data_3TOM # _model_server_result.job_id belSIAe0ThodLxth9O4Dlw _model_server_result.datetime_utc '2025-09-03 22:26:33' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 3tom # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":107}' # _entry.id 3TOM # _exptl.entry_id 3TOM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 65.409 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'ZINC ION' _entity.pdbx_number_of_molecules 6 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 112.61 _cell.angle_gamma 90 _cell.entry_id 3TOM _cell.length_a 95.69 _cell.length_b 37.843 _cell.length_c 138.489 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3TOM _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 PISA tetrameric 4 software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression C,D,J,K,L,M,N,Q,R 1 1 A,B,E,F,G,H,I,O,P 2 1 A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R 3 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 F N N ? 3 H N N ? 3 I N N ? 3 K N N ? 3 M N N ? 3 N N N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order metalc ? metalc1 A SD MET 7 A MET 7 1_555 E FE HEM . A HEM 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.391 ? metalc ? metalc2 A NE2 HIS 63 A HIS 63 1_555 H ZN ZN . B ZN 107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.907 ? metalc ? metalc3 A NE2 HIS 73 A HIS 73 1_555 F ZN ZN . A ZN 107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.989 ? metalc ? metalc4 A NE2 HIS 77 A HIS 77 1_555 F ZN ZN . A ZN 107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.963 ? metalc ? metalc5 A NE2 HIS 102 A HIS 102 1_555 E FE HEM . A HEM 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.954 ? metalc ? metalc6 F ZN ZN . A ZN 107 1_555 B NE2 HIS 63 B HIS 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.007 ? metalc ? metalc7 B O ALA 1 B ALA 1 1_555 I ZN ZN . B ZN 108 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.221 ? metalc ? metalc8 B N ALA 1 B ALA 1 1_555 I ZN ZN . B ZN 108 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.468 ? metalc ? metalc9 B SD MET 7 B MET 7 1_555 G FE HEM . B HEM 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.377 ? metalc ? metalc10 B OD2 ASP 39 B ASP 39 1_555 I ZN ZN . B ZN 108 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? metalc ? metalc11 B OE2 GLU 49 B GLU 49 1_555 N ZN ZN . D ZN 108 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.998 ? metalc ? metalc12 B NE2 HIS 73 B HIS 73 1_555 H ZN ZN . B ZN 107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? metalc ? metalc13 B NE2 HIS 77 B HIS 77 1_555 H ZN ZN . B ZN 107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.238 ? metalc ? metalc14 B NE2 HIS 102 B HIS 102 1_555 G FE HEM . B HEM 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? metalc ? metalc15 I ZN ZN . B ZN 108 1_555 D OE2 GLU 49 D GLU 49 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.804 ? metalc ? metalc16 I ZN ZN . B ZN 108 1_555 R O HOH . D HOH 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.339 ? metalc ? metalc17 C SD MET 7 C MET 7 1_555 J FE HEM . C HEM 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.393 ? metalc ? metalc18 C NE2 HIS 63 C HIS 63 1_555 M ZN ZN . D ZN 107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? metalc ? metalc19 C NE2 HIS 73 C HIS 73 1_555 K ZN ZN . C ZN 107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.169 ? metalc ? metalc20 C NE2 HIS 77 C HIS 77 1_555 K ZN ZN . C ZN 107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.95 ? metalc ? metalc21 C NE2 HIS 102 C HIS 102 1_555 J FE HEM . C HEM 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.945 ? metalc ? metalc22 K ZN ZN . C ZN 107 1_555 D NE2 HIS 63 D HIS 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.107 ? metalc ? metalc23 D O ALA 1 D ALA 1 1_555 N ZN ZN . D ZN 108 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.218 ? metalc ? metalc24 D N ALA 1 D ALA 1 1_555 N ZN ZN . D ZN 108 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.296 ? metalc ? metalc25 D SD MET 7 D MET 7 1_555 L FE HEM . D HEM 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.256 ? metalc ? metalc26 D OD2 ASP 39 D ASP 39 1_555 N ZN ZN . D ZN 108 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.176 ? metalc ? metalc27 D NE2 HIS 73 D HIS 73 1_555 M ZN ZN . D ZN 107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.943 ? metalc ? metalc28 D NE2 HIS 77 D HIS 77 1_555 M ZN ZN . D ZN 107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.105 ? metalc ? metalc29 D NE2 HIS 102 D HIS 102 1_555 L FE HEM . D HEM 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.012 ? metalc ? metalc30 N ZN ZN . D ZN 108 1_555 R O HOH . D HOH 151 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? # _chem_comp.formula 'Zn 2' _chem_comp.formula_weight 65.409 _chem_comp.id ZN _chem_comp.mon_nstd_flag . _chem_comp.name 'ZINC ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 3TOM _atom_sites.fract_transf_matrix[1][1] 0.01045 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004352 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.026425 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.007822 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code E 2 HEM A 1 150 150 HEM HEM . F 3 ZN A 1 107 2 ZN ZN . G 2 HEM B 1 150 150 HEM HEM . H 3 ZN B 1 107 1 ZN ZN . I 3 ZN B 1 108 6 ZN ZN . J 2 HEM C 1 150 150 HEM HEM . K 3 ZN C 1 107 4 ZN ZN . L 2 HEM D 1 150 150 HEM HEM . M 3 ZN D 1 107 3 ZN ZN . N 3 ZN D 1 108 5 ZN ZN . O 4 HOH A 1 108 108 HOH HOH . O 4 HOH A 2 109 2 HOH HOH . O 4 HOH A 3 110 110 HOH HOH . O 4 HOH A 4 111 6 HOH HOH . O 4 HOH A 5 112 7 HOH HOH . O 4 HOH A 6 113 8 HOH HOH . O 4 HOH A 7 114 9 HOH HOH . O 4 HOH A 8 115 115 HOH HOH . O 4 HOH A 9 116 10 HOH HOH . O 4 HOH