Select2 adds class .select2. You can override what script does using css.
Here I’m set select2 to have 100% width, using !important. If I would not do that select2 would have 24px width.
You can further customize other classes that select2 generates using some principle.
$(document).ready(function(){
$("#mySelect").select2();
});.select2 {
width:100%!important;
}<script src="https://ajax.googleapis.com/ajax/libs/jquery/2.1.1/jquery.min.js"></script>
<link href="https://cdnjs.cloudflare.com/ajax/libs/select2/4.0.3/css/select2.css" rel="stylesheet"/>
<script src="https://cdnjs.cloudflare.com/ajax/libs/select2/4.0.3/js/select2.js"></script>
<div class="form-group">
<label class="control-label col-md-3">Select structure</label>
<div class="col-lg-5 col-md-9">
<select class="form-control" id="mySelect" runat="server"></select>
</div>
</div>