Equivalence class DNA_4.0_53550.1 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 | 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 | ||||
| 4 | 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 | ||||
| 5 | 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 | ||||
| 6 | 1TEZ|1|M | 5'-D(*TP*CP*GP*C)-3' | COMPLEX BETWEEN DNA AND THE DNA PHOTOLYASE FROM ANACYSTIS NIDULANS | X-ray diffraction | 1.8 | 2004-12-14 | ||||
| 7 | 1TEZ|1|O | 5'-D(*TP*CP*GP*C)-3' | COMPLEX BETWEEN DNA AND THE DNA PHOTOLYASE FROM ANACYSTIS NIDULANS | X-ray diffraction | 1.8 | 2004-12-14 | ||||
| 8 | 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 | ||||
| 9 | 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 | ||||
| 10 | 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 | ||||
| 11 | 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 | ||||
| 12 | 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 | ||||
| 13 | 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 | ||||
| 14 | 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 | ||||
| 15 | 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 | ||||
| 16 | 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 | ||||
| 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|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 | ||||
| 19 | 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 | ||||
| 20 | 2OA8|1|C | 5'-D(*GP*AP*CP*G)-3' | Crystal Structure of mTREX1 with ssDNA | X-ray diffraction | 2.1 | 2007-02-20 | ||||
| 21 | 2OA8|1|D | 5'-D(*GP*AP*CP*G)-3' | Crystal Structure of mTREX1 with ssDNA | X-ray diffraction | 2.1 | 2007-02-20 | ||||
| 22 | 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 | ||||
| 23 | 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 | ||||
| 24 | 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 | ||||
| 25 | 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 | ||||
| 26 | 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 | ||||
| 27 | 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 | ||||
| 28 | 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 | ||||
| 29 | 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 | ||||
| 30 | 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 | ||||
| 31 | 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 | ||||
| 32 | 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 | ||||
| 33 | 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 | ||||
| 34 | 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 | ||||
| 35 | 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 |
Release history
Parents
| This class | Parent classes | Release id | Intersection | Added to this class | Only in parent |
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Children
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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 | 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 | |
| 2 | 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 | |
| 3 | 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 | |
| 4 | 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 | |
| 5 | 1KDH|1|D | Binary Complex of Murine Terminal Deoxynucleotidyl Transferase with a Primer Single Stranded DNA | X-RAY DIFFRACTION | 3 | 4 | enzyme,polymerase,transferase | |
| 6 | 1RBJ|1|B | RIBONUCLEASE B COMPLEX WITH D(TETRA-(DEOXY-ADENYLATE)) | X-RAY DIFFRACTION | 2.7 | 4 | enzyme,hydrolase,nuclease | |
| 7 | 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 | |
| 8 | 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 | |
| 9 | 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 | |
| 10 | 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 | |
| 11 | 1RTA|1|C | CRYSTAL STRUCTURE DISPOSITION OF THYMIDYLIC ACID TETRAMER IN COMPLEX WITH RIBONUCLEASE A | X-RAY DIFFRACTION | 2.5 | 4 | enzyme,hydrolase,nuclease | |
| 12 | 1KEG|1|A | Antibody 64M-2 Fab complexed with dTT(6-4)TT | X-RAY DIFFRACTION | 2.4 | 4 | antibody,immune system,regulatory | |
| 13 | 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 | |
| 14 | 2OA8|1|D | Crystal Structure of mTREX1 with ssDNA | X-RAY DIFFRACTION | 2.1 | 4 | enzyme,hydrolase,nuclease | |
| 15 | 2OA8|1|C | Crystal Structure of mTREX1 with ssDNA | X-RAY DIFFRACTION | 2.1 | 4 | enzyme,hydrolase,nuclease | |
| 16 | 1DE9|1|X | HUMAN APE1 ENDONUCLEASE WITH BOUND ABASIC DNA AND MN2+ ION | X-RAY DIFFRACTION | 3 | 4 | enzyme,hydrolase,lyase,nuclease | |
| 17 | 1DE9|1|U | HUMAN APE1 ENDONUCLEASE WITH BOUND ABASIC DNA AND MN2+ ION | X-RAY DIFFRACTION | 3 | 4 | enzyme,hydrolase,lyase,nuclease | |
| 18 | 1TEZ|1|M | COMPLEX BETWEEN DNA AND THE DNA PHOTOLYASE FROM ANACYSTIS NIDULANS | X-RAY DIFFRACTION | 1.8 | 4 | enzyme,lyase | |
| 19 | 1TEZ|1|O | COMPLEX BETWEEN DNA AND THE DNA PHOTOLYASE FROM ANACYSTIS NIDULANS | X-RAY DIFFRACTION | 1.8 | 4 | enzyme,lyase | |
| 20 | 3G2C|1|I | Mth0212 in complex with a short ssDNA (CGTA) | X-RAY DIFFRACTION | 2.3 | 4 | enzyme,hydrolase,nuclease | |
| 21 | 3GDD|1|B | An inverted anthraquinone-DNA crystal structure | X-RAY DIFFRACTION | 2.8 | 4 | NAKB_NA_annotation | NAKB_protein_annotation |
| 22 | 3GDD|1|A | An inverted anthraquinone-DNA crystal structure | X-RAY DIFFRACTION | 2.8 | 4 | NAKB_NA_annotation | NAKB_protein_annotation |
| 23 | 1RB8|1|X | The phiX174 DNA binding protein J in two different capsid environments. | X-RAY DIFFRACTION | 3.5 | 4 | structural,virus | |
| 24 | 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 | |
| 25 | 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 | |
| 26 | 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 | |
| 27 | 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 | |
| 28 | 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 | |
| 29 | 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 | |
| 30 | 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 | |
| 31 | 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 | |
| 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 | 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 | |
| 34 | 2I5S|1|A | Crystal structure of onconase with bound nucleic acid | X-RAY DIFFRACTION | 1.9 | 4 | enzyme,hydrolase,nuclease | |
| 35 | 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 |
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