Equivalence class DNA_2.5_77675.1 Obsolete
| # | IFE | Standardized name | Molecule | Organism | Source | Rfam | Title | Method | Res. Å | #NTs | Date |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 1ENN|1|A+ 1ENN|1|B (rep) | DNA (5'-D(*GP*CP*GP*AP*AP*TP*TP*CP*G)-3') | SOLVENT ORGANIZATION IN AN OLIGONUCLEOTIDE CRYSTAL: THE STRUCTURE OF D(GCGAATTCG)2 AT ATOMIC RESOLUTION | X-ray diffraction | 0.89 | 18 | 2000-05-03 | ||||
| 2 | 1XJY|1|A+ 1XJY|1|B | 5'-D(*TP*CP*TP*GP*CP*GP*GP*TP*C)-3', 5'-D(*TP*GP*AP*CP*CP*GP*CP*AP*G)-3' | The crystal structures of the DNA binding sites of the RUNX1 transcription factor | X-ray diffraction | 2 | 18 | 2005-03-15 | ||||
| 3 | 3OQG|1|C+ 3OQG|1|D | DNA 5'-D(*GP*AP*TP*CP*TP*GP*AP*AP*C)-3', DNA 5'-D(*GP*TP*TP*CP*AP*GP*AP*TP*C)-3' | Restriction endonuclease HPY188I in complex with substrate DNA | X-ray diffraction | 1.75 | 18 | 2010-10-20 | ||||
| 4 | 3G00|1|H+ 3G00|1|I | 5'-D(*CP*GP*TP*AP*TP*TP*AP*CP*G)-3', 5'-D(*CP*GP*TP*AP*UP*TP*AP*CP*G)-3' | Mth0212 in complex with a 9bp blunt end dsDNA at 1.7 Angstrom | X-ray diffraction | 1.74 | 18 | 2010-03-09 | ||||
| 5 | 1XJX|1|A+ 1XJX|1|B | 5'-D(*TP*CP*TP*GP*CP*GP*GP*TP*C)-3', 5'-D(*TP*GP*AP*CP*CP*GP*CP*AP*G)-3' | The crystal structures of the DNA binding sites of the RUNX1 transcription factor | X-ray diffraction | 1.7 | 18 | 2005-03-15 | ||||
| 6 | 1UE2|1|A | 5'-D(*GP*(C38)P*GP*AP*AP*AP*GP*CP*T)-3' | Crystal structure of d(GC38GAAAGCT) | X-ray diffraction | 1.4 | 9 | 2004-01-13 | ||||
| 7 | 2GB7|1|E+ 2GB7|1|F | DNA STRAND 1, DNA STRAND 2 | Metal-depleted Ecl18kI in complex with uncleaved, modified DNA | X-ray diffraction | 1.7 | 18 | 2006-06-20 | ||||
| 8 | 2GB7|1|G+ 2GB7|1|H | DNA STRAND 1, DNA STRAND 2 | Metal-depleted Ecl18kI in complex with uncleaved, modified DNA | X-ray diffraction | 1.7 | 18 | 2006-06-20 | ||||
| 9 | 3GV8|1|T+ 3GV8|1|P | 5'-D(*AP*GP*GP*AP*CP*CP*C)-3', 5'-D(*AP*TP*GP*GP*GP*TP*CP*CP*T)-3' | Human DNA polymerase iota in complex with T template DNA and incoming dGTP | X-ray diffraction | 2 | 16 | 2009-06-02 | ||||
| 10 | 3IMB|1|E+ 3IMB|1|F | 5'-D(*CP*GP*CP*CP*CP*GP*GP*AP*C)-3', 5'-D(*GP*TP*CP*CP*GP*GP*GP*CP*G)-3' | Alternative binding mode of restriction endonuclease BcnI to cognate DNA | X-ray diffraction | 1.89 | 18 | 2010-08-11 | ||||
| 11 | 3IMB|1|G+ 3IMB|1|H | 5'-D(*CP*GP*CP*CP*CP*GP*GP*AP*C)-3', 5'-D(*GP*TP*CP*CP*GP*GP*GP*CP*G)-3' | Alternative binding mode of restriction endonuclease BcnI to cognate DNA | X-ray diffraction | 1.89 | 18 | 2010-08-11 | ||||
| 12 | 3IMB|1|I+ 3IMB|1|J | 5'-D(*CP*GP*CP*CP*CP*GP*GP*AP*C)-3', 5'-D(*GP*TP*CP*CP*GP*GP*GP*CP*G)-3' | Alternative binding mode of restriction endonuclease BcnI to cognate DNA | X-ray diffraction | 1.89 | 18 | 2010-08-11 | ||||
| 13 | 3IMB|1|K+ 3IMB|1|L | 5'-D(*CP*GP*CP*CP*CP*GP*GP*AP*C)-3', 5'-D(*GP*TP*CP*CP*GP*GP*GP*CP*G)-3' | Alternative binding mode of restriction endonuclease BcnI to cognate DNA | X-ray diffraction | 1.89 | 18 | 2010-08-11 | ||||
| 14 | 2FQZ|1|E+ 2FQZ|1|F | DNA STRAND 1, DNA STRAND 2 | Metal-depleted Ecl18kI in complex with uncleaved DNA | X-ray diffraction | 2 | 18 | 2006-06-20 | ||||
| 15 | 2FQZ|1|G+ 2FQZ|1|H | DNA STRAND 1, DNA STRAND 2 | Metal-depleted Ecl18kI in complex with uncleaved DNA | X-ray diffraction | 2 | 18 | 2006-06-20 | ||||
| 16 | 3GV7|1|T+ 3GV7|1|P | 5'-D(*AP*GP*GP*AP*CP*CP*C)-3', 5'-D(P*AP*TP*GP*GP*GP*TP*CP*CP*T)-3' | Human DNA polymerase iota in complex with T template DNA and incoming dTTP | X-ray diffraction | 2.2 | 16 | 2009-06-02 | ||||
| 17 | 2W35|1|C | 5'-D(*AP*TP*GP*CP*GP*AP*CP*IP*GP)-3' | synthetic construct | Structures of endonuclease V with DNA reveal initiation of deaminated adenine repair | X-ray diffraction | 2.15 | 4 | 2009-01-20 | |||
| 18 | 2W35|1|F | 5'-D(*AP*TP*GP*CP*GP*AP*CP*IP*GP)-3' | synthetic construct | Structures of endonuclease V with DNA reveal initiation of deaminated adenine repair | X-ray diffraction | 2.15 | 0 | 2009-01-20 | |||
| 19 | 3N1I|1|B | DNA 32-mer ERE32 | Crystal Structure of a StWhy2-ERE32 complex | X-ray diffraction | 2.2 | 9 | 2010-08-11 | ||||
| 20 | 3HR3|1|A | 5'-D(*GP*CP*GP*(US4)P*(OMU))P*AP*CP*GP*C)-3' | synthetic construct | Interplay of Structure, Hydration and Thermal Stability in Formacetal Modified Oligonucleotides: RNA May Tolerate Hydrophobic Modifications Better than DNA | X-ray diffraction | 1.75 | 9 | 2009-10-27 | |||
| 21 | 3H4D|1|T+ 3H4D|1|P | 5'-D(*AP*GP*GP*AP*CP*CP*(DOC)), 5'-D(*TP*(BRU)P*GP*GP*GP*TP*CP*CP*T) | Ternary complex of human DNA polymerase iota with template U/T and incoming dGTP | X-ray diffraction | 2.2 | 16 | 2009-07-21 | ||||
| 22 | 1RXW|1|C+ 1RXW|1|B | 5'-d(*C*pG*pA*pT*pG*pC*pT*pA)-3', 5'-d(*T*pA*pG*pC*pA*pT*pC*pG*pG)-3' | Crystal structure of A. fulgidus FEN-1 bound to DNA | X-ray diffraction | 2 | 15 | 2004-01-27 | ||||
| 23 | 3N1L|1|B | DNA 32-mer rcERE32 | Crystal Structure of a StWhy2-rcERE32 complex | X-ray diffraction | 2.35 | 9 | 2010-08-11 | ||||
| 24 | 2DPJ|1|T+ 2DPJ|1|P | 5'-D(*AP*GP*GP*AP*CP*CP*(DOC))-3', 5'-D(*TP*(EDA)P*GP*GP*GP*TP*CP*CP*T)-3' | structure of hPoli with DNA and dTTP | X-ray diffraction | 2.3 | 16 | 2006-07-04 | ||||
| 25 | 2ALZ|1|T+ 2ALZ|1|P | 5'-D(*AP*GP*GP*AP*CP*CP*(DOC))-3', 5'-D(*TP*GP*GP*GP*GP*TP*CP*CP*T)-3' | Ternary Complex of hPoli with DNA and dCTP | X-ray diffraction | 2.5 | 16 | 2005-10-25 | ||||
| 26 | 3H40|1|T+ 3H40|1|P | 5'-D(*AP*GP*GP*AP*CP*CP*(DOC))-3', 5'-D(*TP*(BRU)P*GP*GP*GP*TP*CP*CP*T)-3' | Binary complex of human DNA polymerase iota with template U/T | X-ray diffraction | 2.3 | 16 | 2009-07-21 | ||||
| 27 | 3G2D|1|H | 5'-D(*CP*GP*CP*G*CP*AP*GP*GP*C)-3' | Complex of Mth0212 and a 4 bp dsDNA with 3'-overhang | X-ray diffraction | 2.3 | 0 | 2010-03-09 | ||||
| 28 | 2DPI|1|T+ 2DPI|1|P | 5'-D(*AP*GP*GP*AP*CP*CP*(DOC))-3', 5'-D(*TP*(EDA)P*GP*GP*GP*TP*CP*CP*T)-3' | Ternary complex of hPoli with DNA and dCTP | X-ray diffraction | 2.3 | 16 | 2006-07-04 | ||||
| 29 | 3G3Y|1|I | 5'-D(*CP*GP*TP*AP*(UPS)P*TP*AP*CP*G)-3' | Mth0212 in complex with ssDNA in space group P32 | X-ray diffraction | 2.5 | 5 | 2010-03-09 | ||||
| 30 | 1RXV|1|C | 5'-d(*T*pA*pG*pC*pA*pT*pC*pG*pG) | Crystal Structure of A. Fulgidus FEN-1 bound to DNA | X-ray diffraction | 2.5 | 2 | 2004-01-27 | ||||
| 31 | 1RXV|1|D | 5'-d(*T*pA*pG*pC*pA*pT*pC*pG*pG) | Crystal Structure of A. Fulgidus FEN-1 bound to DNA | X-ray diffraction | 2.5 | 2 | 2004-01-27 | ||||
| 32 | 208D|1|A+ 208D|1|B | DNA (5'-D(*GP*CP*GP*AP*AP*TP*TP*CP*G)-3') | HIGH-RESOLUTION STRUCTURE OF A DNA HELIX FORMING (C.G)*G BASE TRIPLETS | X-ray diffraction | 2.05 | 18 | 1995-09-15 | ||||
| 33 | 376D|1|A | DNA (5'-D(*GP*(CBR)P*GP*AP*AP*AP*GP*CP*T)-3') | A ZIPPER-LIKE DNA DUPLEX D(GCGAAAGCT) | X-ray diffraction | 2.1 | 9 | 1999-10-26 | ||||
| 34 | 253D|1|A | DNA (5'-D(*GP*CP*GP*TP*AP*CP*GP*CP*G)-3') | CRYSTAL STRUCTURE OF THE B-DNA NONAMER D(GCGTACGCG) WITH A NOVEL D[G*(G.C)] BASE-TRIPLET INVOLVING THE MINOR GROOVE | X-ray diffraction | 2.2 | 9 | 1996-04-15 |
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 | 3G3Y|1|I | Mth0212 in complex with ssDNA in space group P32 | X-RAY DIFFRACTION | 2.5 | 5 | enzyme,hydrolase,nuclease | ||
| 2 | 3N1L|1|B | Crystal Structure of a StWhy2-rcERE32 complex | X-RAY DIFFRACTION | 2.35 | 9 | DNA replication/repair,regulatory | ||
| 3 | 3N1I|1|B | Crystal Structure of a StWhy2-ERE32 complex | X-RAY DIFFRACTION | 2.2 | 9 | DNA replication/repair,regulatory | ||
| 4 | 2GB7|1|G+ 2GB7|1|H | Metal-depleted Ecl18kI in complex with uncleaved, modified DNA | X-RAY DIFFRACTION | 1.7 | 18 | B-form double helix,double helix,structure | enzyme,hydrolase | |
| 5 | 2FQZ|1|G+ 2FQZ|1|H | Metal-depleted Ecl18kI in complex with uncleaved DNA | X-RAY DIFFRACTION | 2 | 18 | B-form double helix,double helix,structure | enzyme,hydrolase | |
| 6 | 2GB7|1|E+ 2GB7|1|F | Metal-depleted Ecl18kI in complex with uncleaved, modified DNA | X-RAY DIFFRACTION | 1.7 | 18 | B-form double helix,double helix,structure | enzyme,hydrolase | |
| 7 | 2FQZ|1|E+ 2FQZ|1|F | Metal-depleted Ecl18kI in complex with uncleaved DNA | X-RAY DIFFRACTION | 2 | 18 | B-form double helix,double helix,structure | enzyme,hydrolase | |
| 8 | 3HR3|1|A | Interplay of Structure, Hydration and Thermal Stability in Formacetal Modified Oligonucleotides: RNA May Tolerate Hydrophobic Modifications Better than DNA | X-RAY DIFFRACTION | 1.75 | 9 | A-form double helix,double helix,structure | ||
| 9 | 3G2D|1|H | Complex of Mth0212 and a 4 bp dsDNA with 3'-overhang | X-RAY DIFFRACTION | 2.3 | 0 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease | |
| 10 | 2DPI|1|T+ 2DPI|1|P | Ternary complex of hPoli with DNA and dCTP | X-RAY DIFFRACTION | 2.3 | 16 | enzyme,polymerase,transferase | ||
| 11 | 2DPJ|1|T+ 2DPJ|1|P | structure of hPoli with DNA and dTTP | X-RAY DIFFRACTION | 2.3 | 16 | enzyme,polymerase,transferase | ||
| 12 | 2ALZ|1|T+ 2ALZ|1|P | Ternary Complex of hPoli with DNA and dCTP | X-RAY DIFFRACTION | 2.5 | 16 | enzyme,polymerase,transferase | ||
| 13 | 3H40|1|T+ 3H40|1|P | Binary complex of human DNA polymerase iota with template U/T | X-RAY DIFFRACTION | 2.3 | 16 | double helix,structure | enzyme,polymerase,transferase | |
| 14 | 3H4D|1|T+ 3H4D|1|P | Ternary complex of human DNA polymerase iota with template U/T and incoming dGTP | X-RAY DIFFRACTION | 2.2 | 16 | double helix,structure | enzyme,polymerase,transferase | |
| 15 | 3GV8|1|T+ 3GV8|1|P | Human DNA polymerase iota in complex with T template DNA and incoming dGTP | X-RAY DIFFRACTION | 2 | 16 | double helix,structure | enzyme,polymerase,transferase | |
| 16 | 3GV7|1|T+ 3GV7|1|P | Human DNA polymerase iota in complex with T template DNA and incoming dTTP | X-RAY DIFFRACTION | 2.2 | 16 | double helix,structure | enzyme,polymerase,transferase | |
| 17 | 208D|1|A+ 208D|1|B | HIGH-RESOLUTION STRUCTURE OF A DNA HELIX FORMING (C.G)*G BASE TRIPLETS | X-RAY DIFFRACTION | 2.05 | 18 | B-form double helix,double helix,structure | ||
| 18 | 1ENN|1|A+ 1ENN|1|B | SOLVENT ORGANIZATION IN AN OLIGONUCLEOTIDE CRYSTAL: THE STRUCTURE OF D(GCGAATTCG)2 AT ATOMIC RESOLUTION | X-RAY DIFFRACTION | 0.89 | 18 | B-form double helix,double helix,structure | ||
| 19 | 1XJX|1|A+ 1XJX|1|B | The crystal structures of the DNA binding sites of the RUNX1 transcription factor | X-RAY DIFFRACTION | 1.7 | 18 | A-form double helix,double helix,structure | ||
| 20 | 3G00|1|H+ 3G00|1|I | Mth0212 in complex with a 9bp blunt end dsDNA at 1.7 Angstrom | X-RAY DIFFRACTION | 1.74 | 18 | B-form double helix,double helix,feature,mispair,structure | enzyme,hydrolase,nuclease | |
