Equivalence class DNA_1.5_21697.1 Obsolete
| # | IFE | Standardized name | Molecule | Organism | Source | Rfam | Title | Method | Res. Å | #NTs | Date |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 1PFE|1|A (rep) | 5'-D(*GP*CP*GP*TP*AP*CP*GP*C)-3' | Echinomycin-(gcgtacgc)2 complex | X-ray diffraction | 1.1 | 8 | 2004-06-08 | ||||
| 2 | 2HC7|1|A | 5'-D(*GP*(2ST)P*GP*TP*AP*CP*AP*C)-3' | 2'-selenium-T A-DNA [G(TSe)GTACAC] | X-ray diffraction | 1.4 | 8 | 2006-07-04 | ||||
| 3 | 3HG8|1|A | 5'-D(*GP*(UMS)P*GP*(US2)P*AP*CP*AP*C)-3' | synthetic construct | Crystal Structure of 5-SMe Derivatized DNA | X-ray diffraction | 1.38 | 8 | 2009-07-21 | |||
| 4 | 1Z7I|1|A | 5'-D(*GP*(UMS)P*GP*TP*AP*CP*AP*C)-3' | 2'-Me-Se Derivitation of A-DNA Octamer G(UMSe)GTACAC | X-ray diffraction | 1.28 | 8 | 2005-04-05 | ||||
| 5 | 3LTU|1|A | 5'-D(*GP*(UMS)P*GP*(T5S)P*AP*CP*AP*C)-3' | synthetic construct | 5-SeMe-dU containing DNA 8mer | X-ray diffraction | 1.4 | 8 | 2010-03-09 | |||
| 6 | 3IKI|1|A | 5'-D(*GP*(UMS)P*GP*(US2)P*AP*CP*AP*C)-3' | 5-SMe-dU containing DNA octamer | X-ray diffraction | 1.38 | 8 | 2010-03-09 | ||||
| 7 | 3IFI|1|A | DNA (5'-D(*GP*TP*(XUG)P*TP*AP*CP*AP*C)-3') | 2'-SeMe-dG modified octamer DNA | X-ray diffraction | 1.2 | 8 | 2009-08-11 | ||||
| 8 | 3IJK|1|A | 5'-D(*GP*(UMS)P*GP*(T5O)P*AP*CP*AP*C)-3' | synthetic construct | 5-OMe modified DNA 8mer | X-ray diffraction | 1.3 | 8 | 2009-10-06 | |||
| 9 | 3GO3|1|A+ 3GO3|1|B | 5'-D(*AP*CP*GP*TP*AP*CP*GP*T)-3' | Interactions of an echinomycin-DNA complex with manganese(II) ions | X-ray diffraction | 1.1 | 16 | 2009-03-31 | ||||
| 10 | 1XVK|1|A | 5'-D(*GP*CP*GP*TP*AP*CP*GP*C)-3' | X-ray structure of an Echinomycin-(GCGTACGC)2 complex | X-ray diffraction | 1.26 | 8 | 2005-04-12 | ||||
| 11 | 3LTR|1|A | 5'-D(*GP*(UMS)P*GP*(T5O)P*AP*CP*AP*C)-3' | 5-OMe-dU containing DNA 8mer | X-ray diffraction | 1.3 | 8 | 2010-03-09 | ||||
| 12 | 2NSK|1|A | 5'-D(*GP*(UMS)P*GP*(T4S)P*AP*CP*AP*C)-3' | Doubled Modified Selenium DNA | X-ray diffraction | 1.5 | 8 | 2006-11-14 | ||||
| 13 | 1WTO|1|B+ 1WTO|1|C | 5'-D(*GP*CP*GP*AP*TP*CP*GP*C)-3' | Hyperthermophile chromosomal protein SAC7D double mutant V26F/M29F in complex with DNA GCGATCGC | X-ray diffraction | 1.5 | 16 | 2005-02-22 | ||||
| 14 | 3K18|1|A | 5'-D(*GP*(UMS)P*GP*(TTI)P*AP*CP*AP*C)-3' | Tellurium modified DNA-8mer | X-ray diffraction | 1.5 | 8 | 2010-10-06 | ||||
| 15 | 1XVN|1|A | 5'-D(*AP*CP*GP*TP*AP*CP*GP*T)-3' | echinomycin (ACGTACGT)2 complex | X-ray diffraction | 1.5 | 8 | 2005-04-12 | ||||
| 16 | 1XYI|1|B+ 1XYI|1|C | 5'-D(*GP*CP*GP*AP*TP*CP*GP*C)-3' | Hyperthermophile chromosomal protein Sac7d double mutant Val26Ala/Met29Ala in complex with DNA GCGATCGC | X-ray diffraction | 1.45 | 16 | 2005-02-08 | ||||
