Equivalence class DNA_4.0_38328.1 Current
| # | IFE | Standardized name | Molecule | Organism | Source | Rfam | Title | Method | Res. Å | Date |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 2VBO|1|C+ 2VBO|1|E (rep) | 5'-D(*TP*CP*TP*GP*CP*CP*TP*TP*TP*TP *TP*TP*GP*AP*AP*GP*GP*AP*TP*CP*CP*TP*AP*A)-3', 5'-D(*TP*TP*AP*GP*GP*AP*TP*CP*CP*TP *TP*CP*AP*AP*AP*AP*AP*AP*GP*GP*CP*AP*GP*A)-3' | Molecular basis of human XPC gene recognition and cleavage by engineered homing endonuclease heterodimers | X-ray diffraction | 1.8 | 2008-10-28 | ||||
| 2 | 2VBJ|1|C+ 2VBJ|1|E | 5'-D(*TP*CP*TP*GP*CP*CP*TP*TP*TP*TP *TP*TP*GP*AP*AP*GP*GP*AP*TP*CP*CP*TP*AP*A)-3', 5'-D(*TP*TP*AP*GP*GP*AP*TP*CP*CP*TP *TP*CP*AP*AP*AP*AP*AP*AP*GP*GP*CP*AP*GP*A)-3' | synthetic construct | Molecular basis of human XPC gene recognition and cleavage by engineered homing endonuclease heterodimers | X-ray diffraction | 1.95 | 2008-10-28 | |||
| 3 | 3MXB|1|C+ 3MXB|1|E | DNA (5'-D(*TP*TP*GP*TP*TP*CP*TP*CP*AP*GP*GP*TP*AP*CP*CP*TP*CP*AP*GP*CP*CP*AP*GP*A)-3'), DNA (5'-D(*TP*CP*TP*GP*GP*CP*TP*GP*AP*GP*GP*TP*AP*CP*CP*TP*GP*AP*GP*AP*AP*CP*AP*A)-3') | Molecular basis of engineered meganuclease targeting of the endogenous human RAG1 locus | X-ray diffraction | 2.3 | 2010-10-06 | ||||
| 4 | 3MXB|1|T+ 3MXB|1|V | DNA (5'-D(*TP*TP*GP*TP*TP*CP*TP*CP*AP*GP*GP*TP*AP*CP*CP*TP*CP*AP*GP*CP*CP*AP*GP*A)-3'), DNA (5'-D(*TP*CP*TP*GP*GP*CP*TP*GP*AP*GP*GP*TP*AP*CP*CP*TP*GP*AP*GP*AP*AP*CP*AP*A)-3') | Molecular basis of engineered meganuclease targeting of the endogenous human RAG1 locus | X-ray diffraction | 2.3 | 2010-10-06 | ||||
| 5 | 2XE0|1|C+ 2XE0|1|D | 24MER DNA | Homo sapiens | Molecular basis of engineered meganuclease targeting of the endogenous human RAG1 locus | X-ray diffraction | 2.31 | 2010-09-29 | |||
| 6 | 1M5X|1|C+ 1M5X|1|D | 5'-D(*GP*CP*AP*GP*AP*AP*CP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*AP*GP*TP*TP*CP*CP*G)-3', 5'-D(*CP*GP*GP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*CP*GP*AP*CP*GP*TP*TP*CP*TP*GP*C)-3' | Crystal structure of the homing endonuclease I-MsoI bound to its DNA substrate | X-ray diffraction | 2.25 | 2003-06-03 | ||||
| 7 | 2FLD|1|C+ 2FLD|1|D | 5'-D(*GP*CP*AP*GP*AP*AP*GP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*CP*GP*TP*TP*CP*CP*G)-3', 5'-D(*CP*GP*GP*AP*AP*CP*GP*GP*TP*CP*TP*CP*AP*CP*GP*AP*CP*CP*TP*TP*CP*TP*GP*C)-3' | I-MsoI Re-Designed for Altered DNA Cleavage Specificity | X-ray diffraction | 2 | 2006-06-06 | ||||
| 8 | 3MX9|1|C+ 3MX9|1|D | DNA (5'-D(*TP*TP*GP*TP*TP*CP*TP*CP*AP*GP*GP*TP*AP*CP*CP*TP*CP*AP*GP*CP*CP*AP*GP*A)-3'), DNA (5'-D(*TP*CP*TP*GP*GP*CP*TP*GP*AP*GP*GP*TP*AP*CP*CP*TP*GP*AP*GP*AP*AP*CP*AP*A)-3') | Molecular basis of engineered meganuclease targeting of the endogenous human RAG1 locus | X-ray diffraction | 2.6 | 2010-10-06 | ||||
