Crystal structure of SARS-cov-2 neutralizing antibody WS6 in complex with spike S2 peptide

Structure

x-ray diffraction · 4 distinct chains · 9% helix, 52% strand (DSSP).

Ligands and binding sites

• ACE · Acetyl group · ligand · 2 copies · chains C, D
• I2J · 2-(2-aminoethoxy)ethan-1-ol · ligand · 2 copies · chains H, L, C, A, B, D
• SO4 · Sulfate ion · ion · 20 copies · chains H, L, B, C, A, D
• PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains L, C

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

Pockets

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

Interfaces

9 interfaces between chains.

• A–B · 1807 Ų buried · 18 hydrogen bonds · protein-protein
• H–L · 1781 Ų buried · 19 hydrogen bonds · protein-protein
• H–A · 397 Ų buried · 12 hydrogen bonds · protein-protein
• H–C · 385 Ų buried · 2 hydrogen bonds · protein-protein
• A–D · 377 Ų buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide, 4 covalent, 1 modified (disulfide, covalent ligand, cyclization).

Compared structures

• 7TCQ · Crystal structure of SARS-CoV-2 neutralizing antibody WS6 in complex with spike S2 peptide · the same entry in another collection · chain H against H, 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 P0DTC2
• Elsewhere: RCSB PDB 7TCQ · PDBe 7TCQ · UniProt P0DTC2