Equivalence class DNA_2.0_45969.3 Current
| # | IFE | Standardized name | Molecule | Organism | Source | Rfam | Title | Method | Res. Å | Date |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 1MNN|1|B+ 1MNN|1|C (rep) | 5'-D(*TP*GP*CP*GP*AP*CP*AP*CP*AP*AP*AP*AP*AP*C)-3', 5'-D(*AP*GP*TP*TP*TP*TP*TP*GP*TP*GP*TP*CP*GP*C)-3' | Structure of the sporulation specific transcription factor Ndt80 bound to DNA | X-ray diffraction | 1.4 | 2002-11-20 | ||||
| 2 | 2VBL|1|C+ 2VBL|1|E+ 2VBL|1|S+ 2VBL|1|T | 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', 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' | Molecular basis of human XPC gene recognition and cleavage by engineered homing endonuclease heterodimers | X-ray diffraction | 1.8 | 2008-10-28 | ||||
| 3 | 2EVG|1|B+ 2EVG|1|C | 5'-D(*TP*GP*CP*GP*AP*CP*AP*CP*AP*TP*AP*AP*AP*C)-3', 5'-D(*AP*GP*TP*TP*TP*AP*TP*GP*TP*GP*TP*CP*GP*C)-3' | Structure of a Ndt80-DNA complex (MSE mutant mA7T) | X-ray diffraction | 1.55 | 2006-03-21 | ||||
| 4 | 2EVF|1|B+ 2EVF|1|C | 5'-D(*TP*GP*CP*GP*AP*CP*AP*CP*TP*AP*AP*AP*AP*C)-3', 5'-D(*AP*GP*TP*TP*TP*TP*AP*GP*TP*GP*TP*CP*GP*C)-3' | Structure of a Ndt80-DNA complex (MSE mutant mA6T) | X-ray diffraction | 1.56 | 2006-03-21 | ||||
| 5 | 2EUZ|1|B+ 2EUZ|1|C | 5'-D(*TP*GP*CP*GP*AP*CP*AP*TP*AP*AP*AP*AP*AP*C)-3', 5'-D(*AP*GP*TP*TP*TP*TP*TP*AP*TP*GP*TP*CP*GP*C)-3' | Structure of a Ndt80-DNA complex (MSE mutant mC5T) | X-ray diffraction | 1.56 | 2006-03-21 | ||||
| 6 | 2ETW|1|B+ 2ETW|1|C | 5'-D(*TP*GP*CP*CP*AP*CP*AP*CP*AP*AP*AP*AP*AP*C)-3', 5'-D(*AP*GP*TP*TP*TP*TP*TP*GP*TP*GP*TP*GP*GP*C)-3' | Principles of protein-DNA recognition revealed in the structural analysis of Ndt80-MSE DNA complexes | X-ray diffraction | 1.67 | 2006-03-21 | ||||
| 7 | 2EUX|1|B+ 2EUX|1|C | 5'-D(*TP*GP*CP*GP*AP*CP*GP*CP*AP*AP*AP*AP*AP*C)-3', 5'-D(*AP*GP*TP*TP*TP*TP*TP*GP*CP*GP*TP*CP*GP*C)-3' | Structure of a Ndt80-DNA complex (MSE VARIANT vA4G) | X-ray diffraction | 1.57 | 2006-03-21 | ||||
| 8 | 2EUW|1|B+ 2EUW|1|C | 5'-D(*TP*GP*CP*GP*AP*CP*TP*CP*AP*AP*AP*AP*AP*C)-3', 5'-D(*AP*GP*TP*TP*TP*TP*TP*GP*AP*GP*TP*CP*GP*C)-3' | Structure of a Ndt80-DNA complex (MSE mutant mA4T) | X-ray diffraction | 1.68 | 2006-03-21 | ||||
| 9 | 2HHS|1|C+ 2HHS|1|B | 5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*GP*CP*AP*TP*GP*A)-3', 5'-D(*CP*AP*TP*(6OG)P*CP*GP*AP*GP*TP*CP*AP*GP*G)-3' | O6-methyl:C pair in the polymerase-10 basepair position | X-ray diffraction | 1.8 | 2006-12-12 | ||||
| 10 | 2EVJ|1|B+ 2EVJ|1|C | 5'-D(*TP*GP*CP*GP*AP*CP*AP*CP*AP*AP*AP*CP*AP*C)-3', 5'-D(*AP*GP*TP*GP*TP*TP*TP*GP*TP*GP*TP*CP*GP*C)-3' | Structure of an Ndt80-DNA complex (MSE mutant mA9C) | X-ray diffraction | 1.89 | 2006-03-21 | ||||
| 11 | 2VBN|1|C+ 2VBN|1|E+ 2VBN|1|S+ 2VBN|1|T | 5'-D(*TP*TP*AP*GP*GP*AP*TP*CP*CP*TP *TP*CP*AP*AP)-3', 5'-D(*TP*CP*TP*GP*CP*CP*TP*TP*TP*TP *TP*TP*GP*AP)-3', 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' | Molecular basis of human XPC gene recognition and cleavage by engineered homing endonuclease heterodimers | X-ray diffraction | 1.9 | 2008-10-28 | ||||
| 12 | 2EVI|1|B+ 2EVI|1|C | 5'-D(*TP*GP*CP*GP*AP*CP*AP*CP*AP*AP*TP*AP*AP*C)-3', 5'-D(*AP*GP*TP*TP*AP*TP*TP*GP*TP*GP*TP*CP*GP*C)-3' | Structure of a Ndt80-DNA complex (MSE mutant mA8T) | X-ray diffraction | 1.8 | 2006-03-21 | ||||
| 13 | 2EVH|1|B+ 2EVH|1|C | 5'-D(*TP*GP*CP*GP*AP*CP*AP*CP*AP*GP*AP*AP*AP*C)-3', 5'-D(*AP*GP*TP*TP*TP*CP*TP*GP*TP*GP*TP*CP*GP*C)-3' | Structure of a Ndt80-DNA complex (MSE mutant mA7G) | X-ray diffraction | 1.989 | 2006-03-21 | ||||
