Equivalence class DNA_2.5_57332.1 Obsolete
| # | IFE | Standardized name | Molecule | Organism | Source | Rfam | Title | Method | Res. Å | #NTs | Date |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 1NK0|1|C+ 1NK0|1|B (rep) | DNA PRIMER STRAND, DNA TEMPLATE STRAND | ADENINE-GUANINE MISMATCH AT THE POLYMERASE ACTIVE SITE | X-ray diffraction | 1.7 | 23 | 2004-03-30 | ||||
| 2 | 3MFI|1|T+ 3MFI|1|P | 5'-D(*GP*TP*CP*CP*TP*CP*CP*CP*CP*TP*(DOC))-3', 5'-D(*TP*AP*AP*(TTD)P*GP*AP*GP*GP*GP*GP*AP*GP*GP*AP*C)-3' | DNA Polymerase Eta in Complex With a cis-syn Thymidine Dimer | X-ray diffraction | 1.76 | 24 | 2010-06-23 | ||||
| 3 | 1NKC|1|B+ 1NKC|1|C | DNA PRIMER STRAND, DNA TEMPLATE STRAND | A BACILLUS DNA POLYMERASE I PRODUCT COMPLEX BOUND TO A GUANINE-THYMINE MISMATCH AFTER FIVE ROUNDS OF PRIMER EXTENSION, FOLLOWING INCORPORATION OF DCTP, DGTP, DTTP, AND DATP. | X-ray diffraction | 1.8 | 30 | 2004-03-30 | ||||
| 4 | 1U4B|1|C+ 1U4B|1|B | DNA primer strand, DNA template strand with 8-oxoguanine | Extension of an adenine-8oxoguanine mismatch | X-ray diffraction | 1.6 | 23 | 2004-09-14 | ||||
| 5 | 1NK8|1|C+ 1NK8|1|B | DNA PRIMER STRAND, DNA TEMPLATE STRAND | A BACILLUS DNA POLYMERASE I PRODUCT COMPLEX BOUND TO A GUANINE-THYMINE MISMATCH AFTER A SINGLE ROUND OF PRIMER EXTENSION, FOLLOWING INCORPORATION OF DCTP. | X-ray diffraction | 1.9 | 23 | 2004-03-30 | ||||
| 6 | 1NJX|1|C+ 1NJX|1|B | DNA PRIMER STRAND, DNA TEMPLATE STRAND | THYMINE-GUANINE MISMATCH AT THE POLYMERASE ACTIVE SITE | X-ray diffraction | 1.65 | 23 | 2004-03-30 | ||||
| 7 | 3FDQ|1|C+ 3FDQ|1|D | 5'-D(*AP*TP*TP*TP*TP*TP*TP*AP*AP*AP*AP*AP*AP*AP*T)-3', 5'-D(*TP*AP*TP*TP*TP*TP*TP*TP*TP*AP*AP*AP*AP*AP*A)-3' | Recognition of AT-rich DNA binding sites by the MogR Repressor | X-ray diffraction | 1.75 | 30 | 2009-06-02 | ||||
| 8 | 1NK7|1|C+ 1NK7|1|B | DNA PRIMER STRAND, DNA TEMPLATE STRAND | GUANINE-ADENINE MISMATCH AT THE POLYMERASE ACTIVE SITE | X-ray diffraction | 1.9 | 20 | 2004-03-30 | ||||
| 9 | 1NK9|1|C+ 1NK9|1|B | DNA PRIMER STRAND, DNA TEMPLATE STRAND | A BACILLUS DNA POLYMERASE I PRODUCT COMPLEX BOUND TO A GUANINE-THYMINE MISMATCH AFTER TWO ROUNDS OF PRIMER EXTENSION, FOLLOWING INCORPORATION OF DCTP AND DGTP. | X-ray diffraction | 1.9 | 24 | 2004-03-30 | ||||
| 10 | 1U45|1|C+ 1U45|1|B | DNA primer strand, DNA template strand with 8-oxoguanine | 8oxoguanine at the pre-insertion site of the polymerase active site | X-ray diffraction | 2.01 | 20 | 2004-09-14 | ||||
| 11 | 1RH6|1|C+ 1RH6|1|D | 5'-D(*CP*TP*AP*TP*GP*TP*AP*GP*TP*CP*TP*GP*TP*TP*G)-3', 5'-D(P*CP*AP*AP*CP*AP*GP*AP*CP*TP*AP*CP*AP*TP*AP*G)-3' | Bacteriophage Lambda Excisionase (Xis)-DNA Complex | X-ray diffraction | 1.7 | 28 | 2004-06-29 | ||||
| 12 | 1NJW|1|C+ 1NJW|1|B | DNA PRIMER STRAND, DNA TEMPLATE STRAND | GUANINE-THYMINE MISMATCH AT THE POLYMERASE ACTIVE SITE | X-ray diffraction | 1.9 | 23 | 2004-03-30 | ||||
| 13 | 2HHQ|1|C+ 2HHQ|1|B | 5'-D(*CP*AP*TP*(6OG)P*CP*GP*AP*GP*TP*CP*AP*GP*G)-3', 5'-D(*GP*CP*CP*TP*GP*AP*CP*TP*CP*GP*TP*AP*TP*GP*A)-3' | O6-methyl-guanine:T pair in the polymerase-10 basepair position | X-ray diffraction | 1.8 | 28 | 2006-12-12 | ||||
| 14 | 1NKB|1|C+ 1NKB|1|B | DNA PRIMER STRAND, DNA TEMPLATE STRAND | A BACILLUS DNA POLYMERASE I PRODUCT COMPLEX BOUND TO A GUANINE-THYMINE MISMATCH AFTER THREE ROUNDS OF PRIMER EXTENSION, FOLLOWING INCORPORATION OF DCTP, DGTP, AND DTTP. | X-ray diffraction | 2 | 27 | 2004-03-30 | ||||
