Crystal structure of MERS-cov papain-like protease in complex with the C-terminal domain of human ISG15

Structure

x-ray diffraction · 2 distinct chains · 26% helix, 38% strand (DSSP).

Ligands and binding sites

• AYE · prop-2-en-1-amine · ligand · 2 copies · chains B, A, D, C
• ZN · Zinc ion · metal · 6 copies · chains A, C
• MPD · (4S)-2-methyl-2,4-pentanediol · additive · 6 copies · chains B, A, D, C

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

Pockets

9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Interfaces

4 interfaces between chains.

• D–C · 1298 Ų buried · 15 hydrogen bonds · protein-protein
• B–A · 1286 Ų buried · 17 hydrogen bonds · protein-protein
• A–C · 435 Ų buried · 10 hydrogen bonds · protein-protein
• A–D · 401 Ų buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 covalent (covalent ligand).

Compared structures

• 5W8T · Crystal structure of MERS-CoV papain-like protease in complex with the C-terminal domain… · the same entry in another collection · chain B against B, TM-score 1.00
• P05161 · AlphaFold monomer V2.0 prediction for ubiquitin-like protein ISG15 (P05161) · a predicted model of the same protein · chain B 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 P05161
• Every structure of UniProt K0BWD0
• Elsewhere: RCSB PDB 5W8T · PDBe 5W8T · UniProt P05161 · UniProt K0BWD0