Equivalence class DNA_4.0_10507.1 Current
| # | IFE | Standardized name | Molecule | Organism | Source | Rfam | Title | Method | Res. Å | Date |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 1RFF|1|D (rep) | 5'-D(*AP*GP*TP*T)-3' | Crystal structure of human Tyrosyl-DNA Phosphodiesterase complexed with vanadate, octapeptide KLNYYDPR, and tetranucleotide AGTT. | X-ray diffraction | 1.7 | 2004-03-02 | ||||
| 2 | 1RFF|1|F | 5'-D(*AP*GP*TP*T)-3' | Crystal structure of human Tyrosyl-DNA Phosphodiesterase complexed with vanadate, octapeptide KLNYYDPR, and tetranucleotide AGTT. | X-ray diffraction | 1.7 | 2004-03-02 | ||||
| 3 | 3OR3|1|E | 5'-D(P*GP*AP*AP*C)-3' | Restriction endonuclease HPY188I in complex with product DNA | X-ray diffraction | 1.95 | 2010-10-20 | ||||
| 4 | 1KEG|1|A | 5'-D(*TP*(64T)P*TP*T)-3' | Antibody 64M-2 Fab complexed with dTT(6-4)TT | X-ray diffraction | 2.4 | 2002-11-15 | ||||
| 5 | 1M07|1|C | 5'-D(*AP*CP*GP*A)-3' | RESIDUES INVOLVED IN THE CATALYSIS AND BASE SPECIFICITY OF CYTOTOXIC RIBONUCLEASE FROM BULLFROG (RANA CATESBEIANA) | X-ray diffraction | 1.8 | 2003-01-21 | ||||
| 6 | 1M07|1|D | 5'-D(*AP*CP*GP*A)-3' | RESIDUES INVOLVED IN THE CATALYSIS AND BASE SPECIFICITY OF CYTOTOXIC RIBONUCLEASE FROM BULLFROG (RANA CATESBEIANA) | X-ray diffraction | 1.8 | 2003-01-21 | ||||
| 7 | 1TEZ|1|M | 5'-D(*TP*CP*GP*C)-3' | synthetic construct | COMPLEX BETWEEN DNA AND THE DNA PHOTOLYASE FROM ANACYSTIS NIDULANS | X-ray diffraction | 1.8 | 2004-12-14 | |||
| 8 | 1TEZ|1|O | 5'-D(*TP*CP*GP*C)-3' | synthetic construct | COMPLEX BETWEEN DNA AND THE DNA PHOTOLYASE FROM ANACYSTIS NIDULANS | X-ray diffraction | 1.8 | 2004-12-14 | |||
| 9 | 1RGT|1|D | 5'-D(*AP*GP*TP*C)-3' | Crystal structure of human Tyrosyl-DNA Phosphodiesterase complexed with vanadate, octopamine, and tetranucleotide AGTC | X-ray diffraction | 2 | 2004-03-02 | ||||
| 10 | 1RGT|1|F | 5'-D(*AP*GP*TP*C)-3' | Crystal structure of human Tyrosyl-DNA Phosphodiesterase complexed with vanadate, octopamine, and tetranucleotide AGTC | X-ray diffraction | 2 | 2004-03-02 | ||||
| 11 | 1RFI|1|D | 5'-D(*AP*GP*TP*C)-3' | Crystal structure of human Tyrosyl-DNA Phosphodiesterase complexed with vanadate, pentapeptide KLNYK, and tetranucleotide AGTC | X-ray diffraction | 2.2 | 2004-03-02 | ||||
| 12 | 1RFI|1|F | 5'-D(*AP*GP*TP*C)-3' | Crystal structure of human Tyrosyl-DNA Phosphodiesterase complexed with vanadate, pentapeptide KLNYK, and tetranucleotide AGTC | X-ray diffraction | 2.2 | 2004-03-02 | ||||