| 17 | 284D|1|A+ 284D|1|B | DNA (5'-CD(*P*AP*TP*TP*CP*AP*TP*TP*C)-3') | THE BI-LOOP, A NEW GENERAL FOUR-STRANDED DNA MOTIF | X-ray diffraction | 1.1 | 16 | 1997-06-11 | ||||
| 18 | 454D|1|A+ 454D|1|B | 5'-D(*GP*(5IU)P*TP*GP*CP*AP*AP*C)-3' | INTERCALATION AND MAJOR GROOVE RECOGNITION IN THE 1.2 A RESOLUTION CRYSTAL STRUCTURE OF RH[ME2TRIEN]PHI BOUND TO 5'-G(5IU)TGCAAC-3' | X-ray diffraction | 1.2 | 16 | 2000-02-21 | ||||
| 19 | 454D|1|C+ 454D|1|D | 5'-D(*GP*(5IU)P*TP*GP*CP*AP*AP*C)-3' | INTERCALATION AND MAJOR GROOVE RECOGNITION IN THE 1.2 A RESOLUTION CRYSTAL STRUCTURE OF RH[ME2TRIEN]PHI BOUND TO 5'-G(5IU)TGCAAC-3' | X-ray diffraction | 1.2 | 16 | 2000-02-21 | ||||
| 20 | 454D|1|E+ 454D|1|F | 5'-D(*GP*(5IU)P*TP*GP*CP*AP*AP*C)-3' | INTERCALATION AND MAJOR GROOVE RECOGNITION IN THE 1.2 A RESOLUTION CRYSTAL STRUCTURE OF RH[ME2TRIEN]PHI BOUND TO 5'-G(5IU)TGCAAC-3' | X-ray diffraction | 1.2 | 16 | 2000-02-21 | ||||
| 21 | 454D|1|G+ 454D|1|H | 5'-D(*GP*(5IU)P*TP*GP*CP*AP*AP*C)-3' | INTERCALATION AND MAJOR GROOVE RECOGNITION IN THE 1.2 A RESOLUTION CRYSTAL STRUCTURE OF RH[ME2TRIEN]PHI BOUND TO 5'-G(5IU)TGCAAC-3' | X-ray diffraction | 1.2 | 16 | 2000-02-21 | ||||
| 22 | 454D|1|I+ 454D|1|J | 5'-D(*GP*(5IU)P*TP*GP*CP*AP*AP*C)-3' | INTERCALATION AND MAJOR GROOVE RECOGNITION IN THE 1.2 A RESOLUTION CRYSTAL STRUCTURE OF RH[ME2TRIEN]PHI BOUND TO 5'-G(5IU)TGCAAC-3' | X-ray diffraction | 1.2 | 16 | 2000-02-21 | ||||
| 23 | 1D78|1|A | DNA (5'-D(*GP*TP*GP*TP*AP*CP*AP*C)-3') | HIGH RESOLUTION REFINEMENT OF THE HEXAGONAL A-DNA OCTAMER D(GTGTACAC) AT 1.4 ANGSTROMS RESOLUTION | X-ray diffraction | 1.4 | 8 | 1993-04-15 | ||||
| 24 | 2PLO|1|A+ 2PLO|1|B | 5'-D(*DGP*DGP*DTP*DAP*DTP*DAP*DCP*DC)-3' | D-(GTATACC) low temperature (100K) | X-ray diffraction | 1.4 | 16 | 2008-05-27 | ||||
| 25 | 1D79|1|A | DNA (5'-D(*GP*TP*GP*TP*AP*CP*AP*C)-3') | HIGH RESOLUTION REFINEMENT OF THE HEXAGONAL A-DNA OCTAMER D(GTGTACAC) AT 1.4 ANGSTROMS RESOLUTION | X-ray diffraction | 1.45 | 8 | 1993-04-15 | ||||
| 26 | 1C8C|1|B+ 1C8C|1|C | 5'-D(*GP*TP*GP*AP*TP*CP*GP*C)-3' | CRYSTAL STRUCTURES OF THE CHROMOSOMAL PROTEINS SSO7D/SAC7D BOUND TO DNA CONTAINING T-G MISMATCHED BASE PAIRS | X-ray diffraction | 1.45 | 16 | 2001-05-04 | ||||
| 27 | 344D|1|A | DNA (5'-D(*AP*CP*GP*TP*AP*CP*GP*(BRU))-3') | DETERMINATION BY MAD-DM OF THE STRUCTURE OF THE DNA DUPLEX D(ACGTACG(5-BRU))2 AT 1.46A AND 100K | X-ray diffraction | 1.46 | 8 | 1997-09-26 | ||||
| 28 | 3FA1|1|A | 5'-D(*DGP*(UMS)P*DGP*(TTI)P*DAP*DCP*DAP*DC)-3' | Crystal Structure of Tellurium Derivatized DNA | X-ray diffraction | 1.5 | 8 | 2009-01-27 | ||||
| 29 | 2DLJ|1|A | 5'-D(*GP*(UMS)P*GP*(BRU)P*AP*CP*AP*C)-3' | 2'-Me-Se and Br Derivitation of A-DNA Octamer G(UMS)G(BRU)ACAC | X-ray diffraction | 1.5 | 8 | 2006-05-23 | ||||
