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 · 25% helix, 38% strand (DSSP).

Ligands and binding sites

• AYE · prop-2-en-1-amine · ligand · 2 copies · chains A, B, C, D
• ZN · Zinc ion · metal · 6 copies · chains A, C
• MPD · (4S)-2-methyl-2,4-pentanediol · additive · 8 copies · chains A, B, C, D

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

Pockets

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

Interfaces

4 interfaces between chains.

• C–D · 1257 Ų buried · 19 hydrogen bonds · protein-protein
• A–B · 1256 Ų buried · 18 hydrogen bonds · protein-protein
• B–C · 492 Ų buried · 4 hydrogen bonds · protein-protein
• A–C · 447 Ų buried · 10 hydrogen bonds · protein-protein

Modifications

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

Compared structures

• 5W8U · Crystal structure of MERS-CoV papain-like protease in complex with the C-terminal domain… · the same entry in another collection · chain A against A, 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 K0BWD0
• Every structure of UniProt P05161
• Elsewhere: RCSB PDB 5W8U · PDBe 5W8U · UniProt K0BWD0 · UniProt P05161