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

Structure

x-ray diffraction · 3 distinct chains.

Ligands and binding sites

• 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 · ligand · chains A, B, C
• 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 · ligand · chains A, B, C
• MG · Magnesium ion · metal · 2 copies · chains A, B
• GOL · Glycerol · additive · 2 copies · chains B, C
• ACT · Acetate ion · additive · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Compared structures

• 5NKL · Crystal structure of the large fragment of DNA polymerase I from Thermus Aquaticus in a… · the same entry in another collection · chain A against A, TM-score 1.00
• P19821 · AlphaFold monomer V2.0 prediction for DNA polymerase I, thermostable (P19821) · a predicted model of the same protein · chain A against A, TM-score 0.96

Analyse

• Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
• Every structure of UniProt P19821
• Elsewhere: RCSB PDB 5NKL · PDBe 5NKL · UniProt P19821