How about a Hash of Arrays (HoA) like so? (Assume your file is called data.txt)

perl -MData::Dumper -lane'push @{ $hash{$F[3]} }, [@F]}{print Dumper \
+%hash' < data.txt
[download]

Output:

$VAR1 = {
          'U2ZRR1' => [
                        [
                          'Secretin_N',
                          'PF03958',
                          '82',
                          'U2ZRR1'
                        ],
                        [
                          'Pfam-B_1479',
                          'PB001479',
                          '704',
                          'U2ZRR1'
                        ],
                        [
                          'Pfam-B_2175',
                          'PB002175',
                          '114',
                          'U2ZRR1'
                        ]
                      ],
          'A1AJD0' => [
                        [
                          'DUF490',
                          'PF04357',
                          '379',
                          'A1AJD0'
                        ],
                        [
                          'Pfam-B_5656',
                          'PB005656',
                          '259',
                          'A1AJD0'
                        ]
                      ],
          'T2MWK7' => [
                        [
                          'STN',
                          'PF07660',
                          '52',
                          'T2MWK7'
                        ]
                      ],
          'T2MVV9' => [
                        [
                          'Pfam-B_2175',
                          'PB002175',
                          '114',
                          'T2MVV9'
                        ]
                      ],
          'T2MZK3' => [
                        [
                          'Secretin_N_2',
                          'PF07655',
                          '98',
                          'T2MZK3'
                        ]
                      ],
          'A0KIJ1' => [
                        [
                          'AsmA_2',
                          'PF13502',
                          '220',
                          'A0KIJ1'
                        ],
                        [
                          'AsmA_2',
                          'PF13502',
                          '220',
                          'A0KIJ1'
                        ]
                      ]
        };
[download]

L-LL-L--L-LL-L--L-LL-L--
-R--R-RR-R--R-RR-R--R-RR
B--B--B--B--B--B--B--B--
H---H---H---H---H---H---
(the triplet paradiddle with high-hat)