Structure of polyphosphate kinase 2 from francisella tularensis with AMPPCH2PPP and polyphosphate

Structure

x-ray diffraction · 1 distinct chain · 53% helix, 15% strand (DSSP).

Ligands and binding sites

• 6YZ · [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-[[oxidanyl-[oxidanyl(phosphonooxy) phosphoryl]oxy-phosphoryl]methyl]phosphinic acid · ligand · 4 copies · chains A, C, B, D
• 6YW · [oxidanyl-[oxidanyl-[oxidanyl(phosphonooxy) phosphoryl]oxy-phosphoryl]oxy-phosphoryl] phosphono hydrogen phosphate · ligand · 4 copies · chains A, B, C, D
• MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
• CL · Chloride ion · ion · 4 copies · chains A, B, C, D

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

Pockets

9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Interfaces

4 interfaces between chains.

• A–B · 1088 Ų buried · 17 hydrogen bonds · protein-protein
• C–D · 1080 Ų buried · 15 hydrogen bonds · protein-protein
• A–C · 755 Ų buried · 5 hydrogen bonds · protein-protein
• B–D · 735 Ų buried · 4 hydrogen bonds · protein-protein

Compared structures

• 5LLB · Structure of Polyphosphate Kinase 2 from Francisella tularensis with AMPPCH2PPP and… · the same entry in another collection · chain A against A, TM-score 1.00

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 Q5NEQ5
• Elsewhere: RCSB PDB 5LLB · PDBe 5LLB · UniProt Q5NEQ5