Equivalence class DNA_3.5_55884.1 Obsolete
| # | IFE | Standardized name | Molecule | Organism | Source | Rfam | Title | Method | Res. Å | #NTs | Date |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 1X9M|1|D+ 1X9M|1|C (rep) | 5'-D(*CP*CP*CP*(8FG)P*AP*TP*CP*AP*CP*AP*CP*TP*AP*CP*CP*AP*AP*TP*CP*AP*CP*TP*CP*TP*CP*C)-3', 5'-D(*GP*GP*AP*GP*AP*GP*TP*GP*AP*TP*TP*GP*GP*TP*AP*GP*TP*GP*TP*GP*AP*(2DT))-3' | T7 DNA polymerase in complex with an N-2-acetylaminofluorene-adducted DNA | X-ray diffraction | 2.1 | 22 | 2004-10-26 | ||||
| 2 | 1TK5|1|T+ 1TK5|1|P | 5'-D(*CP*CP*CP*(8OG)P*CP*TP*GP*GP*CP*AP*CP*TP*GP*GP*CP*CP*GP*TP*CP*GP*TP*TP*TP*TP*CP*G)-3', 5'-D(*CP*GP*AP*AP*A*GP*CP*CP*AP*GP*TP*GP*CP*CP*AP*(DDG)P*TP*GP*CP*AP*A)-3' | T7 DNA polymerase binary complex with 8 oxo guanosine in the templating strand | X-ray diffraction | 2.2 | 24 | 2004-08-31 | ||||
| 3 | 1ZYQ|1|T+ 1ZYQ|1|P | 5'-D(*CP*CP*CP*(8OG)P*CP*TP*GP*GP*CP*AP*CP*TP*GP*GP*CP*CP*GP*TP*CP*GP*TP*TP*TP*TP*CP*G)-3', 5'-D(*CP*GP*AP*AP*AP*AP*CP*GP*AP*CP*GP*GP*CP*CP*AP*GP*TP*GP*CP*CP*AP*(DDG))-3' | T7 DNA polymerase in complex with 8oG and incoming ddATP | X-ray diffraction | 2.7 | 28 | 2005-11-22 | ||||
| 4 | 1X9W|1|D+ 1X9W|1|C | 5'-D(*CP*CP*CP*(AFG)*AP*TP*CP*AP*CP*AP*CP*TP*AP*CP*CP*AP*AP*TP*CP*AP*CP*TP*CP*TP*CP*C)-3', 5'-D(*GP*GP*AP*GP*AP*GP*TP*GP*AP*TP*T*GP*GP*T*AP*GP*TP*GP*TP*GP*AP*(2DT))-3' | T7 DNA polymerase in complex with a primer/template DNA containing a disordered N-2 aminofluorene on the template, crystallized with dideoxy-ATP as the incoming nucleotide. | X-ray diffraction | 2.3 | 22 | 2004-10-26 | ||||
| 5 | 1TK0|1|T+ 1TK0|1|P | 5'-D(*CP*CP*CP*(8OG)P*CP*TP*GP*GP*CP*AP*CP*TP*GP*GP*CP*CP*GP*TP*CP*GP*TP*TP*TP*TP*CP*G)-3', 5'-D(*CP*GP*AP*AP*AP*AP*CP*GP*A*CP*GP*GP*CP*CP*AP*GP*TP*GP*CP*CP*AP*(DDG))-3' | T7 DNA polymerase ternary complex with 8 oxo guanosine and ddCTP at the insertion site | X-ray diffraction | 2.3 | 29 | 2004-08-31 | ||||
| 6 | 1TKD|1|T+ 1TKD|1|P | DNA (5'-D(*CP*CP*CP*AP*(8OG)P*TP*GP*GP*CP*AP*CP*TP*GP*GP*CP*CP*GP*TP*CP*GP*TP*TP*TP*TP*CP*G)-3'), DNA (5'-D(*CP*GP*AP*AP*AP*AP*CP*GP*AP*CP*GP*GP*CP*CP*AP*GP*TP*GP*CP*CP*AP*(DOC))-3') | T7 DNA polymerase ternary complex with 8 oxo guanosine and dCMP at the elongation site | X-ray diffraction | 2.49 | 35 | 2004-08-31 | ||||
| 7 | 1T8E|1|D+ 1T8E|1|C | 25-MER, 5'-D(P*CP*GP*AP*AP*AP*AP*CP*GP*AP*CP*GP*GP*CP*CP*AP*GP*TP*GP*CP*CP*AP*(2DT))-3' | T7 DNA Polymerase Ternary Complex with dCTP at the Insertion Site. | X-ray diffraction | 2.54 | 47 | 2004-10-12 | ||||