| 13 | 1RGU|1|D | 5'-D(*AP*GP*TP*G)-3' | The crystal structure of human Tyrosyl-DNA Phosphodiesterase complexed with vanadate, octopamine, and tetranucleotide AGTG | X-ray diffraction | 2.22 | 2004-03-02 | ||||
| 14 | 1RGU|1|F | 5'-D(*AP*GP*TP*G)-3' | The crystal structure of human Tyrosyl-DNA Phosphodiesterase complexed with vanadate, octopamine, and tetranucleotide AGTG | X-ray diffraction | 2.22 | 2004-03-02 | ||||
| 15 | 2I5S|1|A | 5'-D(*A*(DU)P*GP*A)-3' | Crystal structure of onconase with bound nucleic acid | X-ray diffraction | 1.9 | 2006-09-05 | ||||
| 16 | 1RG2|1|D | 5'-D(*AP*GP*TP*A)-3' | Crystal structure of human Tyrosyl-DNA Phosphodiesterase complexed with vanadate, octopamine, and tetranucleotide AGTA | X-ray diffraction | 2.1 | 2004-03-02 | ||||
| 17 | 1RG2|1|F | 5'-D(*AP*GP*TP*A)-3' | Crystal structure of human Tyrosyl-DNA Phosphodiesterase complexed with vanadate, octopamine, and tetranucleotide AGTA | X-ray diffraction | 2.1 | 2004-03-02 | ||||
| 18 | 1RG1|1|D | 5'-D(*AP*GP*TP*T)-3' | Crystal structure of human Tyrosyl-DNA Phosphodiesterase complexed with vanadate, octopamine, and tetranucleotide AGTT | X-ray diffraction | 2.1 | 2004-03-02 | ||||
| 19 | 1RG1|1|F | 5'-D(*AP*GP*TP*T)-3' | Crystal structure of human Tyrosyl-DNA Phosphodiesterase complexed with vanadate, octopamine, and tetranucleotide AGTT | X-ray diffraction | 2.1 | 2004-03-02 | ||||
| 20 | 3KHC|1|D | DNA (5'-D(P*GP*CP*AP*T)-3') | Crystal Structure of Escherichia coli AlkB in complex with ssDNA containing a 1-methylguanine lesion | X-ray diffraction | 2.2 | 2010-01-12 | ||||
| 21 | 1OJ8|1|B | 5'-D(*AP*CP*GP*AP)-3' | Novel and retro Binding Modes in Cytotoxic Ribonucleases from Rana catesbeiana of Two Crystal Structures Complexed with d(ApCpGpA) and (2',5'CpG) | X-ray diffraction | 1.7 | 2004-07-15 | ||||
| 22 | 2OA8|1|C | 5'-D(*GP*AP*CP*G)-3' | Crystal Structure of mTREX1 with ssDNA | X-ray diffraction | 2.1 | 2007-02-20 | ||||
| 23 | 2OA8|1|D | 5'-D(*GP*AP*CP*G)-3' | Crystal Structure of mTREX1 with ssDNA | X-ray diffraction | 2.1 | 2007-02-20 | ||||
| 24 | 3NGO|1|B | 5'-D(*AP*AP*AP*A)-3' | Crystal structure of the human CNOT6L nuclease domain in complex with poly(A) DNA | X-ray diffraction | 2.2 | 2010-07-28 | ||||
| 25 | 3G2C|1|I | 5'-D(P*CP*GP*TP*A)-3' | Mth0212 in complex with a short ssDNA (CGTA) | X-ray diffraction | 2.3 | 2010-03-09 | ||||
| 26 | 1FYK|1|C | HSE DNA-PHOSPHATE BACKBONE | SERENDIPITOUS CRYSTAL STRUCTURE CONTAINING THE HEAT SHOCK TRANSCRIPTION FACTOR'S DNA BINDING DOMAIN AND COGNATE DNA THAT IS TRANSLATIONALLY DISORDERED | X-ray diffraction | 2.5 | 2001-09-28 | ||||
