Equivalence class DNA_4.0_03502.2 Current
| # | IFE | Standardized name | Molecule | Organism | Source | Rfam | Title | Method | Res. Å | 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 | 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 | 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 | 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 | 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 | 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 | 2004-08-31 | ||||
| 7 | 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 | 2004-08-31 | ||||
| 8 | 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 | 2004-10-12 | ||||
| 9 | 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 | 2009-06-30 | ||||
| 10 | 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 | 2004-07-06 | ||||
| 11 | 2AJQ|1|T+ 2AJQ|1|P | DNA Template, DNA Primer | Structure of replicative DNA polymerase provides insigts into the mechanisms for processivity, frameshifting and editing | X-ray diffraction | 2.6 | 2006-09-26 | ||||
| 12 | 2AJQ|1|Z+ 2AJQ|1|X | DNA Template, DNA Primer | Structure of replicative DNA polymerase provides insigts into the mechanisms for processivity, frameshifting and editing | X-ray diffraction | 2.6 | 2006-09-26 | ||||
| 13 | 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 | 1999-07-13 | ||||
| 14 | 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 | 2004-10-26 | ||||
| 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 | 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 | 2004-08-31 | ||||
| 17 | 3QFQ|1|W | DNA (26-MER) | Asymmetric Assembly of Merkel Cell Polyomavirus Large T-antigen Origin Binding Domains at the Viral Origin | X-ray diffraction | 2.9001 | 2011-04-27 | ||||
| 18 | 3QFQ|1|C | DNA (26-MER) | Asymmetric Assembly of Merkel Cell Polyomavirus Large T-antigen Origin Binding Domains at the Viral Origin | X-ray diffraction | 2.9001 | 2011-04-27 | ||||
| 19 | 1Z1B|1|F+ 1Z1B|1|G | 26-MER DNA | Crystal structure of a lambda integrase dimer bound to a COC' core site | X-ray diffraction | 3.8 | 2005-06-28 | ||||
| 20 | 3GUT|1|I+ 3GUT|1|J+ 3GUT|1|X+ 3GUT|1|Y | HIV-LTR Core Forward Strand, HIV-LTR Core Reverse Strand | Human immunodeficiency virus | Crystal structure of a higher-order complex of p50:RelA bound to the HIV-1 LTR | X-ray diffraction | 3.59 | 2009-09-08 | |||
| 21 | 1H8A|1|D+ 1H8A|1|E | 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'), 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') | Homo sapiens | CRYSTAL STRUCTURE OF TERNARY PROTEIN-DNA COMPLEX3 | X-ray diffraction | 2.23 | 2002-01-28 | |||
| 22 | 1H89|1|D+ 1H89|1|E | 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'), 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') | Homo sapiens | CRYSTAL STRUCTURE OF TERNARY PROTEIN-DNA COMPLEX2 | X-ray diffraction | 2.45 | 2002-01-28 | |||
| 23 | 1H88|1|D+ 1H88|1|E | 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'), 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') | Homo sapiens | CRYSTAL STRUCTURE OF TERNARY PROTEIN-DNA COMPLEX1 | X-ray diffraction | 2.8 | 2002-01-28 | |||
| 24 | 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 | 2001-03-12 | ||||
| 25 | 1HJB|1|G+ 1HJB|1|H+ 1HJB|1|I+ 1HJB|1|J | 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'), 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') | 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 | 2001-03-09 | |||
| 26 | 1RZ9|1|F+ 1RZ9|1|G | 26-MER | Crystal Structure of AAV Rep complexed with the Rep-binding sequence | X-ray diffraction | 3.1 | 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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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 | 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 | 26 | double helix,structure | enzyme,oxidoreductase,polymerase,transferase |
| 2 | 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 | 26 | double helix,structure | enzyme,oxidoreductase,polymerase,transferase |
| 3 | 1SKR|1|T+1SKR|1|P | T7 DNA Polymerase Complexed To DNA Primer/Template and ddATP | X-RAY DIFFRACTION | 2.4 | 26 | B-form double helix,double helix,structure | enzyme,oxidoreductase,polymerase,transferase |
| 4 | 1TK5|1|T+1TK5|1|P | T7 DNA polymerase binary complex with 8 oxo guanosine in the templating strand | X-RAY DIFFRACTION | 2.2 | 26 | B-form double helix,double helix,structure | enzyme,oxidoreductase,polymerase,transferase |
