Equivalence class DNA_2.5_03502.1 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 | 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 | ||||
| 4 | 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 | ||||
| 5 | 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 | ||||
| 6 | 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 | ||||
| 7 | 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 | ||||
| 8 | 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 | ||||
| 9 | 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 | ||||
| 10 | 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 | |||
| 11 | 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 |
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 | 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 |
| 2 | 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 |
| 3 | 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 |
| 4 | 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 |
| 5 | 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 |
| 6 | 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 |
| 7 | 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 |
| 8 | 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 |
| 9 | 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 |
| 10 | 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 |
| 11 | 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 |
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