A 10 117 11 HOH HOH . O 4 HOH A 11 118 12 HOH HOH . O 4 HOH A 12 119 14 HOH HOH . O 4 HOH A 13 120 15 HOH HOH . O 4 HOH A 14 121 16 HOH HOH . O 4 HOH A 15 122 17 HOH HOH . O 4 HOH A 16 123 123 HOH HOH . O 4 HOH A 17 124 124 HOH HOH . O 4 HOH A 18 125 18 HOH HOH . O 4 HOH A 19 126 126 HOH HOH . O 4 HOH A 20 127 127 HOH HOH . O 4 HOH A 21 128 128 HOH HOH . O 4 HOH A 22 129 129 HOH HOH . O 4 HOH A 23 130 130 HOH HOH . O 4 HOH A 24 131 131 HOH HOH . O 4 HOH A 25 132 132 HOH HOH . O 4 HOH A 26 133 133 HOH HOH . O 4 HOH A 27 134 41 HOH HOH . O 4 HOH A 28 135 46 HOH HOH . O 4 HOH A 29 136 49 HOH HOH . O 4 HOH A 30 137 57 HOH HOH . O 4 HOH A 31 138 63 HOH HOH . O 4 HOH A 32 139 64 HOH HOH . O 4 HOH A 33 140 66 HOH HOH . O 4 HOH A 34 141 69 HOH HOH . O 4 HOH A 35 142 72 HOH HOH . O 4 HOH A 36 143 75 HOH HOH . O 4 HOH A 37 144 79 HOH HOH . O 4 HOH A 38 145 88 HOH HOH . O 4 HOH A 39 146 89 HOH HOH . O 4 HOH A 40 147 92 HOH HOH . O 4 HOH A 41 148 95 HOH HOH . O 4 HOH A 42 149 96 HOH HOH . O 4 HOH A 43 151 102 HOH HOH . O 4 HOH A 44 152 105 HOH HOH . O 4 HOH A 45 153 106 HOH HOH . O 4 HOH A 46 154 107 HOH HOH . O 4 HOH A 47 155 155 HOH HOH . O 4 HOH A 48 156 156 HOH HOH . O 4 HOH A 49 157 157 HOH HOH . O 4 HOH A 50 158 158 HOH HOH . O 4 HOH A 51 172 172 HOH HOH . O 4 HOH A 52 173 173 HOH HOH . P 4 HOH B 1 109 109 HOH HOH . P 4 HOH B 2 110 3 HOH HOH . P 4 HOH B 3 111 111 HOH HOH . P 4 HOH B 4 112 112 HOH HOH . P 4 HOH B 5 113 113 HOH HOH . P 4 HOH B 6 114 114 HOH HOH . P 4 HOH B 7 115 4 HOH HOH . P 4 HOH B 8 116 5 HOH HOH . P 4 HOH B 9 117 13 HOH HOH . P 4 HOH B 10 118 19 HOH HOH . P 4 HOH B 11 119 119 HOH HOH . P 4 HOH B 12 120 120 HOH HOH . P 4 HOH B 13 121 121 HOH HOH . P 4 HOH B 14 122 122 HOH HOH . P 4 HOH B 15 123 20 HOH HOH . P 4 HOH B 16 124 21 HOH HOH . P 4 HOH B 17 125 22 HOH HOH . P 4 HOH B 18 126 23 HOH HOH . P 4 HOH B 19 127 24 HOH HOH . P 4 HOH B 20 128 25 HOH HOH . P 4 HOH B 21 129 26 HOH HOH . P 4 HOH B 22 130 42 HOH HOH . P 4 HOH B 23 131 44 HOH HOH . P 4 HOH B 24 132 45 HOH HOH . P 4 HOH B 25 133 47 HOH HOH . P 4 HOH B 26 134 134 HOH HOH . P 4 HOH B 27 135 135 HOH HOH . P 4 HOH B 28 136 136 HOH HOH . P 4 HOH B 29 137 137 HOH HOH . P 4 HOH B 30 138 48 HOH HOH . P 4 HOH B 31 139 53 HOH HOH . P 4 HOH B 32 140 56 HOH HOH . P 4 HOH B 33 141 58 HOH HOH . P 4 HOH B 34 142 60 HOH HOH . P 4 HOH B 35 143 70 HOH HOH . P 4 HOH B 36 144 71 HOH HOH . P 4 HOH B 37 145 74 HOH HOH . P 4 HOH B 38 146 76 HOH HOH . P 4 HOH B 39 147 80 HOH HOH . P 4 HOH B 40 148 81 HOH HOH . P 4 HOH B 41 149 86 HOH HOH . P 4 HOH B 42 151 97 HOH HOH . P 4 HOH B 43 152 98 HOH HOH . P 4 HOH B 44 153 153 HOH HOH . P 4 HOH B 45 154 101 HOH HOH . P 4 HOH B 46 155 103 HOH HOH . P 4 HOH B 47 160 160 HOH HOH . P 4 HOH B 48 161 161 HOH HOH . P 4 HOH B 49 163 163 HOH HOH . P 4 HOH B 50 164 164 HOH HOH . P 4 HOH B 51 165 165 HOH HOH . P 4 HOH B 52 166 166 HOH HOH . P 4 HOH B 53 167 167 HOH HOH . P 4 HOH B 54 168 168 HOH HOH . Q 4 HOH C 1 108 27 HOH HOH . Q 4 HOH C 2 109 28 HOH HOH . Q 4 HOH C 3 110 29 HOH HOH . Q 4 HOH C 4 111 30 HOH HOH . Q 4 HOH C 5 112 32 HOH HOH . Q 4 HOH C 6 113 34 HOH HOH . Q 4 HOH C 7 114 36 HOH HOH . Q 4 HOH C 8 115 38 HOH HOH . Q 4 HOH C 9 116 50 HOH HOH . Q 4 HOH C 10 117 117 HOH HOH . Q 4 HOH C 11 118 118 HOH HOH . Q 4 HOH C 12 119 52 HOH HOH . Q 4 HOH C 13 120 55 HOH HOH . Q 4 HOH C 14 121 59 HOH HOH . Q 4 HOH C 15 122 61 HOH HOH . Q 4 HOH C 16 123 68 HOH HOH . Q 4 HOH C 17 124 77 HOH HOH . Q 4 HOH C 18 125 82 HOH HOH . Q 4 HOH C 19 126 83 HOH HOH . Q 4 HOH C 20 127 91 HOH HOH . Q 4 HOH C 21 128 93 HOH HOH . Q 4 HOH C 22 138 138 HOH HOH . Q 4 HOH C 23 139 139 HOH HOH . Q 4 HOH C 24 140 140 HOH HOH . Q 4 HOH C 25 141 141 HOH HOH . Q 4 HOH C 26 142 142 HOH HOH . Q 4 HOH C 27 143 143 HOH HOH . Q 4 HOH C 28 144 144 HOH HOH . Q 4 HOH C 29 145 145 HOH HOH . Q 4 HOH C 30 146 146 HOH HOH . Q 4 HOH C 31 147 147 HOH HOH . Q 4 HOH C 32 162 162 HOH HOH . Q 4 HOH C 33 170 170 HOH HOH . Q 4 HOH C 34 174 174 HOH HOH . Q 4 HOH C 35 176 176 HOH HOH . R 4 HOH D 1 109 1 HOH HOH . R 4 HOH D 2 110 31 HOH HOH . R 4 HOH D 3 111 33 HOH HOH . R 4 HOH D 4 112 35 HOH HOH . R 4 HOH D 5 113 37 HOH HOH . R 4 HOH D 6 114 39 HOH HOH . R 4 HOH D 7 115 40 HOH HOH . R 4 HOH D 8 116 116 HOH HOH . R 4 HOH D 9 117 43 HOH HOH . R 4 HOH D 10 118 51 HOH HOH . R 4 HOH D 11 119 54 HOH HOH . R 4 HOH D 12 120 62 HOH HOH . R 4 HOH D 13 121 65 HOH HOH . R 4 HOH D 14 122 67 HOH HOH . R 4 HOH D 15 123 73 HOH HOH . R 4 HOH D 16 124 78 HOH HOH . R 4 HOH D 17 125 125 HOH HOH . R 4 HOH D 18 126 84 HOH HOH . R 4 HOH D 19 127 85 HOH HOH . R 4 HOH D 20 128 87 HOH HOH . R 4 HOH D 21 129 90 HOH HOH . R 4 HOH D 22 130 94 HOH HOH . R 4 HOH D 23 131 99 HOH HOH . R 4 HOH D 24 132 100 HOH HOH . R 4 HOH D 25 133 104 HOH HOH . R 4 HOH D 26 134 150 HOH HOH . R 4 HOH D 27 148 148 HOH HOH . R 4 HOH D 28 149 149 HOH HOH . R 4 HOH D 29 151 151 HOH HOH . R 4 HOH D 30 152 152 HOH HOH . R 4 HOH D 31 154 154 HOH HOH . R 4 HOH D 32 159 159 HOH HOH . R 4 HOH D 33 169 169 HOH HOH . R 4 HOH D 34 171 171 HOH HOH . R 4 HOH D 35 175 175 HOH HOH . R 4 HOH D 36 177 177 HOH HOH . R 4 HOH D 37 178 178 HOH HOH . # _atom_site.group_PDB HETATM _atom_site.id 1 _atom_site.type_symbol ZN _atom_site.label_atom_id ZN _atom_site.label_comp_id ZN _atom_site.label_seq_id . _atom_site.label_alt_id . _atom_site.pdbx_PDB_ins_code . _atom_site.label_asym_id F _atom_site.label_entity_id 3 _atom_site.Cartn_x -15.683 _atom_site.Cartn_y 15.723 _atom_site.Cartn_z 49.886 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 27.57 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id ZN _atom_site.auth_comp_id ZN _atom_site.auth_seq_id 107 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 305 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 1 #