9R83
Kod-h4 dna polymerase mutant in a ternary complex with hna:dna containing six hna nucleotides and a 2',3'-dideoxycytidine at the 3'-end of the dna primer complexed to a natural datp in the active site
PDB DOI: 10.2210/pdb9r83/pdb
Classification: TRANSFERASE Organism(s): Thermococcus Kodakarensis Kod1 , Synthetic Construct
Deposited: 2025-05-15 Deposition Author(s): Betz, K. , Gutfreund, C.
Experimental Data Snapshot
Method: X-RAY DIFFRACTION Resolution: 2.8 Å
Kod-h4 dna polymerase mutant in a ternary complex with hna:dna containing six hna nucleotides and a 2',3'-dideoxycytidine at the 3'-end of the dna primer complexed to a natural datp in the active site
Primary Citation of Related Structures: 9R83
| Nucleic Acids / Hybrid | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*CP*AP*C)-3') | f | 12 | NA | GACCACGGCCAC |
| DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*CP*AP*C)-3') | c | 12 | NA | GACCACGGCCAC |
| DNA (5'-D(P*(6HA)P*(6HC)P*(6HT)P*(6HG)P*(6HT)P*GP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3') | d | 16 | NA | AACTGTGGCCGTGGTC |
| DNA (5'-D(P*(6HA)P*(6HC)P*(6HT)P*(6HG)P*(6HT)P*GP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3') | e | 16 | NA | AACTGTGGCCGTGGTC |
| Proteins | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| DNA polymerase | A | 774 | Thermococcus Kodakarensis Kod1 , Synthetic Construct | MILDTDYITEDGKPVIRIFKKENGEFKIEYDRTFEPYFYALLKDDSAIEEVKKITAERHGTVVTVKRVEKVQKKFLGRPVEVWKLYFTHPQDQPAIRDKIREHPAVIDIYEYDTPFAKRYLIDKGLVPMEGDEELKMLAFAIATLYHEGEEFAEGPILMISYADEEGARVITWKNVDLPYVDVVSTEREMIKRFLRVVKEKDPDVLITYNGDNFDFAYLKKRCEKLGINFALGRDGSEPKIQRMGDRFAVEVKGRIHFDLYPVIRRTINLPTYTLEAVYEAVFGQPKEKVYAEEITTAWETGENLERVARYSMEDAKVTYELGKEFLPMEAQLSRLIGQSLWDVSRSSTGNLVEWFLLRKAYERNELAPNKPDEKELARRRQKYEGGYVKEPERGLWENIVYLDFRSLYPSIIITHNVSPDTLNREGCGEYDVAPQVGHRFCKDLPGFIPSLLGDLLEERQKIKKKMKATIDPIERKLLDYRQRLIKILANSVYGHMGFENARWYCKECAESVTAWGREYLTMTIKEIEEKYGFKVIYSDTDGFFATIPGADAETVKKKAMEFLKYINAKLPGALELEYEGFYKRGFFVTKKKYAVIDEEGKITTRGLEIVRRDWSEIAKETQARVLEALLKDGDVEKAVRIVKEVTEKLSKYEVPPEKLVIHKQITRDLKDYKATGPHVAVAKRLAARGVKIRPGTVISYIVLKGSGRIGDRAIPFDEFDPTKHRYDAEYYIEKQVLPAVERILRAFGYRKEDLRYQKTRQVGLSAWLKPKGT |
| DNA polymerase | B | 774 | Thermococcus Kodakarensis Kod1 , Synthetic Construct | MILDTDYITEDGKPVIRIFKKENGEFKIEYDRTFEPYFYALLKDDSAIEEVKKITAERHGTVVTVKRVEKVQKKFLGRPVEVWKLYFTHPQDQPAIRDKIREHPAVIDIYEYDTPFAKRYLIDKGLVPMEGDEELKMLAFAIATLYHEGEEFAEGPILMISYADEEGARVITWKNVDLPYVDVVSTEREMIKRFLRVVKEKDPDVLITYNGDNFDFAYLKKRCEKLGINFALGRDGSEPKIQRMGDRFAVEVKGRIHFDLYPVIRRTINLPTYTLEAVYEAVFGQPKEKVYAEEITTAWETGENLERVARYSMEDAKVTYELGKEFLPMEAQLSRLIGQSLWDVSRSSTGNLVEWFLLRKAYERNELAPNKPDEKELARRRQKYEGGYVKEPERGLWENIVYLDFRSLYPSIIITHNVSPDTLNREGCGEYDVAPQVGHRFCKDLPGFIPSLLGDLLEERQKIKKKMKATIDPIERKLLDYRQRLIKILANSVYGHMGFENARWYCKECAESVTAWGREYLTMTIKEIEEKYGFKVIYSDTDGFFATIPGADAETVKKKAMEFLKYINAKLPGALELEYEGFYKRGFFVTKKKYAVIDEEGKITTRGLEIVRRDWSEIAKETQARVLEALLKDGDVEKAVRIVKEVTEKLSKYEVPPEKLVIHKQITRDLKDYKATGPHVAVAKRLAARGVKIRPGTVISYIVLKGSGRIGDRAIPFDEFDPTKHRYDAEYYIEKQVLPAVERILRAFGYRKEDLRYQKTRQVGLSAWLKPKGT |
Experimental Data
Method: X-RAY DIFFRACTION
Deposited Date: 2025-05-15 Deposition Author(s): Betz, K. , Gutfreund, C.