| 27 | 3GDD|1|A | 5'-D(*(BRU)P*AP*GP*G)-3' | An inverted anthraquinone-DNA crystal structure | X-ray diffraction | 2.8 | 2010-03-09 | ||||
| 28 | 3GDD|1|B | 5'-D(*(BRU)P*AP*GP*G)-3' | An inverted anthraquinone-DNA crystal structure | X-ray diffraction | 2.8 | 2010-03-09 | ||||
| 29 | 1RB8|1|X | DNA (5'-D(P*CP*AP*AP*A)-3') | The phiX174 DNA binding protein J in two different capsid environments. | X-ray diffraction | 3.5 | 2004-04-13 | ||||
| 30 | 1KDH|1|D | 5'-D(P*(BRU)P*(BRU)P*(BRU)P*(BRU))-3' | Binary Complex of Murine Terminal Deoxynucleotidyl Transferase with a Primer Single Stranded DNA | X-ray diffraction | 3 | 2002-05-13 | ||||
| 31 | 1DE9|1|U | 5'-d(*CP*TP*AP*C)-3' | HUMAN APE1 ENDONUCLEASE WITH BOUND ABASIC DNA AND MN2+ ION | X-ray diffraction | 3 | 2000-02-02 | ||||
| 32 | 1DE9|1|X | 5'-d(*CP*TP*AP*C)-3' | HUMAN APE1 ENDONUCLEASE WITH BOUND ABASIC DNA AND MN2+ ION | X-ray diffraction | 3 | 2000-02-02 | ||||
| 33 | 1ZNA|1|A+ 1ZNA|1|B | DNA (5'-D(*CP*GP*CP*G)-3') | CONFORMATION AND DYNAMICS IN A Z-DNA TETRAMER | X-ray diffraction | 1.5 | 1981-03-18 | ||||
| 34 | 1D53|1|C+ 1D53|1|D | DNA (5'-D(*CP*GP*CP*G)-3') | CRYSTAL STRUCTURE AT 1.5 ANGSTROMS RESOLUTION OF D(CGCICICG), AN OCTANUCLEOTIDE CONTAINING INOSINE, AND ITS COMPARISON WITH D(CGCG) AND D(CGCGCG) STRUCTURES | X-ray diffraction | 1.5 | 1993-04-13 | ||||
| 35 | 1FIU|1|G | DNA (5'-D(*TP*GP*CP*G)-3') | TETRAMERIC RESTRICTION ENDONUCLEASE NGOMIV IN COMPLEX WITH CLEAVED DNA | X-ray diffraction | 1.6 | 2001-02-07 | ||||
| 36 | 3BAM|1|D | DNA (5'-D(*TP*AP*TP*G)-3') | RESTRICTION ENDONUCLEASE BAMHI COMPLEX WITH DNA AND MANGANESE IONS (POST-REACTIVE COMPLEX) | X-ray diffraction | 1.8 | 1999-01-13 | ||||
| 37 | 1ANA|1|A | DNA (5'-D(*(C38)P*CP*GP*G)-3') | HELIX GEOMETRY AND HYDRATION IN AN A-DNA TETRAMER. IC-C-G-G | X-ray diffraction | 2 | 1982-07-29 | ||||
| 38 | 1ANA|1|B | DNA (5'-D(*(C38)P*CP*GP*G)-3') | HELIX GEOMETRY AND HYDRATION IN AN A-DNA TETRAMER. IC-C-G-G | X-ray diffraction | 2 | 1982-07-29 | ||||
| 39 | 1RCN|1|D | DNA (5'-D(*AP*TP*AP*A)-3') | CRYSTAL STRUCTURE OF THE RIBONUCLEASE A D(APTPAPAPG) COMPLEX : DIRECT EVIDENCE FOR EXTENDED SUBSTRATE RECOGNITION | X-ray diffraction | 2.32 | 1994-09-30 | ||||
| 40 | 1RTA|1|C | DNA (5'-D(*TP*TP*TP*T)-3') | CRYSTAL STRUCTURE DISPOSITION OF THYMIDYLIC ACID TETRAMER IN COMPLEX WITH RIBONUCLEASE A | X-ray diffraction | 2.5 | 1993-10-31 | ||||
| 41 | 1RBJ|1|B | DNA (5'-D(*AP*AP*AP*A)-3') | RIBONUCLEASE B COMPLEX WITH D(TETRA-(DEOXY-ADENYLATE)) | X-ray diffraction | 2.7 | 1995-12-07 | ||||
