You can simply delete the entire certificate.
Delete the private key and matching public certs along with any specific use of them.
If you are using certbot, you can issue a delete command to have it do the first two parts for you.
Syntax:
certbot delete --cert-name example.com
[so you will need to know the exact cert-name - not the specific FQDN(or domain name) within the cert]
[you can get the cert names with: certbot certificates]
If you use another ACME client, you should review their documentation for a comparable command.
It is always preferable to use the ACME client to remove the cert itself than trying to do so manually.