| 15 | 1U47|1|C+ 1U47|1|B | DNA primer strand, DNA template strand with 8-oxoguanine | cytosine-8-Oxoguanine base pair at the polymerase active site | X-ray diffraction | 2 | 22 | 2004-09-14 | ||||
| 16 | 2XHI|1|B+ 2XHI|1|C | 5'-D(*GP*CP*GP*TP*CP*CP*AP*(8OG)P*GP*TP*CP*TP*AP*CP*C)-3', 5'-D(*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*C)-3' | Separation-of-function mutants unravel the dual reaction mode of human 8-oxoguanine DNA glycosylase | X-ray diffraction | 1.55 | 28 | 2011-01-26 | ||||
| 17 | 1U48|1|C+ 1U48|1|B | DNA primer strand, DNA template strand with 8-oxoguanine | Extension of a cytosine-8-oxoguanine base pair | X-ray diffraction | 2.1 | 23 | 2004-09-14 | ||||
| 18 | 2NOH|1|B+ 2NOH|1|C | 5'-D(*GP*CP*GP*TP*CP*CP*AP*(G42)P*GP*TP*CP*TP*AP*CP*C)-3', 5'-D(*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*C)-3' | Structure of catalytically inactive Q315A human 8-oxoguanine glycosylase complexed to 8-oxoguanine DNA | X-ray diffraction | 2.01 | 29 | 2006-11-21 | ||||
| 19 | 2VS8|1|D+ 2VS8|1|B+ 2VS8|1|C+ 2VS8|1|E | 5'-D(*CP*CP*GP*GP*CP*AP*AP* GP*GP*CP)-3', 5'-D(*CP*GP*CP*GP*CP*CP*GP*GP*AP*AP *CP*TP*TP*AP*C)-3', 5'-D(*GP*CP*CP*TP*TP*GP*CP*CP*GP*GP *GP*TP*AP*A)-3', 5'-D(*GP*TP*TP*CP*CP*GP*GP*CP* DGP*DCP*DGP)-3' | Desulfurococcus mucosus | The crystal structure of I-DmoI in complex with DNA and Mn | X-ray diffraction | 2.1 | 50 | 2008-11-11 | |||
| 20 | 2VS8|1|I+ 2VS8|1|H | 5'-D(*CP*GP*CP*GP*CP*CP*GP*GP*AP*AP *CP*TP*TP*AP*C)-3', 5'-D(*GP*TP*TP*CP*CP*GP*GP*CP* DGP*DCP*DGP)-3' | Desulfurococcus mucosus | The crystal structure of I-DmoI in complex with DNA and Mn | X-ray diffraction | 2.1 | 0 | 2008-11-11 | |||
| 21 | 2VS8|1|N+ 2VS8|1|L+ 2VS8|1|M+ 2VS8|1|O | 5'-D(*CP*CP*GP*GP*CP*AP*AP* GP*GP*CP)-3', 5'-D(*CP*GP*CP*GP*CP*CP*GP*GP*AP*AP *CP*TP*TP*AP*C)-3', 5'-D(*GP*CP*CP*TP*TP*GP*CP*CP*GP*GP *GP*TP*AP*A)-3', 5'-D(*GP*TP*TP*CP*CP*GP*GP*CP* DGP*DCP*DGP)-3' | Desulfurococcus mucosus | The crystal structure of I-DmoI in complex with DNA and Mn | X-ray diffraction | 2.1 | 50 | 2008-11-11 | |||
| 22 | 1XC9|1|C+ 1XC9|1|B | DNA primer strand, DNA template strand with benzo[a]pyrene adduct | Structure of a high-fidelity polymerase bound to a benzo[a]pyrene adduct that blocks replication | X-ray diffraction | 1.9 | 22 | 2004-12-14 | ||||
| 23 | 1NK6|1|C+ 1NK6|1|B | DNA PRIMER STRAND, DNA TEMPLATE STRAND | CYTOSINE-CYTOSINE MISMATCH AT THE POLYMERASE ACTIVE SITE | X-ray diffraction | 2.1 | 18 | 2004-03-30 | ||||
| 24 | 1U49|1|C+ 1U49|1|B | DNA primer strand, DNA template strand with 8-oxoguanine | Adenine-8oxoguanine mismatch at the polymerase active site | X-ray diffraction | 2.15 | 22 | 2004-09-14 | ||||
| 25 | 1LWY|1|D+ 1LWY|1|E | 5'-D(*GP*CP*GP*TP*CP*CP*AP*(PED)P*GP*TP*CP*TP*AP*CP*C)-3', 5'-D(*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*C)-3' | hOgg1 Borohydride-Trapped Intermediate without 8-oxoguanine | X-ray diffraction | 2.01 | 29 | 2003-02-25 | ||||
| 26 | 3IAG|1|A+ 3IAG|1|B | 5'-D(*AP*AP*TP*CP*TP*TP*TP*CP*AP*CP*AP*CP*GP*AP*T)-3', 5'-D(*TP*TP*AP*TP*CP*GP*TP*GP*TP*GP*AP*AP*AP*GP*A)-3' | CSL (RBP-Jk) bound to HES-1 nonconsensus site | X-ray diffraction | 2 | 30 | 2009-11-10 | ||||
| 27 | 1LWW|1|D+ 1LWW|1|E | 5'-D(*GP*CP*GP*TP*CP*CP*AP*(PED)P*GP*TP*CP*TP*AP*CP*C)-3', 5'-D(*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*C)-3' | Borohydride-trapped hOgg1 Intermediate Structure Co-Crystallized with 8-bromoguanine | X-ray diffraction | 2.1 | 29 | 2003-02-25 | ||||