| 42 | 1MVM|1|C | DNA (5'-D(*CP*AP*AP*A)-3') | MVM(STRAIN I), COMPLEX(VIRAL COAT/DNA), VP2, PH=7.5, T=4 DEGREES C | X-ray diffraction | 3.5 | 1998-02-25 |
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 | Length | NAKB NA annotation | NAKB protein annotation |
|---|---|---|---|---|---|---|---|---|
| 1 | 3NGO|1|B | Crystal structure of the human CNOT6L nuclease domain in complex with poly(A) DNA | X-RAY DIFFRACTION | 2.2 | 4 | enzyme,hydrolase,nuclease | ||
| 2 | 1RFI|1|F | Crystal structure of human Tyrosyl-DNA Phosphodiesterase complexed with vanadate, pentapeptide KLNYK, and tetranucleotide AGTC | X-RAY DIFFRACTION | 2.2 | 4 | enzyme,hydrolase,nuclease | ||
| 3 | 3GDD|1|B | An inverted anthraquinone-DNA crystal structure | X-RAY DIFFRACTION | 2.8 | 4 | NAKB_NA_annotation | NAKB_protein_annotation | |
| 4 | 3GDD|1|A | An inverted anthraquinone-DNA crystal structure | X-RAY DIFFRACTION | 2.8 | 4 | NAKB_NA_annotation | NAKB_protein_annotation | |
| 5 | 3G2C|1|I | Mth0212 in complex with a short ssDNA (CGTA) | X-RAY DIFFRACTION | 2.3 | 4 | enzyme,hydrolase,nuclease | ||
| 6 | 1MVM|1|C | MVM(STRAIN I), COMPLEX(VIRAL COAT/DNA), VP2, PH=7.5, T=4 DEGREES C | X-RAY DIFFRACTION | 3.5 | 4 | structural,virus | ||
| 7 | 1KDH|1|D | Binary Complex of Murine Terminal Deoxynucleotidyl Transferase with a Primer Single Stranded DNA | X-RAY DIFFRACTION | 3 | 4 | enzyme,polymerase,transferase | ||
| 8 | 3KHC|1|D | Crystal Structure of Escherichia coli AlkB in complex with ssDNA containing a 1-methylguanine lesion | X-RAY DIFFRACTION | 2.2 | 4 | enzyme,oxidoreductase | ||
| 9 | 1DE9|1|X | HUMAN APE1 ENDONUCLEASE WITH BOUND ABASIC DNA AND MN2+ ION | X-RAY DIFFRACTION | 3 | 4 | enzyme,hydrolase,lyase,nuclease | ||
| 10 | 1DE9|1|U | HUMAN APE1 ENDONUCLEASE WITH BOUND ABASIC DNA AND MN2+ ION | X-RAY DIFFRACTION | 3 | 4 | enzyme,hydrolase,lyase,nuclease | ||
| 11 | 1TEZ|1|M | COMPLEX BETWEEN DNA AND THE DNA PHOTOLYASE FROM ANACYSTIS NIDULANS | X-RAY DIFFRACTION | 1.8 | 4 | enzyme,lyase | ||
| 12 | 1TEZ|1|O | COMPLEX BETWEEN DNA AND THE DNA PHOTOLYASE FROM ANACYSTIS NIDULANS | X-RAY DIFFRACTION | 1.8 | 4 | enzyme,lyase | ||
| 13 | 1ANA|1|B | HELIX GEOMETRY AND HYDRATION IN AN A-DNA TETRAMER. IC-C-G-G | X-RAY DIFFRACTION | 2 | 4 | double helix,structure | ||
| 14 | 1ANA|1|A | HELIX GEOMETRY AND HYDRATION IN AN A-DNA TETRAMER. IC-C-G-G | X-RAY DIFFRACTION | 2 | 4 | double helix,structure | ||
| 15 | 3OR3|1|E | Restriction endonuclease HPY188I in complex with product DNA | X-RAY DIFFRACTION | 1.95 | 4 | double helix,structure | enzyme,hydrolase,nuclease | |
