You might be able to rig up a door, or at least a make-shift covering for that. You might be able to get a dog door and install it if the hole is the right size.I made the mistake of buying a store bought coop and a big design flaw is that the coop doesn't actually have a door! This is what I have:
http://www.waremfginc.com/b-detaildisplay.aspx?itemno=14061
I took the run off because it was too difficult to get to the chickens and to clean it out and the birds were free ranging anyway. I'm wondering if I install a small pet door there that has a plastic piece that slides into it to close it off would be a suitable cheap fix until the spring when I get a new, bigger, better coop.