| 28 | 1M3Q|1|B+ 1M3Q|1|C | 5'-D(*GP*CP*GP*TP*CP*CP*AP*(DRZ)P*GP*TP*CP*TP*AP*CP*C)-3', 5'-D(*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*C)-3' | Crystal Structure of hogg1 D268E Mutant with Base-Excised DNA and 8-aminoguanine | X-ray diffraction | 1.9 | 30 | 2004-02-17 | ||||
| 29 | 2NOE|1|B+ 2NOE|1|C | 5'-D(*G*CP*GP*TP*CP*CP*AP*(G42)P*GP*TP*CP*TP*AP*CP*C)-3', 5'-D(*G*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*C)-3' | Structure of catalytically inactive G42A human 8-oxoguanine glycosylase complexed to 8-oxoguanine DNA | X-ray diffraction | 2.2 | 26 | 2006-11-21 | ||||
| 30 | 2IMW|1|T+ 2IMW|1|S | 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*C)-3', 5'-D(*TP*AP*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3' | Mechanism of Template-Independent Nucleotide Incorporation Catalyzed by a Template-Dependent DNA Polymerase | X-ray diffraction | 2.05 | 28 | 2007-01-16 | ||||
| 31 | 1LWV|1|D+ 1LWV|1|E | 5'-D(*GP*CP*GP*TP*CP*CP*AP*(PED)P*GP*TP*CP*TP*AP*CP*C)-3', 5'-D(*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*C)-3' | Borohydride-trapped hOgg1 Intermediate Structure Co-Crystallized with 8-aminoguanine | X-ray diffraction | 2.3 | 29 | 2003-02-25 | ||||
| 32 | 2NOF|1|B+ 2NOF|1|C | 5'-D(*GP*CP*GP*TP*C*CP*AP*(G42)P*GP*TP*CP*TP*AP*CP*C)-3', 5'-D(*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*C)-3' | Structure of Q315F human 8-oxoguanine glycosylase proximal crosslink to 8-oxoguanine DNA | X-ray diffraction | 2.35 | 16 | 2006-11-21 | ||||
| 33 | 2NOI|1|B+ 2NOI|1|C | 5'-D(*GP*CP*GP*TP*C*CP*AP*GP*GP*TP*CP*TP*AP*CP*C)-3', 5'-D(*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*C)-3' | Structure of G42A human 8-oxoguanine glycosylase crosslinked to undamaged G-containing DNA | X-ray diffraction | 2.35 | 19 | 2006-11-21 | ||||
| 34 | 3BRG|1|A+ 3BRG|1|B | DNA (5'-D(*DAP*DAP*DTP*DCP*DTP*DTP*DTP*DCP*DCP*DCP*DAP*DCP*DAP*DGP*DT)-3'), DNA (5'-D(*DTP*DTP*DAP*DCP*DTP*DGP*DTP*DGP*DGP*DGP*DAP*DAP*DAP*DGP*DA)-3') | CSL (RBP-Jk) bound to DNA | X-ray diffraction | 2.2 | 30 | 2008-04-01 | ||||
| 35 | 3L4J|1|C+ 3L4J|1|B | DNA (5'-D(*CP*GP*CP*GP*GP*TP*AP*GP*CP*AP*GP*TP*AP*GP*G)-3'), DNA (5'-D(P*CP*CP*TP*AP*CP*TP*GP*CP*TP*AP*C)-3') | Topoisomerase II-DNA cleavage complex, apo | X-ray diffraction | 2.48 | 26 | 2010-05-26 | ||||
| 36 | 3L4J|1|E+ 3L4J|1|D | DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*CP*GP*TP*CP*AP*TP*CP*C)-3'), DNA (5'-D(P*GP*GP*AP*TP*GP*AP*CP*GP*AP*TP*)-3') | Topoisomerase II-DNA cleavage complex, apo | X-ray diffraction | 2.48 | 25 | 2010-05-26 | ||||
| 37 | 2RDJ|1|F+ 2RDJ|1|E | DNA (5'-D(*DGP*DGP*DGP*DAP*DCP*DCP*DCP*DTP*DTP*DCP*DGP*DAP*DAP*DT)-3'), DNA (5'-D(P*DTP*DAP*DTP*DTP*DCP*DGP*DAP*DAP*DGP*DGP*DGP*DTP*DCP*DCP*DC)-3') | Snapshots of a Y-family DNA polymerase in replication: Dpo4 in apo and binary/ternary complex forms | X-ray diffraction | 2.2 | 29 | 2008-06-24 | ||||
| 38 | 3BRD|1|B+ 3BRD|1|C | DNA (5'-D(*DAP*DAP*DTP*DCP*DTP*DTP*DTP*DCP*DCP*DCP*DAP*DCP*DAP*DGP*DT)-3'), DNA (5'-D(*DTP*DTP*DAP*DCP*DTP*DGP*DTP*DGP*DGP*DGP*DAP*DAP*DAP*DGP*DA)-3') | CSL (Lag-1) bound to DNA with Lin-12 RAM peptide, P212121 | X-ray diffraction | 2.21 | 30 | 2008-04-01 | ||||
| 39 | 1M3H|1|B+ 1M3H|1|C+ 1M3H|1|D | 5'-D(P*GP*CP*GP*TP*CP*CP*AP*(DDX))-3', 5'-D(P*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*C)-3', 5'-D(P*GP*TP*CP*TP*AP*CP*C)-3' | Crystal Structure of Hogg1 D268E Mutant with Product Oligonucleotide | X-ray diffraction | 2.05 | 30 | 2004-04-20 | ||||