| 16 | 3BAM|1|D | RESTRICTION ENDONUCLEASE BAMHI COMPLEX WITH DNA AND MANGANESE IONS (POST-REACTIVE COMPLEX) | X-RAY DIFFRACTION | 1.8 | 4 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease | |
| 17 | 1FIU|1|G | TETRAMERIC RESTRICTION ENDONUCLEASE NGOMIV IN COMPLEX WITH CLEAVED DNA | X-RAY DIFFRACTION | 1.6 | 4 | enzyme,hydrolase,nuclease | ||
| 18 | 2OA8|1|D | Crystal Structure of mTREX1 with ssDNA | X-RAY DIFFRACTION | 2.1 | 4 | enzyme,hydrolase,nuclease | ||
| 19 | 2OA8|1|C | Crystal Structure of mTREX1 with ssDNA | X-RAY DIFFRACTION | 2.1 | 4 | enzyme,hydrolase,nuclease | ||
| 20 | 1D53|1|C+ 1D53|1|D | CRYSTAL STRUCTURE AT 1.5 ANGSTROMS RESOLUTION OF D(CGCICICG), AN OCTANUCLEOTIDE CONTAINING INOSINE, AND ITS COMPARISON WITH D(CGCG) AND D(CGCGCG) STRUCTURES | X-RAY DIFFRACTION | 1.5 | 4 | Z-form double helix,double helix,structure | ||
| 21 | 1ZNA|1|A+ 1ZNA|1|B | CONFORMATION AND DYNAMICS IN A Z-DNA TETRAMER | X-RAY DIFFRACTION | 1.5 | 4 | Z-form double helix,double helix,structure | ||
| 22 | 1OJ8|1|B | Novel and retro Binding Modes in Cytotoxic Ribonucleases from Rana catesbeiana of Two Crystal Structures Complexed with d(ApCpGpA) and (2',5'CpG) | X-RAY DIFFRACTION | 1.7 | 4 | enzyme,hydrolase,nuclease | ||
| 23 | 1M07|1|D | RESIDUES INVOLVED IN THE CATALYSIS AND BASE SPECIFICITY OF CYTOTOXIC RIBONUCLEASE FROM BULLFROG (RANA CATESBEIANA) | X-RAY DIFFRACTION | 1.8 | 4 | enzyme,hydrolase,nuclease | ||
| 24 | 1M07|1|C | RESIDUES INVOLVED IN THE CATALYSIS AND BASE SPECIFICITY OF CYTOTOXIC RIBONUCLEASE FROM BULLFROG (RANA CATESBEIANA) | X-RAY DIFFRACTION | 1.8 | 4 | enzyme,hydrolase,nuclease | ||
| 25 | 1RTA|1|C | CRYSTAL STRUCTURE DISPOSITION OF THYMIDYLIC ACID TETRAMER IN COMPLEX WITH RIBONUCLEASE A | X-RAY DIFFRACTION | 2.5 | 4 | enzyme,hydrolase,nuclease | ||
| 26 | 1KEG|1|A | Antibody 64M-2 Fab complexed with dTT(6-4)TT | X-RAY DIFFRACTION | 2.4 | 4 | antibody,immune system,regulatory | ||
| 27 | 1RCN|1|D | CRYSTAL STRUCTURE OF THE RIBONUCLEASE A D(APTPAPAPG) COMPLEX : DIRECT EVIDENCE FOR EXTENDED SUBSTRATE RECOGNITION | X-RAY DIFFRACTION | 2.32 | 4 | enzyme,hydrolase,nuclease | ||
| 28 | 1RBJ|1|B | RIBONUCLEASE B COMPLEX WITH D(TETRA-(DEOXY-ADENYLATE)) | X-RAY DIFFRACTION | 2.7 | 4 | enzyme,hydrolase,nuclease | ||
| 29 | 2I5S|1|A | Crystal structure of onconase with bound nucleic acid | X-RAY DIFFRACTION | 1.9 | 4 | enzyme,hydrolase,nuclease | ||
| 30 | 1RG2|1|F | Crystal structure of human Tyrosyl-DNA Phosphodiesterase complexed with vanadate, octopamine, and tetranucleotide AGTA | X-RAY DIFFRACTION | 2.1 | 4 | enzyme,hydrolase,nuclease | ||
