Equivalence class DNA_3.0_45760.1 Current
| # | IFE | Standardized name | Molecule | Organism | Source | Rfam | Title | Method | Res. Å | #NTs | Date |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 1ZS4|1|T+ 1ZS4|1|U (rep) | DNA - 27mer | Structure of bacteriophage lambda cII protein in complex with DNA | X-ray diffraction | 1.7 | 54 | 2005-08-23 | ||||
| 2 | 2XQC|1|E+ 2XQC|1|F | 5'-D(TP*TP*GP*AP*TP*GP)-3', DRA2 TRANSPOSASE LEFT END RECOGNITION SEQUENCE | Deinococcus radiodurans | DEINOCOCCUS RADIODURANS ISDRA2 TRANSPOSASE COMPLEXED WITH LEFT END RECOGNITION AND CLEAVAGE SITE AND ZN | X-ray diffraction | 1.9 | 33 | 2010-10-13 | |||
| 3 | 2XO6|1|E+ 2XO6|1|F | 5'-D(*TP*TP*GP*AP*TP*G)-3', DRA2 TRANSPOSASE LEFT END RECOGNITION SEQUENCE | synthetic construct | DEINOCOCCUS RADIODURANS ISDRA2 TRANSPOSASE Y132F MUTANT COMPLEXED WITH LEFT END RECOGNITION AND CLEAVAGE SITE | X-ray diffraction | 1.9 | 33 | 2010-10-13 | |||
| 4 | 2XO6|1|B+ 2XO6|1|C | 5'-D(*TP*TP*GP*AP*TP*G)-3', DRA2 TRANSPOSASE LEFT END RECOGNITION SEQUENCE | synthetic construct | DEINOCOCCUS RADIODURANS ISDRA2 TRANSPOSASE Y132F MUTANT COMPLEXED WITH LEFT END RECOGNITION AND CLEAVAGE SITE | X-ray diffraction | 1.9 | 33 | 2010-10-13 | |||
| 5 | 2XQC|1|B+ 2XQC|1|C | 5'-D(TP*TP*GP*AP*TP*GP)-3', DRA2 TRANSPOSASE LEFT END RECOGNITION SEQUENCE | Deinococcus radiodurans | DEINOCOCCUS RADIODURANS ISDRA2 TRANSPOSASE COMPLEXED WITH LEFT END RECOGNITION AND CLEAVAGE SITE AND ZN | X-ray diffraction | 1.9 | 33 | 2010-10-13 | |||
| 6 | 3GZ6|1|C+ 3GZ6|1|D | DNA (27-MER) | Crystal structure of Shewanella oneidensis NrtR complexed with a 27mer DNA | X-ray diffraction | 2.901 | 54 | 2009-06-09 | ||||
| 7 | 3IV5|1|C+ 3IV5|1|D | DNA (27-MER) | Crystal structure of Fis bound to 27 bp optimal binding sequence F1 | X-ray diffraction | 2.9 | 54 | 2010-04-28 | ||||
| 8 | 1K78|1|C+ 1K78|1|D | Pax5/Ets Binding Site on the mb-1 promoter | Pax5(1-149)+Ets-1(331-440)+DNA | X-ray diffraction | 2.25 | 54 | 2002-01-04 | ||||
| 9 | 3JRH|1|C+ 3JRH|1|D | DNA (27-MER) | Crystal structure of Fis bound to 27 bp non consensus sequence DNA F21 | X-ray diffraction | 2.88 | 54 | 2010-04-28 | ||||
| 10 | 1K78|1|G+ 1K78|1|H | Pax5/Ets Binding Site on the mb-1 promoter | Pax5(1-149)+Ets-1(331-440)+DNA | X-ray diffraction | 2.25 | 54 | 2002-01-04 | ||||
| 11 | 2XM3|1|K | DRA2 TRANSPOSASE BINDING ELEMENT | synthetic construct | Deinococcus radiodurans ISDra2 Transposase Left end DNA complex | X-ray diffraction | 2.3 | 27 | 2010-10-13 | |||
| 12 | 3JR9|1|C+ 3JR9|1|D | DNA (27-MER) | Crystal structure of Fis bound to 27 bp optimal binding sequence F2 | X-ray diffraction | 2.9 | 54 | 2010-04-28 | ||||
| 13 | 2XM3|1|G | DRA2 TRANSPOSASE BINDING ELEMENT | synthetic construct | Deinococcus radiodurans ISDra2 Transposase Left end DNA complex | X-ray diffraction | 2.3 | 27 | 2010-10-13 | |||
| 14 | 2XM3|1|I | DRA2 TRANSPOSASE BINDING ELEMENT | synthetic construct | Deinococcus radiodurans ISDra2 Transposase Left end DNA complex | X-ray diffraction | 2.3 | 27 | 2010-10-13 | |||
| 15 | 3KK1|1|T+ 3KK1|1|P | 5'-D(*A*TP*GP*GP*TP*GP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP*CP*TP*GP*TP*G)-3', 5'-D(*AP*CP*A*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*GP*CP*GP*CP*CP*(DOC))-3' | HIV-1 reverse transcriptase-DNA complex with nuceotide inhibitor GS-9148-diphosphate bound in nucleotide site | X-ray diffraction | 2.7 | 42 | 2010-03-23 | ||||