| 40 | 2NOZ|1|B+ 2NOZ|1|C | 5'-D(*G*CP*GP*TP*CP*CP*AP*(G42)P*GP*TP*CP*TP*AP*CP*C)-3', 5'-D(*GP*G*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*C)-3' | Structure of Q315F human 8-oxoguanine glycosylase distal crosslink to 8-oxoguanine DNA | X-ray diffraction | 2.43 | 23 | 2006-11-21 | ||||
| 41 | 1HU0|1|D+ 1HU0|1|E | 5'-D(*GP*CP*GP*TP*CP*CP*AP*(PED)P*GP*TP*CP*TP*AP*CP*C)-3', 5'-D(*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*C)-3' | CRYSTAL STRUCTURE OF AN HOGG1-DNA BOROHYDRIDE TRAPPED INTERMEDIATE COMPLEX | X-ray diffraction | 2.35 | 29 | 2003-02-25 | ||||
| 42 | 1K79|1|B+ 1K79|1|C | DNA (5'-D(*CP*AP*CP*AP*TP*TP*TP*CP*CP*GP*GP*CP*AP*CP*T)-3'), DNA (5'-D(*TP*AP*GP*TP*GP*CP*CP*GP*GP*AP*AP*AP*TP*GP*T)-3') | Ets-1(331-440)+GGAA duplex | X-ray diffraction | 2.4 | 30 | 2002-01-04 | ||||
| 43 | 1K79|1|E+ 1K79|1|F | DNA (5'-D(*CP*AP*CP*AP*TP*TP*TP*CP*CP*GP*GP*CP*AP*CP*T)-3'), DNA (5'-D(*TP*AP*GP*TP*GP*CP*CP*GP*GP*AP*AP*AP*TP*GP*T)-3') | Ets-1(331-440)+GGAA duplex | X-ray diffraction | 2.4 | 30 | 2002-01-04 | ||||
| 44 | 2CGP|1|C+ 2CGP|1|B | DNA (5'-D(*AP*TP*TP*AP*AP*TP*GP*TP*GP*AP*CP*AP*TP*AP*T)-3'), DNA (5'-D(*GP*TP*CP*AP*CP*AP*TP*TP*AP*AP*T)-3') | CATABOLITE GENE ACTIVATOR PROTEIN/DNA COMPLEX, ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE | X-ray diffraction | 2.2 | 26 | 1998-02-04 | ||||
| 45 | 2H1K|1|C+ 2H1K|1|D | 15-mer DNA | Crystal structure of the Pdx1 homeodomain in complex with DNA | X-ray diffraction | 2.42 | 30 | 2007-03-20 | ||||
| 46 | 2H1K|1|E+ 2H1K|1|F | 15-mer DNA | Crystal structure of the Pdx1 homeodomain in complex with DNA | X-ray diffraction | 2.42 | 30 | 2007-03-20 | ||||
| 47 | 1QPI|1|M | DNA (5'-D(*CP*CP*TP*AP*TP*CP*AP*AP*TP*GP*AP*TP*AP*GP*A)-3') | CRYSTAL STRUCTURE OF TETRACYCLINE REPRESSOR/OPERATOR COMPLEX | X-ray diffraction | 2.5 | 0 | 2000-02-28 | ||||
| 48 | 1QPI|1|N | DNA (5'-D(*TP*CP*TP*AP*TP*CP*AP*TP*TP*GP*AP*TP*AP*GP*G)-3') | CRYSTAL STRUCTURE OF TETRACYCLINE REPRESSOR/OPERATOR COMPLEX | X-ray diffraction | 2.5 | 0 | 2000-02-28 | ||||
| 49 | 1SKN|1|A+ 1SKN|1|B | DNA (5'-D(*CP*AP*GP*GP*GP*AP*TP*GP*AP*CP*AP*TP*TP*GP*T)-3'), DNA (5'-D(*TP*GP*AP*CP*AP*AP*TP*GP*TP*CP*AP*TP*CP*CP*C)-3') | THE BINDING DOMAIN OF SKN-1 IN COMPLEX WITH DNA: A NEW DNA-BINDING MOTIF | X-ray diffraction | 2.5 | 30 | 1998-06-24 | ||||
| 50 | 3BRF|1|B+ 3BRF|1|C | DNA (5'-D(*DAP*DAP*DTP*DCP*DTP*DTP*DTP*DCP*DCP*DCP*DAP*DCP*DAP*DGP*DT)-3'), DNA (5'-D(*DTP*DTP*DAP*DCP*DTP*DGP*DTP*DGP*DGP*DGP*DAP*DAP*DAP*DGP*DA)-3') | CSL (Lag-1) bound to DNA with Lin-12 RAM peptide, C2221 | X-ray diffraction | 2.47 | 30 | 2008-04-01 | ||||
| 51 | 1DSZ|1|C+ 1DSZ|1|D | DNA (5'-D(*CP*AP*GP*GP*TP*CP*AP*AP*AP*GP*GP*TP*CP*AP*G)-3'), DNA (5'-D(*CP*TP*GP*AP*CP*CP*TP*TP*TP*GP*AP*CP*CP*TP*G)-3') | STRUCTURE OF THE RXR/RAR DNA-BINDING DOMAIN HETERODIMER IN COMPLEX WITH THE RETINOIC ACID RESPONSE ELEMENT DR1 | X-ray diffraction | 1.7 | 30 | 2000-07-10 | ||||
| 52 | 1N39|1|B+ 1N39|1|C | DNA complement strand, DNA inhibitor strand | Structural and biochemical exploration of a critical amino acid in human 8-oxoguanine glycosylase | X-ray diffraction | 2.2 | 30 | 2003-03-04 | ||||
| 53 | 1N3A|1|B+ 1N3A|1|C | DNA complement strand, DNA inhibitor strand | Structural and biochemical exploration of a critical amino acid in human 8-oxoguanine glycosylase | X-ray diffraction | 2.2 | 30 | 2003-03-04 | ||||
| 54 | 1OZJ|1|C+ 1OZJ|1|D | Smad binding element | Crystal structure of Smad3-MH1 bound to DNA at 2.4 A resolution | X-ray diffraction | 2.4 | 30 | 2004-03-23 | ||||