| 31 | 1RFI|1|D | Crystal structure of human Tyrosyl-DNA Phosphodiesterase complexed with vanadate, pentapeptide KLNYK, and tetranucleotide AGTC | X-RAY DIFFRACTION | 2.2 | 4 | enzyme,hydrolase,nuclease | ||
| 32 | 1RGT|1|D | Crystal structure of human Tyrosyl-DNA Phosphodiesterase complexed with vanadate, octopamine, and tetranucleotide AGTC | X-RAY DIFFRACTION | 2 | 4 | enzyme,hydrolase,nuclease | ||
| 33 | 1RFF|1|F | Crystal structure of human Tyrosyl-DNA Phosphodiesterase complexed with vanadate, octapeptide KLNYYDPR, and tetranucleotide AGTT. | X-RAY DIFFRACTION | 1.7 | 4 | enzyme,hydrolase,nuclease | ||
| 34 | 1RGU|1|F | The crystal structure of human Tyrosyl-DNA Phosphodiesterase complexed with vanadate, octopamine, and tetranucleotide AGTG | X-RAY DIFFRACTION | 2.22 | 4 | enzyme,hydrolase,nuclease | ||
| 35 | 1RG2|1|D | Crystal structure of human Tyrosyl-DNA Phosphodiesterase complexed with vanadate, octopamine, and tetranucleotide AGTA | X-RAY DIFFRACTION | 2.1 | 4 | enzyme,hydrolase,nuclease | ||
| 36 | 1RB8|1|X | The phiX174 DNA binding protein J in two different capsid environments. | X-RAY DIFFRACTION | 3.5 | 4 | structural,virus | ||
| 37 | 1RG1|1|D | Crystal structure of human Tyrosyl-DNA Phosphodiesterase complexed with vanadate, octopamine, and tetranucleotide AGTT | X-RAY DIFFRACTION | 2.1 | 4 | enzyme,hydrolase,nuclease | ||
| 38 | 1RGU|1|D | The crystal structure of human Tyrosyl-DNA Phosphodiesterase complexed with vanadate, octopamine, and tetranucleotide AGTG | X-RAY DIFFRACTION | 2.22 | 4 | enzyme,hydrolase,nuclease | ||
| 39 | 1RFF|1|D | Crystal structure of human Tyrosyl-DNA Phosphodiesterase complexed with vanadate, octapeptide KLNYYDPR, and tetranucleotide AGTT. | X-RAY DIFFRACTION | 1.7 | 4 | enzyme,hydrolase,nuclease | ||
| 40 | 1RG1|1|F | Crystal structure of human Tyrosyl-DNA Phosphodiesterase complexed with vanadate, octopamine, and tetranucleotide AGTT | X-RAY DIFFRACTION | 2.1 | 4 | enzyme,hydrolase,nuclease | ||
| 41 | 1RGT|1|F | Crystal structure of human Tyrosyl-DNA Phosphodiesterase complexed with vanadate, octopamine, and tetranucleotide AGTC | X-RAY DIFFRACTION | 2 | 4 | enzyme,hydrolase,nuclease | ||
| 42 | 1FYK|1|C | SERENDIPITOUS CRYSTAL STRUCTURE CONTAINING THE HEAT SHOCK TRANSCRIPTION FACTOR'S DNA BINDING DOMAIN AND COGNATE DNA THAT IS TRANSLATIONALLY DISORDERED | X-RAY DIFFRACTION | 2.5 | 4 | DNA-binding transcription factor (TF),helix-turn-helix (HTH),regulatory,transcription,winged helix/forkhead |
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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