Crystal structure of HCV NS5B genotype 2A jfh-1 isolate with S15G E86Q E87Q C223H V321I mutations in complex with RNA template 5'-agcc, RNA primer 5'-pgg, MN2+, and cdp

Structure

x-ray diffraction · 3 distinct chains · 49% helix, 16% strand (DSSP).

Ligands and binding sites

• CDP · Cytidine-5'-diphosphate · ligand · chains T, P, A
• MN · Manganese (II) ion · metal · 3 copies · chains P, A
• CL · Chloride ion · ion · chains A
• PG6 · 1-(2-methoxy-ethoxy)-2-{2-[2-(2-methoxy-ethoxy]-ethoxy}-ethane · additive · chains A
• B3P · 2-[3-(2-hydroxy-1,1-dihydroxymethyl-ethylamino)-propylamino]-2-hydroxymethyl-propane-1,3-diol · additive · chains A
• EDO · 1,2-ethanediol · additive · chains A

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

Pockets

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

Interfaces

3 interfaces between chains.

• T–A · 541 Ų buried · 13 hydrogen bonds · protein-nucleic
• P–A · 407 Ų buried · 7 hydrogen bonds · protein-nucleic
• T–P · 107 Ų buried · 8 hydrogen bonds · nucleic-nucleic

Compared structures

• 4WTK · Crystal structure of HCV NS5B genotype 2A jfh-1 isolate with S15G E86Q E87Q C223H V321I… · the same entry in another collection · chain T against T, 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 Q99IB8
• Elsewhere: RCSB PDB 4WTK · PDBe 4WTK · UniProt Q99IB8