| 55 | 1B8I|1|C+ 1B8I|1|D | DNA (5'-D(*AP*CP*GP*TP*GP*AP*TP*TP*TP*AP*TP*GP*GP*CP*G)-3'), DNA (5'-D(*GP*TP*CP*GP*CP*CP*AP*TP*AP*AP*AP*TP*CP*AP*C)-3') | STRUCTURE OF THE HOMEOTIC UBX/EXD/DNA TERNARY COMPLEX | X-ray diffraction | 2.4 | 30 | 1999-04-12 | ||||
| 56 | 9ANT|1|C+ 9ANT|1|D | DNA (5'-D(*AP*GP*AP*AP*AP*GP*CP*CP*AP*TP*TP*AP*GP*AP*G)-3'), DNA (5'-D(*TP*CP*TP*CP*TP*AP*AP*TP*GP*GP*CP*TP*TP*TP*C)-3') | ANTENNAPEDIA HOMEODOMAIN-DNA COMPLEX | X-ray diffraction | 2.4 | 30 | 1998-10-14 | ||||
| 57 | 9ANT|1|E+ 9ANT|1|F | DNA (5'-D(*AP*GP*AP*AP*AP*GP*CP*CP*AP*TP*TP*AP*GP*AP*G)-3'), DNA (5'-D(*TP*CP*TP*CP*TP*AP*AP*TP*GP*GP*CP*TP*TP*TP*C)-3') | ANTENNAPEDIA HOMEODOMAIN-DNA COMPLEX | X-ray diffraction | 2.4 | 30 | 1998-10-14 | ||||
| 58 | 1PDN|1|A+ 1PDN|1|B | DNA (5'-D(*AP*AP*CP*GP*TP*CP*AP*CP*GP*GP*TP*TP*GP*AP*C)-3'), DNA (5'-D(*TP*TP*GP*TP*CP*AP*AP*CP*CP*GP*TP*GP*AP*CP*G)-3') | CRYSTAL STRUCTURE OF A PAIRED DOMAIN-DNA COMPLEX AT 2.5 ANGSTROMS RESOLUTION REVEALS STRUCTURAL BASIS FOR PAX DEVELOPMENTAL MUTATIONS | X-ray diffraction | 2.5 | 30 | 1995-07-31 |
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 | 3L4J|1|C+ 3L4J|1|B | Topoisomerase II-DNA cleavage complex, apo | X-RAY DIFFRACTION | 2.48 | 26 | double helix,structure | enzyme,isomerase | |
| 2 | 3L4J|1|E+ 3L4J|1|D | Topoisomerase II-DNA cleavage complex, apo | X-RAY DIFFRACTION | 2.48 | 25 | double helix,structure | enzyme,isomerase | |
| 3 | 2NOF|1|B+ 2NOF|1|C | Structure of Q315F human 8-oxoguanine glycosylase proximal crosslink to 8-oxoguanine DNA | X-RAY DIFFRACTION | 2.35 | 16 | B-form double helix,double helix,structure | enzyme,hydrolase | |
| 4 | 2NOI|1|B+ 2NOI|1|C | Structure of G42A human 8-oxoguanine glycosylase crosslinked to undamaged G-containing DNA | X-RAY DIFFRACTION | 2.35 | 19 | B-form double helix,double helix,structure | enzyme,hydrolase | |
| 5 | 2XHI|1|B+ 2XHI|1|C | Separation-of-function mutants unravel the dual reaction mode of human 8-oxoguanine DNA glycosylase | X-RAY DIFFRACTION | 1.55 | 28 | B-form double helix,double helix,structure | enzyme,hydrolase | |
| 6 | 2NOH|1|B+ 2NOH|1|C | Structure of catalytically inactive Q315A human 8-oxoguanine glycosylase complexed to 8-oxoguanine DNA | X-RAY DIFFRACTION | 2.01 | 29 | B-form double helix,double helix,structure | enzyme,hydrolase | |
| 7 | 2NOZ|1|B+ 2NOZ|1|C | Structure of Q315F human 8-oxoguanine glycosylase distal crosslink to 8-oxoguanine DNA | X-RAY DIFFRACTION | 2.43 | 23 | B-form double helix,double helix,structure | enzyme,hydrolase | |
| 8 | 1M3H|1|B+ 1M3H|1|C+ 1M3H|1|D | Crystal Structure of Hogg1 D268E Mutant with Product Oligonucleotide | X-RAY DIFFRACTION | 2.05 | 30 | B-form double helix,double helix,structure | enzyme,hydrolase | |
| 9 | 1N39|1|B+ 1N39|1|C | Structural and biochemical exploration of a critical amino acid in human 8-oxoguanine glycosylase | X-RAY DIFFRACTION | 2.2 | 30 | B-form double helix,double helix,structure | enzyme,hydrolase | |
| 10 | 1N3A|1|B+ 1N3A|1|C | Structural and biochemical exploration of a critical amino acid in human 8-oxoguanine glycosylase | X-RAY DIFFRACTION | 2.2 | 30 | B-form double helix,double helix,structure | enzyme,hydrolase | |
| 11 | 1M3Q|1|B+ 1M3Q|1|C | Crystal Structure of hogg1 D268E Mutant with Base-Excised DNA and 8-aminoguanine | X-RAY DIFFRACTION | 1.9 | 30 | B-form double helix,double helix,structure | enzyme,hydrolase | |
| 12 | 1LWY|1|D+ 1LWY|1|E | hOgg1 Borohydride-Trapped Intermediate without 8-oxoguanine | X-RAY DIFFRACTION | 2.01 | 29 | B-form double helix,double helix,structure | enzyme,hydrolase | |
