Crystal structure of spike protein receptor-binding domain from a predicted SARS coronavirus civet strain complexed with human-civet chimeric receptor ACE2

Structure

x-ray diffraction · 2 distinct chains · 48% helix, 7% strand (DSSP).

Ligands and binding sites

• ZN · Zinc ion · metal · 2 copies · chains A, B
• CL · Chloride ion · ion · 2 copies · chains A, B

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

Pockets

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

Interfaces

3 interfaces between chains.

• A–E · 984 Ų buried · 14 hydrogen bonds · protein-protein
• B–F · 958 Ų buried · 15 hydrogen bonds · protein-protein
• A–B · 129 Ų buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 disulfide (disulfide).

Compared structures

• 3SCK · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · the same entry in another collection · chain A against A, TM-score 1.00
• 3SCL · Crystal structure of spike protein receptor-binding domain from SARS coronavirus epidemic… · an experimental structure of the same protein · chain A against A, TM-score 1.00
• 3SCL · Crystal structure of spike protein receptor-binding domain from SARS coronavirus epidemic… · an experimental structure of the same protein · chain A against A, TM-score 1.00
• 2AJF · Structure of SARS coronavirus spike receptor-binding domain complexed with its receptor · an experimental structure of the same protein · chain A against A, TM-score 1.00
• 2AJF · Structure of SARS coronavirus spike receptor-binding domain complexed with its receptor · an experimental structure of the same protein · chain A against A, TM-score 1.00
• 7ZF7 · SARS-CoV-2 Omicron BA.2 RBD in complex with ACE2 · an experimental structure of the same protein · chain A against A, TM-score 0.99
• 7ZF7 · SARS-cov-2 omicron BA.2 rbd in complex with ACE2 · an experimental structure of the same protein · chain A against A, TM-score 0.99
• 6M0J · Crystal structure of SARS-cov-2 spike receptor-binding domain bound with ACE2 · an experimental structure of the same protein · chain A against A, TM-score 0.99
• 6M0J · Crystal structure of SARS-CoV-2 spike receptor-binding domain bound with ACE2 · an experimental structure of the same protein · chain A against A, TM-score 0.99

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 Q56NL1
• Every structure of UniProt Q9BYF1
• Every structure of UniProt P59594
• Elsewhere: RCSB PDB 3SCK · PDBe 3SCK · UniProt Q56NL1 · AlphaFold DB Q56NL1 · UniProt Q9BYF1 · AlphaFold DB Q9BYF1 · UniProt P59594 · AlphaFold DB P59594