| 9 | 2I3Q|1|C+ 2I3Q|1|D | 5'-D(*GP*CP*AP*AP*AP*AP*CP*GP*AP*CP*GP*TP*GP*AP*GP*TP*CP*AP*GP*TP*TP*TP*CP*G)-3', 5'-D(*CP*GP*AP*AP*AP*CP*TP*GP*AP*CP*TP*CP*AP*CP*GP*TP*CP*GP*TP*TP*TP*TP*GP*C)-3' | Q44V mutant of Homing Endonuclease I-CreI | X-ray diffraction | 2.3 | 2006-09-05 | ||||
| 10 | 3MIP|1|C+ 3MIP|1|D | DNA (5'-D(*GP*CP*AP*GP*GP*CP*GP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*CP*GP*CP*TP*CP*CP*G)-3'), DNA (5'-D(*CP*GP*GP*AP*GP*CP*GP*GP*TP*CP*TP*CP*AP*CP*GP*AP*CP*CP*GP*CP*CP*TP*GP*C)-3') | I-MsoI re-designed for altered DNA cleavage specificity (-8GCG) | X-ray diffraction | 2.4 | 2010-05-19 | ||||
| 11 | 3MIS|1|C+ 3MIS|1|D | DNA (5'-D(*GP*CP*AP*GP*GP*AP*CP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*AP*GP*CP*TP*CP*CP*G)-3'), DNA (5'-D(*CP*GP*GP*AP*GP*CP*TP*GP*TP*CP*TP*CP*AP*CP*GP*AP*CP*GP*TP*CP*CP*TP*GP*C)-3') | I-MsoI re-designed for altered DNA cleavage specificity (-8G) | X-ray diffraction | 2.3 | 2010-05-19 | ||||
| 12 | 2I3P|1|C+ 2I3P|1|D | 5'-D(*GP*CP*AP*AP*AP*TP*CP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*AP*AP*TP*TP*TP*CP*G)-3', 5'-D(*CP*GP*AP*AP*AP*TP*TP*GP*TP*CP*TP*CP*AP*CP*GP*AP*CP*GP*AP*TP*TP*TP*GP*C)-3' | K28R mutant of Homing Endonuclease I-CreI | X-ray diffraction | 2.3 | 2006-09-05 | ||||
| 13 | 3FD2|1|B+ 3FD2|1|C | 5'-D(*GP*CP*AP*GP*AP*AP*CP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*AP*GP*TP*TP*CP*CP*G)-3', 5'-D(*CP*GP*GP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*CP*GP*AP*CP*GP*TP*TP*CP*TP*GP*C)-3' | synthetic construct | Crystal structure of mMsoI/DNA complex with calcium | X-ray diffraction | 2.69 | 2009-06-30 | |||
| 14 | 3KO2|1|C+ 3KO2|1|D | 5'-D(*GP*CP*AP*GP*AP*CP*CP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*AP*GP*TP*TP*CP*CP*G)-3', 5'-D(*CP*GP*GP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*CP*GP*AP*CP*GP*GP*TP*CP*TP*GP*C)-3' | I-MsoI re-designed for altered DNA cleavage specificity (-7C) | X-ray diffraction | 2.9 | 2010-05-19 | ||||
| 15 | 3KO2|1|H+ 3KO2|1|I | 5'-D(*GP*CP*AP*GP*AP*CP*CP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*AP*GP*TP*TP*CP*CP*G)-3', 5'-D(*CP*GP*GP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*CP*GP*AP*CP*GP*GP*TP*CP*TP*GP*C)-3' | I-MsoI re-designed for altered DNA cleavage specificity (-7C) | X-ray diffraction | 2.9 | 2010-05-19 | ||||
| 16 | 1U0D|1|C+ 1U0D|1|D | 5'-D(*GP*CP*GP*AP*AP*AP*CP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*AP*GP*TP*TP*CP*CP*G)-3', 5'-D(*CP*GP*GP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*CP*GP*AP*CP*GP*TP*TP*TP*CP*GP*C)-3' | Y33H Mutant of Homing endonuclease I-CreI | X-ray diffraction | 2.9 | 2004-11-02 | ||||
| 17 | 1T9I|1|C+ 1T9I|1|D | 5'-D(*GP*CP*AP*AP*AP*AP*CP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*AP*GP*TP*TP*TP*CP*G)-3', 5'-D(*CP*GP*AP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*CP*GP*AP*CP*GP*TP*TP*TP*TP*GP*C)-3' | I-CreI(D20N)/DNA complex | X-ray diffraction | 1.6 | 2004-11-16 | ||||