| 13 | 1HU0|1|D+ 1HU0|1|E | CRYSTAL STRUCTURE OF AN HOGG1-DNA BOROHYDRIDE TRAPPED INTERMEDIATE COMPLEX | X-RAY DIFFRACTION | 2.35 | 29 | B-form double helix,double helix,structure | enzyme,hydrolase | |
| 14 | 1LWW|1|D+ 1LWW|1|E | Borohydride-trapped hOgg1 Intermediate Structure Co-Crystallized with 8-bromoguanine | X-RAY DIFFRACTION | 2.1 | 29 | B-form double helix,double helix,structure | enzyme,hydrolase | |
| 15 | 1LWV|1|D+ 1LWV|1|E | Borohydride-trapped hOgg1 Intermediate Structure Co-Crystallized with 8-aminoguanine | X-RAY DIFFRACTION | 2.3 | 29 | B-form double helix,double helix,structure | enzyme,hydrolase | |
| 16 | 2NOE|1|B+ 2NOE|1|C | Structure of catalytically inactive G42A human 8-oxoguanine glycosylase complexed to 8-oxoguanine DNA | X-RAY DIFFRACTION | 2.2 | 26 | double helix,structure | enzyme,hydrolase | |
| 17 | 1U4B|1|C+ 1U4B|1|B | Extension of an adenine-8oxoguanine mismatch | X-RAY DIFFRACTION | 1.6 | 23 | enzyme,polymerase,transferase | ||
| 18 | 1NKB|1|C+ 1NKB|1|B | A BACILLUS DNA POLYMERASE I PRODUCT COMPLEX BOUND TO A GUANINE-THYMINE MISMATCH AFTER THREE ROUNDS OF PRIMER EXTENSION, FOLLOWING INCORPORATION OF DCTP, DGTP, AND DTTP. | X-RAY DIFFRACTION | 2 | 27 | B-form double helix,double helix,feature,mispair,structure | enzyme,polymerase,transferase | |
| 19 | 1XC9|1|C+ 1XC9|1|B | Structure of a high-fidelity polymerase bound to a benzo[a]pyrene adduct that blocks replication | X-RAY DIFFRACTION | 1.9 | 22 | B-form double helix,double helix,structure | enzyme,polymerase,transferase | |
| 20 | 2IMW|1|T+ 2IMW|1|S | Mechanism of Template-Independent Nucleotide Incorporation Catalyzed by a Template-Dependent DNA Polymerase | X-RAY DIFFRACTION | 2.05 | 28 | B-form double helix,double helix,structure | enzyme,polymerase,transferase | |
| 21 | 1U47|1|C+ 1U47|1|B | cytosine-8-Oxoguanine base pair at the polymerase active site | X-RAY DIFFRACTION | 2 | 22 | B-form double helix,double helix,structure | enzyme,polymerase,transferase | |
| 22 | 1U48|1|C+ 1U48|1|B | Extension of a cytosine-8-oxoguanine base pair | X-RAY DIFFRACTION | 2.1 | 23 | B-form double helix,double helix,structure | enzyme,polymerase,transferase | |
| 23 | 1NJX|1|C+ 1NJX|1|B | THYMINE-GUANINE MISMATCH AT THE POLYMERASE ACTIVE SITE | X-RAY DIFFRACTION | 1.65 | 23 | B-form double helix,double helix,feature,mispair,structure | enzyme,polymerase,transferase | |
| 24 | 1NJW|1|C+ 1NJW|1|B | GUANINE-THYMINE MISMATCH AT THE POLYMERASE ACTIVE SITE | X-RAY DIFFRACTION | 1.9 | 23 | B-form double helix,double helix,feature,mispair,structure | enzyme,polymerase,transferase | |
| 25 | 2HHQ|1|C+ 2HHQ|1|B | O6-methyl-guanine:T pair in the polymerase-10 basepair position | X-RAY DIFFRACTION | 1.8 | 28 | B-form double helix,double helix,structure | enzyme,polymerase,transferase | |
| 26 | 3BRF|1|B+ 3BRF|1|C | CSL (Lag-1) bound to DNA with Lin-12 RAM peptide, C2221 | X-RAY DIFFRACTION | 2.47 | 30 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),P53 like,cell signaling,immunoglobulin (Ig) fold,regulatory,transcription | |
| 27 | 3BRD|1|B+ 3BRD|1|C | CSL (Lag-1) bound to DNA with Lin-12 RAM peptide, P212121 | X-RAY DIFFRACTION | 2.21 | 30 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),cell signaling,immunoglobulin (Ig) fold,regulatory,rel homology,transcription | |
| 28 | 1B8I|1|C+ 1B8I|1|D | STRUCTURE OF THE HOMEOTIC UBX/EXD/DNA TERNARY COMPLEX | X-RAY DIFFRACTION | 2.4 | 30 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),homeodomain,regulatory,transcription | |
