Brand  (β version)

PDB ID: 5NKL

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Ligands
Code Name Style Show Link
91R [[(2~{R},3~{S},5~{R})-5-[4-[(4~{S})-4,5-bis(oxidanyl)pent-1-ynyl]-2-nitro-pyrrol-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate PoSSuM
91T [[(2~{R},3~{S},5~{R})-5-[4-[(4~{R})-4,5-bis(oxidanyl)pent-1-ynyl]-2-nitro-pyrrol-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate PoSSuM
ACT Acetate ion PoSSuM
GOL Glycerol PoSSuM
MG Magnesium ion PoSSuM
Non-standard Residues
Code Name Show
DOC 2',3'-dideoxycytidine-5'-monophosphate
Glycosylation
Code Name Emphasize
Modification
Code Name Show
91N [(2~{R},3~{S},5~{R})-3-oxidanyl-5-(7-thiophen-2-ylimidazo[4,5-B]pyridin-3-yl)oxolan-2-yl]methyl dihydrogen phosphate

Structure summary

Code : 5NKL   PDBj   RCSB PDB   PDBe
Header : TRANSFERASE
Title : Crystal structure of the large fragment of DNA polymerase I from Thermus Aquaticus in a closed ternary complex with the artificial base pair dDs-dPxTP
Release Data : 2017-06-28
Compound :
mol_id molecule chains synonym
1 DNA polymerase I, thermostable A Taq polymerase 1
ec: 2.7.7.7
mol_id molecule chains
2 DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DOC))-3') B
mol_id molecule chains
3 DNA (5'-D(*AP*AP*AP*(DNU)P*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3') C
Source :
mol_id organism_scientific expression_system
1 Thermus aquaticus  (taxid:271) Escherichia coli  (taxid:562)
gene: polA, pol1
mol_id organism_scientific
2 Synthetic construct  (taxid:32630)
synthetic: yes
mol_id organism_scientific
3 Synthetic construct  (taxid:32630)
synthetic: yes
Authors : Betz, K., Marx, A., Diederichs, K., Hirao, I., Kimoto, M.
Keywords : DNA polymerase, artificial base pair, unnatural base pair, ternary complex, transferase
Exp. method : X-RAY DIFFRACTION ( 1.700 Å )
Citation :

Structural Basis for Expansion of the Genetic Alphabet with an Artificial Nucleobase Pair.

Betz, K.,Kimoto, M.,Diederichs, K.  et al.
(2017)  Angew. Chem. Int. Ed. Engl.  56 : 12000 - 12003

PubMed: 28594080
DOI: 10.1002/anie.201704190

Reaction

Chain : A
UniProt : P19821 (DPO1_THEAQ)
Reaction: EC: Evidence:
Physiological Direction:
a 2'-deoxyribonucleoside 5'-triphosphate + DNA(n) = diphosphate + DNA(n+1) 2.7.7.7 -
-