| 8 | 1TK8|1|T+ 1TK8|1|P | 5'-D(*CP*CP*CP*AP*(8OG)P*TP*GP*GP*CP*AP*CP*TP*GP*GP*CP*CP*GP*TP*CP*GP*TP*TP*TP*TP*CP*G)-3', 5'-D(*CP*GP*AP*AP*AP*AP*CP*GP*AP*CP*GP*GP*CP*CP*AP*GP*TP*GP*CP*CP*AP*(2DA))-3' | T7 DNA polymerase ternary complex with 8 oxo guanosine and dAMP at the elongation site | X-ray diffraction | 2.5 | 37 | 2004-08-31 | ||||
| 9 | 1SKR|1|T+ 1SKR|1|P | 5'-D(*CP*CP*CP*TP*TP*TP*GP*GP*CP*AP*CP*TP*GP*GP*CP*CP*GP*TP*CP*GP*TP*TP*TP*TP*CP*G)-3', 5'-D(*CP*GP*AP*AP*AP*AP*CP*GP*AP*C*GP*GP*CP*CP*AP*GP*TP*GP*CP*CP*AP*(2DA))-3' | T7 DNA Polymerase Complexed To DNA Primer/Template and ddATP | X-ray diffraction | 2.4 | 24 | 2004-07-06 | ||||
| 10 | 3H0D|1|C+ 3H0D|1|D | DNA (26-MER) | Crystal structure of CtsR in complex with a 26bp DNA duplex | X-ray diffraction | 2.4 | 52 | 2009-06-30 | ||||
| 11 | 2AJQ|1|T+ 2AJQ|1|P | DNA Primer, DNA Template | Structure of replicative DNA polymerase provides insigts into the mechanisms for processivity, frameshifting and editing | X-ray diffraction | 2.6 | 42 | 2006-09-26 | ||||
| 12 | 2AJQ|1|Z+ 2AJQ|1|X | DNA Primer, DNA Template | Structure of replicative DNA polymerase provides insigts into the mechanisms for processivity, frameshifting and editing | X-ray diffraction | 2.6 | 46 | 2006-09-26 | ||||
| 13 | 1X9S|1|T+ 1X9S|1|P | 5'-D(*CP*CP*CP*(AFG)P*AP*TP*CP*AP*CP*AP*CP*TP*AP*CP*CP*AP*AP*TP*CP*AP*CP*TP*CP*TP*CP*C)-3', 5'-D(*GP*GP*AP*GP*AP*GP*TP*GP*AP*TP*T*GP*GP*TP*AP*GP*TP*GP*TP*GP*AP*(2DT))-3' | T7 DNA polymerase in complex with a primer/template DNA containing a disordered N-2 aminofluorene on the template, crystallized with dideoxy-CTP as the incoming nucleotide. | X-ray diffraction | 2.7 | 22 | 2004-10-26 | ||||
| 14 | 6PAX|1|B+ 6PAX|1|C | 26 NUCLEOTIDE DNA | CRYSTAL STRUCTURE OF THE HUMAN PAX-6 PAIRED DOMAIN-DNA COMPLEX REVEALS A GENERAL MODEL FOR PAX PROTEIN-DNA INTERACTIONS | X-ray diffraction | 2.5 | 52 | 1999-07-13 | ||||
| 15 | 1MDM|1|C+ 1MDM|1|D | PAX5/ETS BINDING SITE ON THE MB-1 PROMOTER | INHIBITED FRAGMENT OF ETS-1 AND PAIRED DOMAIN OF PAX5 BOUND TO DNA | X-ray diffraction | 2.8 | 52 | 2002-12-11 | ||||
| 16 | 1U78|1|B+ 1U78|1|C | 26-MER | Structure of the bipartite DNA-binding domain of Tc3 transposase bound to transposon DNA | X-ray diffraction | 2.69 | 52 | 2004-08-31 | ||||
| 17 | 1H8A|1|D+ 1H8A|1|E | DNA(5'-(*CP*CP*AP*GP*TP*CP*CP*GP*TP*TP*AP* AP*GP*GP*AP*TP*TP*GP*CP*GP*CP*CP*AP*CP*AP*T)-3'), DNA(5'-(*GP*AP*TP*GP*TP*GP*GP*CP*GP*CP*AP* AP*TP*CP*CP*TP*TP*AP*AP*CP*GP*GP*AP*CP*TP*G)-3') | Homo sapiens | CRYSTAL STRUCTURE OF TERNARY PROTEIN-DNA COMPLEX3 | X-ray diffraction | 2.23 | 52 | 2002-01-28 | |||