| 29 | 1QPI|1|N | CRYSTAL STRUCTURE OF TETRACYCLINE REPRESSOR/OPERATOR COMPLEX | X-RAY DIFFRACTION | 2.5 | 0 | B-form double helix,double helix,feature,mispair,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),regulatory,tetR family,transcription | |
| 30 | 1QPI|1|M | CRYSTAL STRUCTURE OF TETRACYCLINE REPRESSOR/OPERATOR COMPLEX | X-RAY DIFFRACTION | 2.5 | 0 | B-form double helix,double helix,feature,mispair,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),regulatory,tetR family,transcription | |
| 31 | 1PDN|1|A+ 1PDN|1|B | CRYSTAL STRUCTURE OF A PAIRED DOMAIN-DNA COMPLEX AT 2.5 ANGSTROMS RESOLUTION REVEALS STRUCTURAL BASIS FOR PAX DEVELOPMENTAL MUTATIONS | X-RAY DIFFRACTION | 2.5 | 30 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),homeodomain,regulatory,transcription | |
| 32 | 9ANT|1|E+ 9ANT|1|F | ANTENNAPEDIA HOMEODOMAIN-DNA COMPLEX | X-RAY DIFFRACTION | 2.4 | 30 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),homeodomain,regulatory,transcription | |
| 33 | 9ANT|1|C+ 9ANT|1|D | ANTENNAPEDIA HOMEODOMAIN-DNA COMPLEX | X-RAY DIFFRACTION | 2.4 | 30 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),homeodomain,regulatory,transcription | |
| 34 | 2H1K|1|C+ 2H1K|1|D | Crystal structure of the Pdx1 homeodomain in complex with DNA | X-RAY DIFFRACTION | 2.42 | 30 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),homeodomain,regulatory,transcription | |
| 35 | 1RH6|1|C+ 1RH6|1|D | Bacteriophage Lambda Excisionase (Xis)-DNA Complex | X-RAY DIFFRACTION | 1.7 | 28 | B-form double helix,double helix,structure | enzyme,recombinase | |
| 36 | 2VS8|1|D+ 2VS8|1|B+ 2VS8|1|C+ 2VS8|1|E | The crystal structure of I-DmoI in complex with DNA and Mn | X-RAY DIFFRACTION | 2.1 | 50 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease | |
| 37 | 2VS8|1|N+ 2VS8|1|L+ 2VS8|1|M+ 2VS8|1|O | The crystal structure of I-DmoI in complex with DNA and Mn | X-RAY DIFFRACTION | 2.1 | 50 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease | |
| 38 | 2VS8|1|I+ 2VS8|1|H | The crystal structure of I-DmoI in complex with DNA and Mn | X-RAY DIFFRACTION | 2.1 | 0 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease | |
| 39 | 1K79|1|B+ 1K79|1|C | Ets-1(331-440)+GGAA duplex | X-RAY DIFFRACTION | 2.4 | 30 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),regulatory,transcription,winged helix/forkhead | |
| 40 | 1NK9|1|C+ 1NK9|1|B | A BACILLUS DNA POLYMERASE I PRODUCT COMPLEX BOUND TO A GUANINE-THYMINE MISMATCH AFTER TWO ROUNDS OF PRIMER EXTENSION, FOLLOWING INCORPORATION OF DCTP AND DGTP. | X-RAY DIFFRACTION | 1.9 | 24 | double helix,feature,mispair,structure | enzyme,polymerase,transferase | |
| 41 | 1K79|1|E+ 1K79|1|F | Ets-1(331-440)+GGAA duplex | X-RAY DIFFRACTION | 2.4 | 30 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),regulatory,transcription,winged helix/forkhead | |
| 42 | 3FDQ|1|C+ 3FDQ|1|D | Recognition of AT-rich DNA binding sites by the MogR Repressor | X-RAY DIFFRACTION | 1.75 | 30 | B-form double helix,double helix,structure | regulatory,transcription | |
| 43 | 2CGP|1|C+ 2CGP|1|B | CATABOLITE GENE ACTIVATOR PROTEIN/DNA COMPLEX, ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE | X-RAY DIFFRACTION | 2.2 | 26 | double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),regulatory,transcription,winged helix/forkhead | |