| 18 | 1T9J|1|C+ 1T9J|1|D | 5'-D(*GP*CP*AP*AP*AP*AP*CP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*AP*GP*TP*TP*TP*CP*G)-3', 5'-D(*CP*GP*AP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*CP*GP*AP*CP*GP*TP*TP*TP*TP*GP*C)-3' | I-CreI(Q47E)/DNA complex | X-ray diffraction | 2 | 2004-11-16 | ||||
| 19 | 1G9Y|1|C+ 1G9Y|1|D | 5'-D(*CP*GP*AP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*CP*GP*AP*CP*GP*TP*TP*TP*TP*GP*C)-3', 5'-D(*GP*CP*AP*AP*AP*AP*CP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*AP*GP*TP*TP*TP*CP*G)-3' | HOMING ENDONUCLEASE I-CREI / DNA SUBSTRATE COMPLEX WITH CALCIUM | X-ray diffraction | 2.05 | 2001-04-02 | ||||
| 20 | 1U0C|1|C+ 1U0C|1|D | 5'-D(*GP*CP*TP*AP*AP*AP*CP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*AP*GP*TP*TP*AP*CP*G)-3', 5'-D(*CP*GP*TP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*CP*GP*AP*CP*GP*TP*TP*TP*AP*GP*C)-3' | Y33C Mutant of Homing endonuclease I-CreI | X-ray diffraction | 2.5 | 2004-11-02 | ||||
| 21 | 1BP7|1|1+ 1BP7|1|2 | DNA (5'-D(*GP*CP*AP*AP*AP*AP*CP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*AP*GP*TP*TP*TP* CP*G)-3'), DNA (5'-D(*CP*GP*AP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*CP*GP*AP*CP*GP*TP*TP*TP*TP* GP*C)-3') | GROUP I MOBILE INTRON ENDONUCLEASE I-CREI COMPLEXED WITH HOMING SITE DNA | X-ray diffraction | 3 | 1999-01-06 | ||||
| 22 | 1BP7|1|3+ 1BP7|1|4 | DNA (5'-D(*GP*CP*AP*AP*AP*AP*CP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*AP*GP*TP*TP*TP* CP*G)-3'), DNA (5'-D(*CP*GP*AP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*CP*GP*AP*CP*GP*TP*TP*TP*TP* GP*C)-3') | GROUP I MOBILE INTRON ENDONUCLEASE I-CREI COMPLEXED WITH HOMING SITE DNA | X-ray diffraction | 3 | 1999-01-06 |
Release history
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 | 2VBJ|1|C+2VBJ|1|E | Molecular basis of human XPC gene recognition and cleavage by engineered homing endonuclease heterodimers | X-RAY DIFFRACTION | 1.95 | 24 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease |
| 2 | 2VBO|1|C+2VBO|1|E | Molecular basis of human XPC gene recognition and cleavage by engineered homing endonuclease heterodimers | X-RAY DIFFRACTION | 1.8 | 24 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease |
| 3 | 2XE0|1|C+2XE0|1|D | Molecular basis of engineered meganuclease targeting of the endogenous human RAG1 locus | X-RAY DIFFRACTION | 2.31 | 24 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease |
| 4 | 3MX9|1|C+3MX9|1|D | Molecular basis of engineered meganuclease targeting of the endogenous human RAG1 locus | X-RAY DIFFRACTION | 2.6 | 24 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease |
| 5 | 3MXB|1|C+3MXB|1|E | Molecular basis of engineered meganuclease targeting of the endogenous human RAG1 locus | X-RAY DIFFRACTION | 2.3 | 24 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease |
| 6 | 3MXB|1|T+3MXB|1|V | Molecular basis of engineered meganuclease targeting of the endogenous human RAG1 locus | X-RAY DIFFRACTION | 2.3 | 24 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease |
| 7 | 1BP7|1|3+1BP7|1|4 | GROUP I MOBILE INTRON ENDONUCLEASE I-CREI COMPLEXED WITH HOMING SITE DNA | X-RAY DIFFRACTION | 3 | 24 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease |
| 8 | 1BP7|1|1+1BP7|1|2 | GROUP I MOBILE INTRON ENDONUCLEASE I-CREI COMPLEXED WITH HOMING SITE DNA | X-RAY DIFFRACTION | 3 | 24 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease |
| 9 | 1G9Y|1|C+1G9Y|1|D | HOMING ENDONUCLEASE I-CREI / DNA SUBSTRATE COMPLEX WITH CALCIUM | X-RAY DIFFRACTION | 2.05 | 24 | double helix,structure | enzyme,hydrolase,nuclease |
| 10 | 2I3P|1|C+2I3P|1|D | K28R mutant of Homing Endonuclease I-CreI | X-RAY DIFFRACTION | 2.3 | 24 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease |
| 11 | 2I3Q|1|C+2I3Q|1|D | Q44V mutant of Homing Endonuclease I-CreI | X-RAY DIFFRACTION | 2.3 | 24 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease |
| 12 | 1T9J|1|C+1T9J|1|D | I-CreI(Q47E)/DNA complex | X-RAY DIFFRACTION | 2 | 24 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease |
| 13 | 1T9I|1|C+1T9I|1|D | I-CreI(D20N)/DNA complex | X-RAY DIFFRACTION | 1.6 | 24 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease |
| 14 | 1U0C|1|C+1U0C|1|D | Y33C Mutant of Homing endonuclease I-CreI | X-RAY DIFFRACTION | 2.5 | 24 | double helix,structure | enzyme,hydrolase,nuclease |
| 15 | 3MIP|1|C+3MIP|1|D | I-MsoI re-designed for altered DNA cleavage specificity (-8GCG) | X-RAY DIFFRACTION | 2.4 | 24 | double helix,structure | enzyme,hydrolase,nuclease |
| 16 | 2FLD|1|C+2FLD|1|D | I-MsoI Re-Designed for Altered DNA Cleavage Specificity | X-RAY DIFFRACTION | 2 | 24 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease |
| 17 | 1M5X|1|C+1M5X|1|D | Crystal structure of the homing endonuclease I-MsoI bound to its DNA substrate | X-RAY DIFFRACTION | 2.25 | 24 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease |
| 18 | 3FD2|1|B+3FD2|1|C | Crystal structure of mMsoI/DNA complex with calcium | X-RAY DIFFRACTION | 2.69 | 24 | double helix,structure | enzyme,hydrolase,nuclease |
| 19 | 3MIS|1|C+3MIS|1|D | I-MsoI re-designed for altered DNA cleavage specificity (-8G) | X-RAY DIFFRACTION | 2.3 | 24 | double helix,structure | enzyme,hydrolase,nuclease |
| 20 | 3KO2|1|H+3KO2|1|I | I-MsoI re-designed for altered DNA cleavage specificity (-7C) | X-RAY DIFFRACTION | 2.9 | 24 | double helix,structure | enzyme,hydrolase,nuclease |
| 21 | 3KO2|1|C+3KO2|1|D | I-MsoI re-designed for altered DNA cleavage specificity (-7C) | X-RAY DIFFRACTION | 2.9 | 24 | double helix,structure | enzyme,hydrolase,nuclease |
| 22 | 1U0D|1|C+1U0D|1|D | Y33H Mutant of Homing endonuclease I-CreI | X-RAY DIFFRACTION | 2.9 | 24 | double helix,structure | enzyme,hydrolase,nuclease |
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