| 16 | 3KK2|1|T+ 3KK2|1|P | 5'-D(*A*TP*GP*GP*TP*GP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP*CP*TP*GP*TP*G)-3', 5'-D(*AP*CP*A*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*GP*CP*GP*CP*CP*(DOC))-3' | HIV-1 reverse transcriptase-DNA complex with dATP bound in the nucleotide binding site | X-ray diffraction | 2.9 | 42 | 2010-03-23 | ||||
| 17 | 2XM3|1|M | DRA2 TRANSPOSASE BINDING ELEMENT | synthetic construct | Deinococcus radiodurans ISDra2 Transposase Left end DNA complex | X-ray diffraction | 2.3 | 27 | 2010-10-13 | |||
| 18 | 2WWY|1|Q+ 2WWY|1|P | 5'-D(*DA DG DC DG DT DC DG DA DG DA DT DC DCP)-3', DNA OLIGO (27BP) | synthetic construct | Structure of human RECQ-like helicase in complex with a DNA substrate | X-ray diffraction | 2.9 | 33 | 2009-12-29 | |||
| 19 | 3KK3|1|T+ 3KK3|1|P | 5'-D(*AP*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*GP*CP*GP*CP*C*(URT))-3', 5'-D(*AP*TP*GP*GP*TP*TP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP*CP*TP*GP*TP*G)-3' | HIV-1 reverse transcriptase-DNA complex with GS-9148 terminated primer | X-ray diffraction | 2.9 | 41 | 2010-03-23 | ||||
| 20 | 3KLH|1|E+ 3KLH|1|F | DNA (5'-D(*AP*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*(MRG)P*CP*GP*CP*CP*(ATM))-3'), DNA (5'-D(*AP*T*GP*CP*TP*AP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP*CP*TP*GP*TP*G)-3') | Crystal structure of AZT-Resistant HIV-1 Reverse Transcriptase crosslinked to post-translocation AZTMP-Terminated DNA (COMPLEX P) | X-ray diffraction | 2.9 | 45 | 2010-09-22 | ||||
| 21 | 1N6Q|1|T+ 1N6Q|1|P | 5'-D(*A*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*(MRG)P*CP*GP*CP*CP*AP*(ATM))-3', 5'-D(*AP*T*GP*CP*AP*TP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP*CP*TP*GP*TP*G)-3' | HIV-1 Reverse Transcriptase Crosslinked to pre-translocation AZTMP-terminated DNA (complex N) | X-ray diffraction | 3 | 44 | 2003-01-14 | ||||
| 22 | 1T05|1|T+ 1T05|1|P | oligonucleotide primer, oligonucleotide template | HIV-1 reverse transcriptase crosslinked to template-primer with tenofovir-diphosphate bound as the incoming nucleotide substrate | X-ray diffraction | 3 | 44 | 2004-05-11 | ||||
| 23 | 3JSM|1|T+ 3JSM|1|P | DNA (5'-D(*A*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*(MRG)P*CP*GP*CP*CP*(DDG))-3'), DNA (5'-D(*A*TP*GP*GP*TP*CP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP*CP*TP*GP*TP*G)-3') | K65R mutant HIV-1 reverse transcriptase cross-linked to DS-DNA and complexed with tenofovir-diphosphate as the incoming nucleotide substrate | X-ray diffraction | 3 | 44 | 2009-09-29 | ||||
| 24 | 2XM3|1|Q | DRA2 TRANSPOSASE BINDING ELEMENT | synthetic construct | Deinococcus radiodurans ISDra2 Transposase Left end DNA complex | X-ray diffraction | 2.3 | 27 | 2010-10-13 | |||
| 25 | 2XM3|1|O | DRA2 TRANSPOSASE BINDING ELEMENT | synthetic construct | Deinococcus radiodurans ISDra2 Transposase Left end DNA complex | X-ray diffraction | 2.3 | 27 | 2010-10-13 | |||
| 26 | 2WWY|1|T+ 2WWY|1|S | 5'-D(*DA DG DC DG DT DC DG DA DG DA DT DC DCP)-3', DNA OLIGO (27BP) | synthetic construct | Structure of human RECQ-like helicase in complex with a DNA substrate | X-ray diffraction | 2.9 | 30 | 2009-12-29 | |||
| 27 | 3H25|1|C | SINGLE STRANDED INITIATOR DNA (SSIA) | Crystal structure of the catalytic domain of primase Repb' in complex with initiator DNA | X-ray diffraction | 2.7 | 27 | 2009-04-28 | ||||
| 28 | 2WWY|1|O | DNA OLIGO (27BP) | synthetic construct | Structure of human RECQ-like helicase in complex with a DNA substrate | X-ray diffraction | 2.9 | 5 | 2009-12-29 | |||
| 29 | 2WWY|1|R | DNA OLIGO (27BP) | synthetic construct | Structure of human RECQ-like helicase in complex with a DNA substrate | X-ray diffraction | 2.9 | 3 | 2009-12-29 | |||
| 30 | 1R0A|1|T+ 1R0A|1|P | 5'-D(*A*TP*GP*CP*AP*TP*CP*GP*GP*CP*GP*CP*TP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP*CP*GP*GP*T)-3', 5'-D(*C*CP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*AP*GP*CP*GP*CP*CP*GP*(2DA))-3' | Crystal structure of HIV-1 reverse transcriptase covalently tethered to DNA template-primer solved to 2.8 angstroms | X-ray diffraction | 2.8 | 44 | 2004-08-03 |
Release history
| Release | 0.6 |
|---|---|
| Date | 2011-03-05 |
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 |
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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 | 2WWY|1|R | Structure of human RECQ-like helicase in complex with a DNA substrate | X-RAY DIFFRACTION | 2.9 | 3 | enzyme,helicase,hydrolase | ||
| 2 | 2XO6|1|B+ 2XO6|1|C | DEINOCOCCUS RADIODURANS ISDRA2 TRANSPOSASE Y132F MUTANT COMPLEXED WITH LEFT END RECOGNITION AND CLEAVAGE SITE | X-RAY DIFFRACTION | 1.9 | 33 | enzyme,recombinase | ||
| 3 | 2XQC|1|B+ 2XQC|1|C | DEINOCOCCUS RADIODURANS ISDRA2 TRANSPOSASE COMPLEXED WITH LEFT END RECOGNITION AND CLEAVAGE SITE AND ZN | X-RAY DIFFRACTION | 1.9 | 33 | enzyme,recombinase | ||
| 4 | 2XM3|1|K | Deinococcus radiodurans ISDra2 Transposase Left end DNA complex | X-RAY DIFFRACTION | 2.3 | 27 | enzyme,recombinase | ||
| 5 | 2XM3|1|G | Deinococcus radiodurans ISDra2 Transposase Left end DNA complex | X-RAY DIFFRACTION | 2.3 | 27 | enzyme,recombinase | ||
| 6 | 2XM3|1|O | Deinococcus radiodurans ISDra2 Transposase Left end DNA complex | X-RAY DIFFRACTION | 2.3 | 27 | enzyme,recombinase | ||
| 7 | 2XM3|1|Q | Deinococcus radiodurans ISDra2 Transposase Left end DNA complex | X-RAY DIFFRACTION | 2.3 | 27 | enzyme,recombinase | ||
| 8 | 2XM3|1|I | Deinococcus radiodurans ISDra2 Transposase Left end DNA complex | X-RAY DIFFRACTION | 2.3 | 27 | enzyme,recombinase | ||
| 9 | 2XM3|1|M | Deinococcus radiodurans ISDra2 Transposase Left end DNA complex | X-RAY DIFFRACTION | 2.3 | 27 | enzyme,recombinase | ||
| 10 | 2XO6|1|E+ 2XO6|1|F | DEINOCOCCUS RADIODURANS ISDRA2 TRANSPOSASE Y132F MUTANT COMPLEXED WITH LEFT END RECOGNITION AND CLEAVAGE SITE | X-RAY DIFFRACTION | 1.9 | 33 | enzyme,recombinase | ||
| 11 | 2XQC|1|E+ 2XQC|1|F | DEINOCOCCUS RADIODURANS ISDRA2 TRANSPOSASE COMPLEXED WITH LEFT END RECOGNITION AND CLEAVAGE SITE AND ZN | X-RAY DIFFRACTION | 1.9 | 33 | enzyme,recombinase | ||
| 12 | 3H25|1|C | Crystal structure of the catalytic domain of primase Repb' in complex with initiator DNA | X-RAY DIFFRACTION | 2.7 | 27 | DNA replication/repair,regulatory | ||
| 13 | 2WWY|1|O | Structure of human RECQ-like helicase in complex with a DNA substrate | X-RAY DIFFRACTION | 2.9 | 5 | enzyme,helicase,hydrolase | ||
| 14 | 3KK1|1|T+ 3KK1|1|P | HIV-1 reverse transcriptase-DNA complex with nuceotide inhibitor GS-9148-diphosphate bound in nucleotide site | X-RAY DIFFRACTION | 2.7 | 42 | enzyme,polymerase,transferase | ||
| 15 | 3KK2|1|T+ 3KK2|1|P | HIV-1 reverse transcriptase-DNA complex with dATP bound in the nucleotide binding site | X-RAY DIFFRACTION | 2.9 | 42 | double helix,structure | enzyme,polymerase,transferase | |
| 16 | 3KK3|1|T+ 3KK3|1|P | HIV-1 reverse transcriptase-DNA complex with GS-9148 terminated primer | X-RAY DIFFRACTION | 2.9 | 41 | enzyme,polymerase,transferase | ||
| 17 | 1T05|1|T+ 1T05|1|P | HIV-1 reverse transcriptase crosslinked to template-primer with tenofovir-diphosphate bound as the incoming nucleotide substrate | X-RAY DIFFRACTION | 3 | 44 | double helix,structure | enzyme,polymerase,transferase | |
| 18 | 3JSM|1|T+ 3JSM|1|P | K65R mutant HIV-1 reverse transcriptase cross-linked to DS-DNA and complexed with tenofovir-diphosphate as the incoming nucleotide substrate | X-RAY DIFFRACTION | 3 | 44 | double helix,structure | enzyme,polymerase,transferase | |
| 19 | 1R0A|1|T+ 1R0A|1|P | Crystal structure of HIV-1 reverse transcriptase covalently tethered to DNA template-primer solved to 2.8 angstroms | X-RAY DIFFRACTION | 2.8 | 44 | double helix,structure | antibody,enzyme,immune system,polymerase,regulatory,transferase | |
| 20 | 1N6Q|1|T+ 1N6Q|1|P | HIV-1 Reverse Transcriptase Crosslinked to pre-translocation AZTMP-terminated DNA (complex N) | X-RAY DIFFRACTION | 3 | 44 | double helix,structure | antibody,enzyme,immune system,polymerase,regulatory,transferase | |
| 21 | 3KLH|1|E+ 3KLH|1|F | Crystal structure of AZT-Resistant HIV-1 Reverse Transcriptase crosslinked to post-translocation AZTMP-Terminated DNA (COMPLEX P) | X-RAY DIFFRACTION | 2.9 | 45 | double helix,structure | antibody,enzyme,immune system,polymerase,regulatory,transferase | |
| 22 | 3JR9|1|C+ 3JR9|1|D | Crystal structure of Fis bound to 27 bp optimal binding sequence F2 | X-RAY DIFFRACTION | 2.9 | 54 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),homeodomain,regulatory,transcription | |
| 23 | 3IV5|1|C+ 3IV5|1|D | Crystal structure of Fis bound to 27 bp optimal binding sequence F1 | X-RAY DIFFRACTION | 2.9 | 54 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),homeodomain,regulatory,transcription | |
| 24 | 3JRH|1|C+ 3JRH|1|D | Crystal structure of Fis bound to 27 bp non consensus sequence DNA F21 | X-RAY DIFFRACTION | 2.88 | 54 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),homeodomain,regulatory,transcription | |
| 25 | 3GZ6|1|C+ 3GZ6|1|D | Crystal structure of Shewanella oneidensis NrtR complexed with a 27mer DNA | X-RAY DIFFRACTION | 2.901 | 54 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),regulatory,transcription,winged helix/forkhead | |
| 26 | 1ZS4|1|T+ 1ZS4|1|U | Structure of bacteriophage lambda cII protein in complex with DNA | X-RAY DIFFRACTION | 1.7 | 54 | DNA-binding transcription factor (TF),helix-turn-helix (HTH),lambda repressor-like,regulatory,transcription | ||
| 27 | 1K78|1|G+ 1K78|1|H | Pax5(1-149)+Ets-1(331-440)+DNA | X-RAY DIFFRACTION | 2.25 | 54 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),homeodomain,regulatory,transcription,winged helix/forkhead | |
| 28 | 1K78|1|C+ 1K78|1|D | Pax5(1-149)+Ets-1(331-440)+DNA | X-RAY DIFFRACTION | 2.25 | 54 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),homeodomain,regulatory,transcription,winged helix/forkhead | |
| 29 | 2WWY|1|Q+ 2WWY|1|P | Structure of human RECQ-like helicase in complex with a DNA substrate | X-RAY DIFFRACTION | 2.9 | 33 | enzyme,helicase,hydrolase | ||
| 30 | 2WWY|1|T+ 2WWY|1|S | Structure of human RECQ-like helicase in complex with a DNA substrate | X-RAY DIFFRACTION | 2.9 | 30 | enzyme,helicase,hydrolase |
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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