| 44 | 2H1K|1|E+ 2H1K|1|F | Crystal structure of the Pdx1 homeodomain in complex with DNA | X-RAY DIFFRACTION | 2.42 | 30 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),homeodomain,regulatory,transcription | |
| 45 | 1NK8|1|C+ 1NK8|1|B | A BACILLUS DNA POLYMERASE I PRODUCT COMPLEX BOUND TO A GUANINE-THYMINE MISMATCH AFTER A SINGLE ROUND OF PRIMER EXTENSION, FOLLOWING INCORPORATION OF DCTP. | X-RAY DIFFRACTION | 1.9 | 23 | B-form double helix,double helix,feature,mispair,structure | enzyme,polymerase,transferase | |
| 46 | 1NK0|1|C+ 1NK0|1|B | ADENINE-GUANINE MISMATCH AT THE POLYMERASE ACTIVE SITE | X-RAY DIFFRACTION | 1.7 | 23 | B-form double helix,double helix,feature,mispair,structure | enzyme,polymerase,transferase | |
| 47 | 1NK6|1|C+ 1NK6|1|B | CYTOSINE-CYTOSINE MISMATCH AT THE POLYMERASE ACTIVE SITE | X-RAY DIFFRACTION | 2.1 | 18 | B-form double helix,double helix,structure | enzyme,polymerase,transferase | |
| 48 | 3MFI|1|T+ 3MFI|1|P | DNA Polymerase Eta in Complex With a cis-syn Thymidine Dimer | X-RAY DIFFRACTION | 1.76 | 24 | B-form double helix,double helix,structure | enzyme,polymerase,transferase | |
| 49 | 1NK7|1|C+ 1NK7|1|B | GUANINE-ADENINE MISMATCH AT THE POLYMERASE ACTIVE SITE | X-RAY DIFFRACTION | 1.9 | 20 | B-form double helix,double helix,structure | enzyme,polymerase,transferase | |
| 50 | 1U45|1|C+ 1U45|1|B | 8oxoguanine at the pre-insertion site of the polymerase active site | X-RAY DIFFRACTION | 2.01 | 20 | B-form double helix,double helix,structure | enzyme,polymerase,transferase | |
| 51 | 1U49|1|C+ 1U49|1|B | Adenine-8oxoguanine mismatch at the polymerase active site | X-RAY DIFFRACTION | 2.15 | 22 | enzyme,polymerase,transferase | ||
| 52 | 1SKN|1|A+ 1SKN|1|B | THE BINDING DOMAIN OF SKN-1 IN COMPLEX WITH DNA: A NEW DNA-BINDING MOTIF | X-RAY DIFFRACTION | 2.5 | 30 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),basic transcription factor,leucine zipper (bZIP),regulatory,transcription | |
| 53 | 1NKC|1|B+ 1NKC|1|C | A BACILLUS DNA POLYMERASE I PRODUCT COMPLEX BOUND TO A GUANINE-THYMINE MISMATCH AFTER FIVE ROUNDS OF PRIMER EXTENSION, FOLLOWING INCORPORATION OF DCTP, DGTP, DTTP, AND DATP. | X-RAY DIFFRACTION | 1.8 | 30 | B-form double helix,double helix,feature,mispair,structure | enzyme,polymerase,transferase | |
| 54 | 1OZJ|1|C+ 1OZJ|1|D | Crystal structure of Smad3-MH1 bound to DNA at 2.4 A resolution | X-RAY DIFFRACTION | 2.4 | 30 | B-form double helix,double helix,structure | β-sheet,DNA-binding transcription factor (TF),SMAD-like,regulatory,transcription | |
| 55 | 1DSZ|1|C+ 1DSZ|1|D | STRUCTURE OF THE RXR/RAR DNA-BINDING DOMAIN HETERODIMER IN COMPLEX WITH THE RETINOIC ACID RESPONSE ELEMENT DR1 | X-RAY DIFFRACTION | 1.7 | 30 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),Zinc-coordinating,nuclear receptor ZnC4,regulatory,transcription | |
| 56 | 3BRG|1|A+ 3BRG|1|B | CSL (RBP-Jk) bound to DNA | X-RAY DIFFRACTION | 2.2 | 30 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),immunoglobulin (Ig) fold,regulatory,rel homology,transcription | |
| 57 | 3IAG|1|A+ 3IAG|1|B | CSL (RBP-Jk) bound to HES-1 nonconsensus site | X-RAY DIFFRACTION | 2 | 30 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),immunoglobulin (Ig) fold,regulatory,rel homology,transcription | |
| 58 | 2RDJ|1|F+ 2RDJ|1|E | Snapshots of a Y-family DNA polymerase in replication: Dpo4 in apo and binary/ternary complex forms | X-RAY DIFFRACTION | 2.2 | 29 | B-form double helix,double helix,structure | enzyme,polymerase,transferase |
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.
Coloring options: