
| 18 | 3CMY|1|B+ 3CMY|1|C | 5'-D(*DAP*DCP*DAP*DTP*DAP*DAP*DP*DCP*DGP*DAP*DTP*DTP*DAP*DC)-3', 5'-D(*DTP*DGP*DTP*DAP*DAP*DTP*DCP*DGP*DAP*DTP*DTP*DAP*DTP*DG)-3' | Structure of a homeodomain in complex with DNA | X-ray diffraction | 1.95 | 15 | 2009-02-17 | ||||
| 19 | 1LV5|1|D+ 1LV5|1|C | 5'-D(*AP*CP*GP*TP*CP*GP*CP*TP*GP*AP*TP*CP*CP*G)-3', 5'-D(*GP*GP*AP*TP*CP*AP*GP*CP*GP*A)-3' | Crystal Structure of the Closed Conformation of Bacillus DNA Polymerase I Fragment Bound to DNA and dCTP | X-ray diffraction | 1.95 | 24 | 2003-03-25 | ||||
| 20 | 1LV5|1|F+ 1LV5|1|E | 5'-D(*AP*CP*GP*TP*CP*GP*CP*TP*GP*AP*TP*CP*CP*G)-3', 5'-D(*GP*GP*AP*TP*CP*AP*GP*CP*GP*A)-3' | Crystal Structure of the Closed Conformation of Bacillus DNA Polymerase I Fragment Bound to DNA and dCTP | X-ray diffraction | 1.95 | 24 | 2003-03-25 | ||||
| 21 | 3AAF|1|C+ 3AAF|1|D | DNA (5'-D(*AP*CP*CP*CP*TP*AP*AP*TP*TP*AP*GP*GP*GP*T)-3') | Structure of WRN RQC domain bound to double-stranded DNA | X-ray diffraction | 1.9 | 28 | 2010-02-16 | ||||
| 22 | 2D5V|1|C+ 2D5V|1|D | 5'-D(*AP*TP*TP*AP*TP*TP*GP*AP*CP*TP*TP*AP*GP*A)-3', 5'-D(*TP*CP*TP*AP*AP*GP*TP*CP*AP*AP*TP*AP*AP*T)-3' | Crystal structure of HNF-6alpha DNA-binding domain in complex with the TTR promoter | X-ray diffraction | 2 | 27 | 2006-12-05 | ||||
| 23 | 2D5V|1|E+ 2D5V|1|F | 5'-D(*AP*TP*TP*AP*TP*TP*GP*AP*CP*TP*TP*AP*GP*A)-3', 5'-D(*TP*CP*TP*AP*AP*GP*TP*CP*AP*AP*TP*AP*AP*T)-3' | Crystal structure of HNF-6alpha DNA-binding domain in complex with the TTR promoter | X-ray diffraction | 2 | 26 | 2006-12-05 | ||||
| 24 | 2H7G|1|Z+ 2H7G|1|Y | 5'-D(*TP*AP*AP*TP*AP*AP*GP*GP*GP*CP*GP*AP*CP*A)-3', 5'-D(*TP*TP*GP*TP*CP*GP*CP*CP*CP*TP*TP*A)-3' | Structure of variola topoisomerase non-covalently bound to DNA | X-ray diffraction | 1.9 | 26 | 2006-08-15 | ||||
| 25 | 1G9Z|1|C+ 1G9Z|1|E+ 1G9Z|1|D+ 1G9Z|1|F | 5'-D(*CP*GP*AP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*C)-3', 5'-D(*GP*CP*AP*AP*AP*AP*CP*GP*TP*CP*GP*TP*GP*A)-3', 5'-D(P*GP*AP*CP*AP*GP*TP*TP*TP*CP*G)-3', 5'-D(P*GP*AP*CP*GP*TP*TP*TP*TP*GP*C)-3' | LAGLIDADG HOMING ENDONUCLEASE I-CREI / DNA PRODUCT COMPLEX WITH MAGNESIUM | X-ray diffraction | 1.8 | 48 | 2001-04-02 | ||||
| 26 | 1FJL|1|D+ 1FJL|1|E | DNA (5'-D(*AP*AP*TP*AP*AP*TP*CP*TP*GP*AP*TP*TP*AP*C)-3'), DNA (5'-D(*TP*GP*TP*AP*AP*TP*CP*AP*GP*AP*TP*TP*AP*T)-3') | HOMEODOMAIN FROM THE DROSOPHILA PAIRED PROTEIN BOUND TO A DNA OLIGONUCLEOTIDE | X-ray diffraction | 2 | 28 | 1996-06-20 | ||||
| 27 | 1FJL|1|F | DNA (5'-D(*TP*GP*TP*AP*AP*TP*CP*TP*GP*AP*TP*TP*AP*C)-3') | HOMEODOMAIN FROM THE DROSOPHILA PAIRED PROTEIN BOUND TO A DNA OLIGONUCLEOTIDE | X-ray diffraction | 2 | 14 | 1996-06-20 |
Parents
| This class | Parent classes | Release id | Intersection | Added to this class | Only in parent |
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Children
| This class | Descendant classes | Release id | Intersection | Only in this class | Added to child |
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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 | 3CMY|1|B+ 3CMY|1|C | Structure of a homeodomain in complex with DNA | X-RAY DIFFRACTION | 1.95 | 15 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),homeodomain,regulatory,transcription | |
| 2 | 1N3F|1|C+ 1N3F|1|E+ 1N3F|1|D+ 1N3F|1|F | Crystal structure of I-CreI bound to a palindromic DNA sequence II (palindrome of right side of wildtype DNA target sequence) | X-RAY DIFFRACTION | 2 | 48 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease | |
| 3 | 1N3F|1|I+ 1N3F|1|K+ 1N3F|1|J+ 1N3F|1|L | Crystal structure of I-CreI bound to a palindromic DNA sequence II (palindrome of right side of wildtype DNA target sequence) | X-RAY DIFFRACTION | 2 | 48 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease | |
| 4 | 1G9Z|1|C+ 1G9Z|1|E+ 1G9Z|1|D+ 1G9Z|1|F | LAGLIDADG HOMING ENDONUCLEASE I-CREI / DNA PRODUCT COMPLEX WITH MAGNESIUM | X-RAY DIFFRACTION | 1.8 | 48 | double helix,structure | enzyme,hydrolase,nuclease | |
| 5 | 2VBN|1|C+ 2VBN|1|E+ 2VBN|1|S+ 2VBN|1|T | Molecular basis of human XPC gene recognition and cleavage by engineered homing endonuclease heterodimers | X-RAY DIFFRACTION | 1.9 | 48 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease | |
| 6 | 2VBL|1|C+ 2VBL|1|E+ 2VBL|1|S+ 2VBL|1|T | Molecular basis of human XPC gene recognition and cleavage by engineered homing endonuclease heterodimers | X-RAY DIFFRACTION | 1.8 | 48 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease | |
| 7 | 2HHS|1|C+ 2HHS|1|B | O6-methyl:C pair in the polymerase-10 basepair position | X-RAY DIFFRACTION | 1.8 | 27 | B-form double helix,double helix,structure | enzyme,polymerase,transferase | |
| 8 | 1FJL|1|D+ 1FJL|1|E | HOMEODOMAIN FROM THE DROSOPHILA PAIRED PROTEIN BOUND TO A DNA OLIGONUCLEOTIDE | X-RAY DIFFRACTION | 2 | 28 | B-form double helix,double helix,feature,mispair,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),homeodomain,regulatory,transcription | |
| 9 | 1FJL|1|F | HOMEODOMAIN FROM THE DROSOPHILA PAIRED PROTEIN BOUND TO A DNA OLIGONUCLEOTIDE | X-RAY DIFFRACTION | 2 | 14 | B-form double helix,double helix,feature,mispair,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),homeodomain,regulatory,transcription | |
| 10 | 3AAF|1|C+ 3AAF|1|D | Structure of WRN RQC domain bound to double-stranded DNA | X-RAY DIFFRACTION | 1.9 | 28 | double helix,structure | enzyme,helicase,hydrolase | |
| 11 | 2D5V|1|E+ 2D5V|1|F | Crystal structure of HNF-6alpha DNA-binding domain in complex with the TTR promoter | X-RAY DIFFRACTION | 2 | 26 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),homeodomain,regulatory,transcription | |
| 12 | 2D5V|1|C+ 2D5V|1|D | Crystal structure of HNF-6alpha DNA-binding domain in complex with the TTR promoter | X-RAY DIFFRACTION | 2 | 27 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),homeodomain,regulatory,transcription | |
| 13 | 2EVF|1|B+ 2EVF|1|C | Structure of a Ndt80-DNA complex (MSE mutant mA6T) | X-RAY DIFFRACTION | 1.56 | 27 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),P53 like,immunoglobulin (Ig) fold,regulatory,transcription | |
| 14 | 2EVI|1|B+ 2EVI|1|C | Structure of a Ndt80-DNA complex (MSE mutant mA8T) | X-RAY DIFFRACTION | 1.8 | 27 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),P53 like,immunoglobulin (Ig) fold,regulatory,transcription | |
| 15 | 1MNN|1|B+ 1MNN|1|C | Structure of the sporulation specific transcription factor Ndt80 bound to DNA | X-RAY DIFFRACTION | 1.4 | 28 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),P53 like,immunoglobulin (Ig) fold,regulatory,transcription | |
| 16 | 2EUZ|1|B+ 2EUZ|1|C | Structure of a Ndt80-DNA complex (MSE mutant mC5T) | X-RAY DIFFRACTION | 1.56 | 27 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),P53 like,immunoglobulin (Ig) fold,regulatory,transcription | |
| 17 | 2EVJ|1|B+ 2EVJ|1|C | Structure of an Ndt80-DNA complex (MSE mutant mA9C) | X-RAY DIFFRACTION | 1.89 | 27 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),P53 like,immunoglobulin (Ig) fold,regulatory,transcription | |
| 18 | 2EVG|1|B+ 2EVG|1|C | Structure of a Ndt80-DNA complex (MSE mutant mA7T) | X-RAY DIFFRACTION | 1.55 | 27 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),P53 like,immunoglobulin (Ig) fold,regulatory,transcription | |
| 19 | 2EVH|1|B+ 2EVH|1|C | Structure of a Ndt80-DNA complex (MSE mutant mA7G) | X-RAY DIFFRACTION | 1.989 | 27 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),P53 like,immunoglobulin (Ig) fold,regulatory,transcription | |
| 20 | 2EUW|1|B+ 2EUW|1|C | Structure of a Ndt80-DNA complex (MSE mutant mA4T) | X-RAY DIFFRACTION | 1.68 | 27 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),P53 like,immunoglobulin (Ig) fold,regulatory,transcription | |
| 21 | 2EUX|1|B+ 2EUX|1|C | Structure of a Ndt80-DNA complex (MSE VARIANT vA4G) | X-RAY DIFFRACTION | 1.57 | 28 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),P53 like,immunoglobulin (Ig) fold,regulatory,transcription | |
| 22 | 2EUV|1|B+ 2EUV|1|C | Principles of protein-DNA recognition revealed in the structural analysis of Ndt80-MSE DNA complexes | X-RAY DIFFRACTION | 1.94 | 25 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),P53 like,immunoglobulin (Ig) fold,regulatory,transcription | |
| 23 | 2ETW|1|B+ 2ETW|1|C | Principles of protein-DNA recognition revealed in the structural analysis of Ndt80-MSE DNA complexes | X-RAY DIFFRACTION | 1.67 | 27 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),P53 like,immunoglobulin (Ig) fold,regulatory,transcription | |
| 24 | 2H7G|1|Z+ 2H7G|1|Y | Structure of variola topoisomerase non-covalently bound to DNA | X-RAY DIFFRACTION | 1.9 | 26 | B-form double helix,double helix,structure | enzyme,isomerase | |
| 25 | 1UA1|1|C+ 1UA1|1|B | Structure of aminofluorene adduct paired opposite cytosine at the polymerase active site. | X-RAY DIFFRACTION | 2 | 23 | B-form double helix,double helix,structure | enzyme,polymerase,transferase | |
| 26 | 1LV5|1|F+ 1LV5|1|E | Crystal Structure of the Closed Conformation of Bacillus DNA Polymerase I Fragment Bound to DNA and dCTP | X-RAY DIFFRACTION | 1.95 | 24 | double helix,structure | enzyme,polymerase,transferase | |
| 27 | 1LV5|1|D+ 1LV5|1|C | Crystal Structure of the Closed Conformation of Bacillus DNA Polymerase I Fragment Bound to DNA and dCTP | X-RAY DIFFRACTION | 1.95 | 24 | double helix,structure | enzyme,polymerase,transferase |
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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