diff -r 8428d15cbeff Lib/idlelib/pyshell.py
--- a/Lib/idlelib/pyshell.py	Sat Jun 04 07:13:38 2016 +0000
+++ b/Lib/idlelib/pyshell.py	Sat Jun 04 14:15:39 2016 +0300
@@ -1548,6 +1548,15 @@ def main():
     flist = PyShellFileList(root)
     macosx.setupApp(root, flist)
 
+    if root._windowingsystem == 'x11':
+        # Pasting from the clipboard doesn't delete the current selection
+        # on X11.
+        # See issue #5124.
+        for cls in 'Text', 'Entry', 'Spinbox':
+            root.bind_class(cls, '<<Paste>>',
+                            'catch {%W delete sel.first sel.last}\n' +
+                            root.bind_class(cls, '<<Paste>>'))
+
     if macosx.isAquaTk():
         # There are some screwed up <2> class bindings for text
         # widgets defined in Tk which we need to do away with.