Easy:

use Modern::Perl;
use Data::Dump qw/dump/;

my %data;
my $ac;
while (<DATA>) {
    if (/^#=GF AC\s+(.*)$/) {
        $ac = $1;
        next;
    }
    if (/^#=GS ([^_]*)/) {
        push @{ $data{$1} }, $ac;
        next;
    }
}
say dump(%data);

__DATA__
# STOCKHOLM 1.0
#=GF ID   1-cysPrx_C
#=GF AC   PF10417.4
#=GF DE   C-terminal domain of 1-Cys peroxiredoxin
#=GF AU   Finn RD, Coggill PC
#=GF SE   Gene3D, pdb_1prx
...
#=GS A3EU39_9BACT/160-195  AC A3EU39.1
#=GS Q7VQB3_BLOFL/159-194  AC Q7VQB3.1
#=GS Q057V5_BUCCC/160-195  AC Q057V5.1
#=GS A5CDZ8_ORITB/160-195  AC A5CDZ8.1
...
//
# LONDON 1.0
#=GF ID   1-cysPrx_C
#=GF AC   PF10000.3
#=GF DE   C-terminal domain of 1-Cys peroxiredoxin
#=GF AU   Finn RD, Coggill PC
#=GF SE   Gene3D, pdb_1prx
...
#=GS A3EU39_9BACT/160-195  AC A3EU39.1
#=GS Q7VQB8_BLOFL/159-194  AC Q7VQB3.1
#=GS Q057V5_BUCCC/160-195  AC Q057V5.1
#=GS A5CDZ8_ORITB/160-195  AC A5CDZ8.1
//
# AMSTERDAM 1.0
#=GF ID   1-cysPrx_C
#=GF AC   PF10999.3
#=GF DE   C-terminal domain of 1-Cys peroxiredoxin
#=GF AU   Finn RD, Coggill PC
#=GF SE   Gene3D, pdb_1prx
...
#=GS A3EU39_9BACT/160-195  AC A3EU39.1
#=GS Q7VQB8_BLOFL/159-194  AC Q7VQB3.1
#=GS Q057V5_BUCCC/160-195  AC Q057V5.1
#=GS A5CDZ8_ORITB/160-195  AC A5CDZ8.1
[download]

Output:

(
  "Q7VQB8",  ["PF10000.3", "PF10999.3"],
  "Q7VQB3",  ["PF10417.4"],
  "A3EU39",  ["PF10417.4", "PF10000.3", "PF10999.3"],
  "Q057V5",  ["PF10417.4", "PF10000.3", "PF10999.3"],
  "A5CDZ8",  ["PF10417.4", "PF10000.3", "PF10999.3"],
)
[download]

The formatting of the output is left as an exercise for the reader.