| 18 | 1H89|1|D+ 1H89|1|E | DNA(5'-(*CP*CP*AP*GP*TP*CP*CP*GP*TP*TP*AP* AP*GP*GP*AP*TP*TP*GP*CP*GP*CP*CP*AP*CP*AP*T)-3'), DNA(5'-(*GP*AP*TP*GP*TP*GP*GP*CP*GP*CP*AP* AP*TP*CP*CP*TP*TP*AP*AP*CP*GP*GP*AP*CP*TP*G)-3') | Homo sapiens | CRYSTAL STRUCTURE OF TERNARY PROTEIN-DNA COMPLEX2 | X-ray diffraction | 2.45 | 52 | 2002-01-28 | |||
| 19 | 1H88|1|D+ 1H88|1|E | DNA(5'-(*CP*CP*AP*GP*TP*CP*CP*GP*TP*TP*AP* AP*GP*GP*AP*TP*TP*GP*CP*GP*CP*CP*AP*CP*AP*T)-3'), DNA(5'-(*GP*AP*TP*GP*TP*GP*GP*CP*GP*CP*AP* AP*TP*CP*CP*TP*TP*AP*AP*CP*GP*GP*AP*CP*TP*G)-3') | Homo sapiens | CRYSTAL STRUCTURE OF TERNARY PROTEIN-DNA COMPLEX1 | X-ray diffraction | 2.8 | 52 | 2002-01-28 | |||
| 20 | 1IO4|1|E+ 1IO4|1|F | CSF-1R PROMOTER | CRYSTAL STRUCTURE OF RUNX-1/AML1/CBFALPHA RUNT DOMAIN-CBFBETA CORE DOMAIN HETERODIMER AND C/EBPBETA BZIP HOMODIMER BOUND TO A DNA FRAGMENT FROM THE CSF-1R PROMOTER | X-ray diffraction | 3 | 52 | 2001-03-12 | ||||
| 21 | 1HJB|1|G+ 1HJB|1|H | DNA (5'-(*CP*CP*GP*CP*AP*AP*CP*CP*AP*CP* AP*GP*AP*GP*TP*TP*TP*GP*GP*AP*AP*AP*TP*CP*TP*T)-3'), DNA (5'-(*GP*AP*AP*GP*AP*TP*TP*TP*CP*CP* AP*AP*AP*CP*TP*CP*TP*GP*TP*GP*GP*TP*TP*GP*CP*G)-3') | Homo sapiens | CRYSTAL STRUCTURE OF RUNX-1/AML1/CBFALPHA RUNT DOMAIN AND C/EBPBETA BZIP HOMODIMER BOUND TO A DNA FRAGMENT FROM THE CSF-1R PROMOTER | X-ray diffraction | 3 | 52 | 2001-03-09 | |||
| 22 | 1HJB|1|I+ 1HJB|1|J | DNA (5'-(*CP*CP*GP*CP*AP*AP*CP*CP*AP*CP* AP*GP*AP*GP*TP*TP*TP*GP*GP*AP*AP*AP*TP*CP*TP*T)-3'), DNA (5'-(*GP*AP*AP*GP*AP*TP*TP*TP*CP*CP* AP*AP*AP*CP*TP*CP*TP*GP*TP*GP*GP*TP*TP*GP*CP*G)-3') | Homo sapiens | CRYSTAL STRUCTURE OF RUNX-1/AML1/CBFALPHA RUNT DOMAIN AND C/EBPBETA BZIP HOMODIMER BOUND TO A DNA FRAGMENT FROM THE CSF-1R PROMOTER | X-ray diffraction | 3 | 52 | 2001-03-09 | |||
| 23 | 1RZ9|1|F+ 1RZ9|1|G | 26-MER | Crystal Structure of AAV Rep complexed with the Rep-binding sequence | X-ray diffraction | 3.1 | 52 | 2004-02-17 |
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 | 1H88|1|D+ 1H88|1|E | CRYSTAL STRUCTURE OF TERNARY PROTEIN-DNA COMPLEX1 | X-RAY DIFFRACTION | 2.8 | 52 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),basic transcription factor,leucine zipper (bZIP),regulatory,transcription | |
| 2 | 1H89|1|D+ 1H89|1|E | CRYSTAL STRUCTURE OF TERNARY PROTEIN-DNA COMPLEX2 | X-RAY DIFFRACTION | 2.45 | 52 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),basic transcription factor,leucine zipper (bZIP),regulatory,transcription | |
| 3 | 1H8A|1|D+ 1H8A|1|E | CRYSTAL STRUCTURE OF TERNARY PROTEIN-DNA COMPLEX3 | X-RAY DIFFRACTION | 2.23 | 52 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),basic transcription factor,leucine zipper (bZIP),regulatory,transcription | |