| 30 | 295D|1|A | DNA (5'-D(*AP*TP*GP*CP*GP*CP*AP*T)-3') | CRYSTAL AND SOLUTION STRUCTURES OF THE OLIGONUCLEOTIDE D(ATGCGCAT)2: A COMBINED X-RAY AND NMR STUDY | X-ray diffraction | 1.5 | 8 | 1996-12-04 |
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 | 454D|1|C+ 454D|1|D | INTERCALATION AND MAJOR GROOVE RECOGNITION IN THE 1.2 A RESOLUTION CRYSTAL STRUCTURE OF RH[ME2TRIEN]PHI BOUND TO 5'-G(5IU)TGCAAC-3' | X-RAY DIFFRACTION | 1.2 | 16 | B-form double helix,double helix,structure | ||
| 2 | 454D|1|A+ 454D|1|B | INTERCALATION AND MAJOR GROOVE RECOGNITION IN THE 1.2 A RESOLUTION CRYSTAL STRUCTURE OF RH[ME2TRIEN]PHI BOUND TO 5'-G(5IU)TGCAAC-3' | X-RAY DIFFRACTION | 1.2 | 16 | B-form double helix,double helix,structure | ||
| 3 | 454D|1|E+ 454D|1|F | INTERCALATION AND MAJOR GROOVE RECOGNITION IN THE 1.2 A RESOLUTION CRYSTAL STRUCTURE OF RH[ME2TRIEN]PHI BOUND TO 5'-G(5IU)TGCAAC-3' | X-RAY DIFFRACTION | 1.2 | 16 | B-form double helix,double helix,structure | ||
| 4 | 454D|1|G+ 454D|1|H | INTERCALATION AND MAJOR GROOVE RECOGNITION IN THE 1.2 A RESOLUTION CRYSTAL STRUCTURE OF RH[ME2TRIEN]PHI BOUND TO 5'-G(5IU)TGCAAC-3' | X-RAY DIFFRACTION | 1.2 | 16 | B-form double helix,double helix,structure | ||
| 5 | 454D|1|I+ 454D|1|J | INTERCALATION AND MAJOR GROOVE RECOGNITION IN THE 1.2 A RESOLUTION CRYSTAL STRUCTURE OF RH[ME2TRIEN]PHI BOUND TO 5'-G(5IU)TGCAAC-3' | X-RAY DIFFRACTION | 1.2 | 16 | B-form double helix,double helix,structure | ||
| 6 | 3IJK|1|A | 5-OMe modified DNA 8mer | X-RAY DIFFRACTION | 1.3 | 8 | A-form double helix,double helix,structure | ||
| 7 | 3LTR|1|A | 5-OMe-dU containing DNA 8mer | X-RAY DIFFRACTION | 1.3 | 8 | A-form double helix,double helix,structure | ||
| 8 | 3LTU|1|A | 5-SeMe-dU containing DNA 8mer | X-RAY DIFFRACTION | 1.4 | 8 | A-form double helix,double helix,structure | ||
| 9 | 3HG8|1|A | Crystal Structure of 5-SMe Derivatized DNA | X-RAY DIFFRACTION | 1.38 | 8 | A-form double helix,double helix,structure | ||
| 10 | 3IKI|1|A | 5-SMe-dU containing DNA octamer | X-RAY DIFFRACTION | 1.38 | 8 | A-form double helix,double helix,structure | ||
| 11 | 3K18|1|A | Tellurium modified DNA-8mer | X-RAY DIFFRACTION | 1.5 | 8 | A-form double helix,double helix,structure | ||
| 12 | 3FA1|1|A | Crystal Structure of Tellurium Derivatized DNA | X-RAY DIFFRACTION | 1.5 | 8 | A-form double helix,double helix,structure | ||
| 13 | 2NSK|1|A | Doubled Modified Selenium DNA | X-RAY DIFFRACTION | 1.5 | 8 | A-form double helix,double helix,structure | ||
| 14 | 2DLJ|1|A | 2'-Me-Se and Br Derivitation of A-DNA Octamer G(UMS)G(BRU)ACAC | X-RAY DIFFRACTION | 1.5 | 8 | A-form double helix,double helix,structure | ||
| 15 | 2HC7|1|A | 2'-selenium-T A-DNA [G(TSe)GTACAC] | X-RAY DIFFRACTION | 1.4 | 8 | A-form double helix,double helix,structure | ||
| 16 | 1Z7I|1|A | 2'-Me-Se Derivitation of A-DNA Octamer G(UMSe)GTACAC | X-RAY DIFFRACTION | 1.28 | 8 | A-form double helix,double helix,structure | ||
| 17 | 295D|1|A | CRYSTAL AND SOLUTION STRUCTURES OF THE OLIGONUCLEOTIDE D(ATGCGCAT)2: A COMBINED X-RAY AND NMR STUDY | X-RAY DIFFRACTION | 1.5 | 8 | A-form double helix,double helix,structure | ||
| 18 | 344D|1|A | DETERMINATION BY MAD-DM OF THE STRUCTURE OF THE DNA DUPLEX D(ACGTACG(5-BRU))2 AT 1.46A AND 100K | X-RAY DIFFRACTION | 1.46 | 8 | A-form double helix,double helix,structure | ||
| 19 | 3IFI|1|A | 2'-SeMe-dG modified octamer DNA | X-RAY DIFFRACTION | 1.2 | 8 | double helix,structure | ||
| 20 | 1D79|1|A | HIGH RESOLUTION REFINEMENT OF THE HEXAGONAL A-DNA OCTAMER D(GTGTACAC) AT 1.4 ANGSTROMS RESOLUTION | X-RAY DIFFRACTION | 1.45 | 8 | A-form double helix,double helix,structure | ||
| 21 | 1D78|1|A | HIGH RESOLUTION REFINEMENT OF THE HEXAGONAL A-DNA OCTAMER D(GTGTACAC) AT 1.4 ANGSTROMS RESOLUTION | X-RAY DIFFRACTION | 1.4 | 8 | A-form double helix,double helix,structure | ||
| 22 | 2PLO|1|A+ 2PLO|1|B | D-(GTATACC) low temperature (100K) | X-RAY DIFFRACTION | 1.4 | 16 | A-form double helix,double helix,structure | ||
| 23 | 1C8C|1|B+ 1C8C|1|C | CRYSTAL STRUCTURES OF THE CHROMOSOMAL PROTEINS SSO7D/SAC7D BOUND TO DNA CONTAINING T-G MISMATCHED BASE PAIRS | X-RAY DIFFRACTION | 1.45 | 16 | double helix,feature,mispair,structure | chromatin,nucleosome,structural | |
| 24 | 1WTO|1|B+ 1WTO|1|C | Hyperthermophile chromosomal protein SAC7D double mutant V26F/M29F in complex with DNA GCGATCGC | X-RAY DIFFRACTION | 1.5 | 16 | B-form double helix,double helix,structure | chromatin,nucleosome,structural | |
| 25 | 1XYI|1|B+ 1XYI|1|C | Hyperthermophile chromosomal protein Sac7d double mutant Val26Ala/Met29Ala in complex with DNA GCGATCGC | X-RAY DIFFRACTION | 1.45 | 16 | B-form double helix,double helix,structure | chromatin,nucleosome,structural | |
| 26 | 1XVN|1|A | echinomycin (ACGTACGT)2 complex | X-RAY DIFFRACTION | 1.5 | 8 | double helix,structure | ||
| 27 | 3GO3|1|A+ 3GO3|1|B | Interactions of an echinomycin-DNA complex with manganese(II) ions | X-RAY DIFFRACTION | 1.1 | 16 | double helix,structure | ||
| 28 | 1XVK|1|A | X-ray structure of an Echinomycin-(GCGTACGC)2 complex | X-RAY DIFFRACTION | 1.26 | 8 | double helix,structure | ||
| 29 | 1PFE|1|A | Echinomycin-(gcgtacgc)2 complex | X-RAY DIFFRACTION | 1.1 | 8 | double helix,structure | ||
| 30 | 284D|1|A+ 284D|1|B | THE BI-LOOP, A NEW GENERAL FOUR-STRANDED DNA MOTIF | X-RAY DIFFRACTION | 1.1 | 16 | cyclic,feature,structure |
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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