| 14 | 2EUV|1|B+ 2EUV|1|C | 5'-D(*TP*GP*CP*AP*AP*CP*AP*CP*AP*AP*AP*TP*AP*C)-3', 5'-D(*AP*GP*TP*AP*TP*TP*TP*GP*TP*GP*TP*TP*GP*C)-3' | Principles of protein-DNA recognition revealed in the structural analysis of Ndt80-MSE DNA complexes | X-ray diffraction | 1.94 | 2006-03-21 | ||||
| 15 | 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 | 2003-06-03 | ||||
| 16 | 1UA1|1|C+ 1UA1|1|B | DNA template strand with aminofluorene adduct, DNA primer strand | Structure of aminofluorene adduct paired opposite cytosine at the polymerase active site. | X-ray diffraction | 2 | 2004-09-28 | ||||
| 17 | 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 | 2003-06-03 | ||||
| 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 | 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 | 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 | 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 | 2010-02-16 | ||||
| 22 | 2D5V|1|C+ 2D5V|1|D | 5'-D(*TP*CP*TP*AP*AP*GP*TP*CP*AP*AP*TP*AP*AP*T)-3', 5'-D(*AP*TP*TP*AP*TP*TP*GP*AP*CP*TP*TP*AP*GP*A)-3' | Crystal structure of HNF-6alpha DNA-binding domain in complex with the TTR promoter | X-ray diffraction | 2 | 2006-12-05 | ||||
| 23 | 2D5V|1|E+ 2D5V|1|F | 5'-D(*TP*CP*TP*AP*AP*GP*TP*CP*AP*AP*TP*AP*AP*T)-3', 5'-D(*AP*TP*TP*AP*TP*TP*GP*AP*CP*TP*TP*AP*GP*A)-3' | Crystal structure of HNF-6alpha DNA-binding domain in complex with the TTR promoter | X-ray diffraction | 2 | 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 | 2006-08-15 | ||||
| 25 | 1G9Z|1|C+ 1G9Z|1|E+ 1G9Z|1|D+ 1G9Z|1|F | 5'-D(*GP*CP*AP*AP*AP*AP*CP*GP*TP*CP*GP*TP*GP*A)-3', 5'-D(*CP*GP*AP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*C)-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 | 2001-04-02 | ||||
| 26 | 1FJL|1|D+ 1FJL|1|E+ 1FJL|1|F | 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'), 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 | 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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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 | 2HHS|1|C+2HHS|1|B | O6-methyl:C pair in the polymerase-10 basepair position | X-RAY DIFFRACTION | 1.8 | 14 | B-form double helix,double helix,structure | enzyme,polymerase,transferase |
| 2 | 2D5V|1|E+2D5V|1|F | Crystal structure of HNF-6alpha DNA-binding domain in complex with the TTR promoter | X-RAY DIFFRACTION | 2 | 14 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),homeodomain,regulatory,transcription |
| 3 | 3AAF|1|C+3AAF|1|D | Structure of WRN RQC domain bound to double-stranded DNA | X-RAY DIFFRACTION | 1.9 | 14 | double helix,structure | enzyme,helicase,hydrolase |
| 4 | 1FJL|1|D+1FJL|1|E+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 |
| 5 | 2D5V|1|C+2D5V|1|D | Crystal structure of HNF-6alpha DNA-binding domain in complex with the TTR promoter | X-RAY DIFFRACTION | 2 | 14 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),homeodomain,regulatory,transcription |
| 6 | 2EUZ|1|B+2EUZ|1|C | Structure of a Ndt80-DNA complex (MSE mutant mC5T) | X-RAY DIFFRACTION | 1.56 | 14 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),P53 like,immunoglobulin (Ig) fold,regulatory,transcription |
| 7 | 2EVG|1|B+2EVG|1|C | Structure of a Ndt80-DNA complex (MSE mutant mA7T) | X-RAY DIFFRACTION | 1.55 | 14 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),P53 like,immunoglobulin (Ig) fold,regulatory,transcription |