| 4 | 6PAX|1|B+ 6PAX|1|C | CRYSTAL STRUCTURE OF THE HUMAN PAX-6 PAIRED DOMAIN-DNA COMPLEX REVEALS A GENERAL MODEL FOR PAX PROTEIN-DNA INTERACTIONS | X-RAY DIFFRACTION | 2.5 | 52 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),homeodomain,regulatory,transcription | |
| 5 | 1HJB|1|I+ 1HJB|1|J | CRYSTAL STRUCTURE OF RUNX-1/AML1/CBFALPHA RUNT DOMAIN AND C/EBPBETA BZIP HOMODIMER BOUND TO A DNA FRAGMENT FROM THE CSF-1R PROMOTER | X-RAY DIFFRACTION | 3 | 52 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),basic transcription factor,immunoglobulin (Ig) fold,leucine zipper (bZIP),regulatory,runt,transcription | |
| 6 | 1HJB|1|G+ 1HJB|1|H | CRYSTAL STRUCTURE OF RUNX-1/AML1/CBFALPHA RUNT DOMAIN AND C/EBPBETA BZIP HOMODIMER BOUND TO A DNA FRAGMENT FROM THE CSF-1R PROMOTER | X-RAY DIFFRACTION | 3 | 52 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),basic transcription factor,immunoglobulin (Ig) fold,leucine zipper (bZIP),regulatory,runt,transcription | |
| 7 | 1IO4|1|E+ 1IO4|1|F | CRYSTAL STRUCTURE OF RUNX-1/AML1/CBFALPHA RUNT DOMAIN-CBFBETA CORE DOMAIN HETERODIMER AND C/EBPBETA BZIP HOMODIMER BOUND TO A DNA FRAGMENT FROM THE CSF-1R PROMOTER | X-RAY DIFFRACTION | 3 | 52 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),basic transcription factor,immunoglobulin (Ig) fold,leucine zipper (bZIP),regulatory,runt,transcription | |
| 8 | 3H0D|1|C+ 3H0D|1|D | Crystal structure of CtsR in complex with a 26bp DNA duplex | X-RAY DIFFRACTION | 2.4 | 52 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),regulatory,transcription,winged helix/forkhead | |
| 9 | 1MDM|1|C+ 1MDM|1|D | INHIBITED FRAGMENT OF ETS-1 AND PAIRED DOMAIN OF PAX5 BOUND TO DNA | X-RAY DIFFRACTION | 2.8 | 52 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),homeodomain,regulatory,transcription,winged helix/forkhead | |
| 10 | 1RZ9|1|F+ 1RZ9|1|G | Crystal Structure of AAV Rep complexed with the Rep-binding sequence | X-RAY DIFFRACTION | 3.1 | 52 | double helix,structure | enzyme,helicase,hydrolase,regulatory,transcription | |
| 11 | 1TK5|1|T+ 1TK5|1|P | T7 DNA polymerase binary complex with 8 oxo guanosine in the templating strand | X-RAY DIFFRACTION | 2.2 | 24 | B-form double helix,double helix,structure | enzyme,oxidoreductase,polymerase,transferase | |
| 12 | 1ZYQ|1|T+ 1ZYQ|1|P | T7 DNA polymerase in complex with 8oG and incoming ddATP | X-RAY DIFFRACTION | 2.7 | 28 | B-form double helix,double helix,structure | enzyme,oxidoreductase,polymerase,transferase | |
| 13 | 1TK8|1|T+ 1TK8|1|P | T7 DNA polymerase ternary complex with 8 oxo guanosine and dAMP at the elongation site | X-RAY DIFFRACTION | 2.5 | 37 | B-form double helix,double helix,structure | enzyme,oxidoreductase,polymerase,transferase | |
