<p.It looks like your data is column oriented. If it is, the substr() would be a better choice.
#!/usr/bin/perl
use strict;
use warnings;
use Data::Dumper;
# Make Data::Dumper pretty
$Data::Dumper::Sortkeys = 1;
$Data::Dumper::Indent = 1;
# Set maximum depth for Data::Dumper, zero means unlimited
local $Data::Dumper::Maxdepth = 0;
my @data;
while( <DATA> ){
print;
chomp;
@data = ();
$data[0] = substr( $_, 0, 7 );
$data[1] = substr( $_, 9, 35 );
$data[2] = substr( $_, 45, 8 );
$data[3] = substr( $_, 54, 1 );
$data[4] = substr( $_, 56, 1 );
$data[5] = substr( $_, 58, 1 );
print '@data ', Dumper \@data;
}
__DATA__
1xny_01 PROPIONYL-COA CARBOXYLASE COMPLEX B -0.8192 A A A
1xqd_00 CYTOCHROME P450 55A1 -46.5601 A B A
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