| 21 | 1XJY|1|A+ 1XJY|1|B | The crystal structures of the DNA binding sites of the RUNX1 transcription factor | X-RAY DIFFRACTION | 2 | 18 | A-form double helix,double helix,structure | ||
| 22 | 3OQG|1|C+ 3OQG|1|D | Restriction endonuclease HPY188I in complex with substrate DNA | X-RAY DIFFRACTION | 1.75 | 18 | double helix,structure | enzyme,hydrolase,nuclease | |
| 23 | 253D|1|A | CRYSTAL STRUCTURE OF THE B-DNA NONAMER D(GCGTACGCG) WITH A NOVEL D[G*(G.C)] BASE-TRIPLET INVOLVING THE MINOR GROOVE | X-RAY DIFFRACTION | 2.2 | 9 | B-form double helix,double helix,structure | ||
| 24 | 1RXW|1|C+ 1RXW|1|B | Crystal structure of A. fulgidus FEN-1 bound to DNA | X-RAY DIFFRACTION | 2 | 15 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease,regulatory,transcription | |
| 25 | 3IMB|1|K+ 3IMB|1|L | Alternative binding mode of restriction endonuclease BcnI to cognate DNA | X-RAY DIFFRACTION | 1.89 | 18 | double helix,structure | enzyme,hydrolase,nuclease | |
| 26 | 3IMB|1|G+ 3IMB|1|H | Alternative binding mode of restriction endonuclease BcnI to cognate DNA | X-RAY DIFFRACTION | 1.89 | 18 | double helix,structure | enzyme,hydrolase,nuclease | |
| 27 | 3IMB|1|E+ 3IMB|1|F | Alternative binding mode of restriction endonuclease BcnI to cognate DNA | X-RAY DIFFRACTION | 1.89 | 18 | double helix,structure | enzyme,hydrolase,nuclease | |
| 28 | 3IMB|1|I+ 3IMB|1|J | Alternative binding mode of restriction endonuclease BcnI to cognate DNA | X-RAY DIFFRACTION | 1.89 | 18 | double helix,structure | enzyme,hydrolase,nuclease | |
| 29 | 2W35|1|F | Structures of endonuclease V with DNA reveal initiation of deaminated adenine repair | X-RAY DIFFRACTION | 2.15 | 0 | enzyme,hydrolase,nuclease | ||
| 30 | 2W35|1|C | Structures of endonuclease V with DNA reveal initiation of deaminated adenine repair | X-RAY DIFFRACTION | 2.15 | 4 | enzyme,hydrolase,nuclease | ||
| 31 | 376D|1|A | A ZIPPER-LIKE DNA DUPLEX D(GCGAAAGCT) | X-RAY DIFFRACTION | 2.1 | 9 | NAKB_NA_annotation | NAKB_protein_annotation | |
| 32 | 1UE2|1|A | Crystal structure of d(GC38GAAAGCT) | X-RAY DIFFRACTION | 1.4 | 9 | NAKB_NA_annotation | NAKB_protein_annotation | |
| 33 | 1RXV|1|D | Crystal Structure of A. Fulgidus FEN-1 bound to DNA | X-RAY DIFFRACTION | 2.5 | 2 | enzyme,hydrolase,nuclease,regulatory,transcription | ||
| 34 | 1RXV|1|C | Crystal Structure of A. Fulgidus FEN-1 bound to DNA | X-RAY DIFFRACTION | 2.5 | 2 | enzyme,hydrolase,nuclease,regulatory,transcription |
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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