| 14 | 1TKD|1|T+ 1TKD|1|P | T7 DNA polymerase ternary complex with 8 oxo guanosine and dCMP at the elongation site | X-RAY DIFFRACTION | 2.49 | 35 | B-form double helix,double helix,structure | enzyme,oxidoreductase,polymerase,transferase | |
| 15 | 1TK0|1|T+ 1TK0|1|P | T7 DNA polymerase ternary complex with 8 oxo guanosine and ddCTP at the insertion site | X-RAY DIFFRACTION | 2.3 | 29 | double helix,structure | enzyme,oxidoreductase,polymerase,transferase | |
| 16 | 1T8E|1|D+ 1T8E|1|C | T7 DNA Polymerase Ternary Complex with dCTP at the Insertion Site. | X-RAY DIFFRACTION | 2.54 | 47 | double helix,structure | enzyme,oxidoreductase,polymerase,transferase | |
| 17 | 1SKR|1|T+ 1SKR|1|P | T7 DNA Polymerase Complexed To DNA Primer/Template and ddATP | X-RAY DIFFRACTION | 2.4 | 24 | B-form double helix,double helix,structure | enzyme,oxidoreductase,polymerase,transferase | |
| 18 | 2AJQ|1|T+ 2AJQ|1|P | Structure of replicative DNA polymerase provides insigts into the mechanisms for processivity, frameshifting and editing | X-RAY DIFFRACTION | 2.6 | 42 | double helix,structure | enzyme,oxidoreductase,polymerase,transferase | |
| 19 | 2AJQ|1|Z+ 2AJQ|1|X | Structure of replicative DNA polymerase provides insigts into the mechanisms for processivity, frameshifting and editing | X-RAY DIFFRACTION | 2.6 | 46 | double helix,structure | enzyme,oxidoreductase,polymerase,transferase | |
| 20 | 1X9S|1|T+ 1X9S|1|P | T7 DNA polymerase in complex with a primer/template DNA containing a disordered N-2 aminofluorene on the template, crystallized with dideoxy-CTP as the incoming nucleotide. | X-RAY DIFFRACTION | 2.7 | 22 | double helix,structure | enzyme,oxidoreductase,polymerase,transferase | |
| 21 | 1X9M|1|D+ 1X9M|1|C | T7 DNA polymerase in complex with an N-2-acetylaminofluorene-adducted DNA | X-RAY DIFFRACTION | 2.1 | 22 | B-form double helix,double helix,structure | enzyme,oxidoreductase,polymerase,transferase | |
| 22 | 1X9W|1|D+ 1X9W|1|C | T7 DNA polymerase in complex with a primer/template DNA containing a disordered N-2 aminofluorene on the template, crystallized with dideoxy-ATP as the incoming nucleotide. | X-RAY DIFFRACTION | 2.3 | 22 | double helix,structure | enzyme,oxidoreductase,polymerase,transferase | |
| 23 | 1U78|1|B+ 1U78|1|C | Structure of the bipartite DNA-binding domain of Tc3 transposase bound to transposon DNA | X-RAY DIFFRACTION | 2.69 | 52 | double helix,structure | enzyme,recombinase |
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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