#!/usr/bin/perl -w
use strict;
use Data::Dumper;

my @this_record;  #lines of the record
my @records;      #array of array

while (<DATA>)
{
   chomp;
   if (my $line = m|^LOCUS|...m|^//|)
   {     
      if ($line =~ m/E0$/)   #don't push the trailing "//"
      {
          push (@records, [@this_record]); #record complete
          @this_record = ();
      }
      else
      {
          push (@this_record,$_); #just another record line
      }
   }
}

print Dumper \@records;

__DATA__
LOCUS       NP_644805                770 aa            linear   PRI 06-FEB-2011
...following lines deleted for brevity ...