| 5 | 1T8E|1|D+1T8E|1|C | T7 DNA Polymerase Ternary Complex with dCTP at the Insertion Site. | X-RAY DIFFRACTION | 2.54 | 26 | double helix,structure | enzyme,oxidoreductase,polymerase,transferase |
| 6 | 1ZYQ|1|T+1ZYQ|1|P | T7 DNA polymerase in complex with 8oG and incoming ddATP | X-RAY DIFFRACTION | 2.7 | 26 | B-form double helix,double helix,structure | enzyme,oxidoreductase,polymerase,transferase |
| 7 | 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 | 26 | double helix,structure | enzyme,oxidoreductase,polymerase,transferase |
| 8 | 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 | 26 | B-form double helix,double helix,structure | enzyme,oxidoreductase,polymerase,transferase |
| 9 | 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 | 26 | B-form double helix,double helix,structure | enzyme,oxidoreductase,polymerase,transferase |
| 10 | 1X9M|1|D+1X9M|1|C | T7 DNA polymerase in complex with an N-2-acetylaminofluorene-adducted DNA | X-RAY DIFFRACTION | 2.1 | 26 | B-form double helix,double helix,structure | enzyme,oxidoreductase,polymerase,transferase |
| 11 | 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 | 26 | double helix,structure | enzyme,oxidoreductase,polymerase,transferase |
| 12 | 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 | 26 | double helix,structure | enzyme,oxidoreductase,polymerase,transferase |
| 13 | 1Z1B|1|F+1Z1B|1|G | Crystal structure of a lambda integrase dimer bound to a COC' core site | X-RAY DIFFRACTION | 3.8 | 26 | Holliday junction,structure | DNA replication/repair,enzyme,recombinase,regulatory |
| 14 | 1H88|1|D+1H88|1|E | CRYSTAL STRUCTURE OF TERNARY PROTEIN-DNA COMPLEX1 | X-RAY DIFFRACTION | 2.8 | 26 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),basic transcription factor,leucine zipper (bZIP),regulatory,transcription |
| 15 | 3QFQ|1|W | Asymmetric Assembly of Merkel Cell Polyomavirus Large T-antigen Origin Binding Domains at the Viral Origin | X-RAY DIFFRACTION | 2.9001 | 28 | double helix,structure | DNA replication/repair,regulatory |
| 16 | 3QFQ|1|C | Asymmetric Assembly of Merkel Cell Polyomavirus Large T-antigen Origin Binding Domains at the Viral Origin | X-RAY DIFFRACTION | 2.9001 | 27 | double helix,structure | DNA replication/repair,regulatory |
| 17 | 1RZ9|1|F+1RZ9|1|G | Crystal Structure of AAV Rep complexed with the Rep-binding sequence | X-RAY DIFFRACTION | 3.1 | 26 | double helix,structure | enzyme,helicase,hydrolase,regulatory,transcription |
| 18 | 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 | 26 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),homeodomain,regulatory,transcription |
| 19 | 1H8A|1|D+1H8A|1|E | CRYSTAL STRUCTURE OF TERNARY PROTEIN-DNA COMPLEX3 | X-RAY DIFFRACTION | 2.23 | 26 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),basic transcription factor,leucine zipper (bZIP),regulatory,transcription |
| 20 | 1H89|1|D+1H89|1|E | CRYSTAL STRUCTURE OF TERNARY PROTEIN-DNA COMPLEX2 | X-RAY DIFFRACTION | 2.45 | 26 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),basic transcription factor,leucine zipper (bZIP),regulatory,transcription |
| 21 | 1HJB|1|G+1HJB|1|H+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 | 26 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),basic transcription factor,immunoglobulin (Ig) fold,leucine zipper (bZIP),regulatory,runt,transcription |
| 22 | 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 | 26 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),basic transcription factor,immunoglobulin (Ig) fold,leucine zipper (bZIP),regulatory,runt,transcription |
| 23 | 3H0D|1|C+3H0D|1|D | Crystal structure of CtsR in complex with a 26bp DNA duplex | X-RAY DIFFRACTION | 2.4 | 26 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),regulatory,transcription,winged helix/forkhead |
| 24 | 1MDM|1|C+1MDM|1|D | INHIBITED FRAGMENT OF ETS-1 AND PAIRED DOMAIN OF PAX5 BOUND TO DNA | X-RAY DIFFRACTION | 2.8 | 26 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),homeodomain,regulatory,transcription,winged helix/forkhead |
| 25 | 3GUT|1|I+3GUT|1|J+3GUT|1|X+3GUT|1|Y | Crystal structure of a higher-order complex of p50:RelA bound to the HIV-1 LTR | X-RAY DIFFRACTION | 3.59 | 26 | double helix,structure | DNA-binding transcription factor (TF),immunoglobulin (Ig) fold,regulatory,rel homology,transcription |
| 26 | 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 | 26 | double helix,structure | enzyme,recombinase |
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