Not so easy, since your spec changes depending on whether you have 'e' (two decimal places) or not (three decimal places). Best I could come up with is:

printf ((/e/?"%04.2e":"%05.3f")."\n", $number);
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Use sprintf if you wish to convert the number and place into another variable:

my $var = sprintf ((/e/?"%04.2e":"%05.3f"), $number);
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Update: removed stupid "\n" from sprintf