| 8 | 1MNN|1|B+1MNN|1|C | Structure of the sporulation specific transcription factor Ndt80 bound to DNA | X-RAY DIFFRACTION | 1.4 | 14 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),P53 like,immunoglobulin (Ig) fold,regulatory,transcription |
| 9 | 2EVF|1|B+2EVF|1|C | Structure of a Ndt80-DNA complex (MSE mutant mA6T) | X-RAY DIFFRACTION | 1.56 | 14 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),P53 like,immunoglobulin (Ig) fold,regulatory,transcription |
| 10 | 2EVI|1|B+2EVI|1|C | Structure of a Ndt80-DNA complex (MSE mutant mA8T) | X-RAY DIFFRACTION | 1.8 | 14 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),P53 like,immunoglobulin (Ig) fold,regulatory,transcription |
| 11 | 2EVJ|1|B+2EVJ|1|C | Structure of an Ndt80-DNA complex (MSE mutant mA9C) | X-RAY DIFFRACTION | 1.89 | 14 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),P53 like,immunoglobulin (Ig) fold,regulatory,transcription |
| 12 | 2EVH|1|B+2EVH|1|C | Structure of a Ndt80-DNA complex (MSE mutant mA7G) | X-RAY DIFFRACTION | 1.989 | 14 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),P53 like,immunoglobulin (Ig) fold,regulatory,transcription |
| 13 | 2EUW|1|B+2EUW|1|C | Structure of a Ndt80-DNA complex (MSE mutant mA4T) | X-RAY DIFFRACTION | 1.68 | 14 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),P53 like,immunoglobulin (Ig) fold,regulatory,transcription |
| 14 | 2EUX|1|B+2EUX|1|C | Structure of a Ndt80-DNA complex (MSE VARIANT vA4G) | X-RAY DIFFRACTION | 1.57 | 14 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),P53 like,immunoglobulin (Ig) fold,regulatory,transcription |
| 15 | 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 | 14 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),P53 like,immunoglobulin (Ig) fold,regulatory,transcription |
| 16 | 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 | 14 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),P53 like,immunoglobulin (Ig) fold,regulatory,transcription |
| 17 | 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 | 14 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease |
| 18 | 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 | 14 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease |
| 19 | 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 | 14 | double helix,structure | enzyme,hydrolase,nuclease |
| 20 | 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 | 14 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease |
| 21 | 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 | 14 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease |
| 22 | 3CMY|1|B+3CMY|1|C | Structure of a homeodomain in complex with DNA | X-RAY DIFFRACTION | 1.95 | 14 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),homeodomain,regulatory,transcription |
| 23 | 2H7G|1|Z+2H7G|1|Y | Structure of variola topoisomerase non-covalently bound to DNA | X-RAY DIFFRACTION | 1.9 | 14 | B-form double helix,double helix,structure | enzyme,isomerase |
| 24 | 1UA1|1|C+1UA1|1|B | Structure of aminofluorene adduct paired opposite cytosine at the polymerase active site. | X-RAY DIFFRACTION | 2 | 14 | B-form double helix,double helix,structure | enzyme,polymerase,transferase |
| 25 | 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 | 14 | double helix,structure | enzyme,polymerase,transferase |
| 26 | 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 | 14 | double helix,structure | enzyme,polymerase,transferase |
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