There are a number of ways you can approach this problem. One is to simply remove Apache all together. You can serve phpMyAdmin with Nginx as well. Check out:

• How To Install and Secure phpMyAdmin with Nginx on an Ubuntu 14.04 Server

If your setup is working fine as it is, and you just want to make Apache listen on port 3000, you can easily do that too. You’ll need to edit two files and change 80 to 3000

# If you just change the port or add more ports here, you will likely also
# have to change the VirtualHost statement in
# /etc/apache2/sites-enabled/000-default.conf

Listen 3000

<IfModule ssl_module>
        Listen 443
</IfModule>

<IfModule mod_gnutls.c>
        Listen 443
</IfModule>

and

<VirtualHost *:3000>
# [...]

Finally, restart Apache with sudo service apache2 restart Now your phpMyAdmin interface can be reached at: http://your.ip.addr:3000/phpmyadmin