A hash of arrays of arrays seems to fit the bill:

#! perl -slw
use strict;
use Data::Dump qw[ pp ];

my %data;

while( <DATA> ) {
    my @bits = split;
    push @{ $data{ pop @bits } }, \@bits;
}

pp \%data;

__DATA__
AsmA_2               PF13502      220 A0KIJ1
AsmA_2               PF13502      220 A0KIJ1
DUF490               PF04357      379 A1AJD0
Pfam-B_5656          PB005656     259 A1AJD0
STN                  PF07660       52 T2MWK7
Secretin_N_2         PF07655       98 T2MZK3
Pfam-B_2175          PB002175     114 T2MVV9
Secretin_N           PF03958       82 U2ZRR1
Pfam-B_1479          PB001479     704 U2ZRR1
Pfam-B_2175          PB002175     114 U2ZRR1
[download]

Gives:

[16:26:56.39] C:\test>junk56
{
  A0KIJ1 => [
              ["AsmA_2", "PF13502", 220], 
              ["AsmA_2", "PF13502", 220]
            ],
  A1AJD0 => [
              ["DUF490", "PF04357", 379], 
              ["Pfam-B_5656", "PB005656", 259]
            ],
  T2MVV9 => [
              ["Pfam-B_2175", "PB002175", 114]
            ],
  T2MWK7 => [ 
              ["STN", "PF07660", 52]
            ],
  T2MZK3 => [ 
              ["Secretin_N_2", "PF07655", 98]
            ],
  U2ZRR1 => [
              ["Secretin_N", "PF03958", 82],
              ["Pfam-B_1479", "PB001479", 704],
              ["Pfam-B_2175", "PB002175", 114],
            ],
}
[download]