data_5Z71 # _model_server_result.job_id hEvx71w2xrrehkHMCwHckw _model_server_result.datetime_utc '2024-10-12 14:26:32' _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 5z71 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":201}' # _entry.id 5Z71 # _exptl.entry_id 5Z71 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 496.552 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description GENETICIN _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 5Z71 _cell.length_a 30.924 _cell.length_b 90.106 _cell.length_c 46.701 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5Z71 _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 hydrog WATSON-CRICK hydrog1 A N1 G 2 A G 3 1_555 B N3 C 22 B C 46 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 A N2 G 2 A G 3 1_555 B O2 C 22 B C 46 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A O6 G 2 A G 3 1_555 B N4 C 22 B C 46 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 A N3 C 3 A C 4 1_555 B N1 G 21 B G 45 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 A N4 C 3 A C 4 1_555 B O6 G 21 B G 45 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A O2 C 3 A C 4 1_555 B N2 G 21 B G 45 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A N1 G 4 A G 5 1_555 B N3 C 20 B C 44 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A N2 G 4 A G 5 1_555 B O2 C 20 B C 44 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A O6 G 4 A G 5 1_555 B N4 C 20 B C 44 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'U-U MISPAIR' hydrog10 A O4 U 5 A U 6 1_555 B N3 U 19 B U 43 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 A N3 C 6 A C 7 1_555 B N1 G 18 B G 42 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 A N4 C 6 A C 7 1_555 B O6 G 18 B G 42 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 A O2 C 6 A C 7 1_555 B N2 G 18 B G 42 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'C-A MISPAIR' hydrog14 A N4 C 8 A C 9 1_555 B N1 A 15 B A 39 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 A N3 U 9 A U 10 1_555 B N1 A 14 B A 38 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 A O4 U 9 A U 10 1_555 B N6 A 14 B A 38 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 A N3 C 10 A C 11 1_555 B N1 G 13 B G 37 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 A N4 C 10 A C 11 1_555 B O6 G 13 B G 37 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 A O2 C 10 A C 11 1_555 B N2 G 13 B G 37 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 A N3 C 11 A C 12 1_555 B N1 G 12 B G 36 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 A N4 C 11 A C 12 1_555 B O6 G 12 B G 36 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 A O2 C 11 A C 12 1_555 B N2 G 12 B G 36 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 A N1 G 12 A G 13 1_555 B N3 C 11 B C 35 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 A N2 G 12 A G 13 1_555 B O2 C 11 B C 35 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 A O6 G 12 A G 13 1_555 B N4 C 11 B C 35 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 A N1 G 13 A G 14 1_555 B N3 C 10 B C 34 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 A N2 G 13 A G 14 1_555 B O2 C 10 B C 34 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 A O6 G 13 A G 14 1_555 B N4 C 10 B C 34 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog29 A N1 A 14 A A 15 1_555 B N3 U 9 B U 33 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog30 A N6 A 14 A A 15 1_555 B O4 U 9 B U 33 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog31 A N1 G 18 A G 19 1_555 B N3 C 6 B C 30 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog32 A N2 G 18 A G 19 1_555 B O2 C 6 B C 30 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog33 A O6 G 18 A G 19 1_555 B N4 C 6 B C 30 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_16_PAIR hydrog34 A N3 U 19 A U 20 1_555 B O4 U 5 B U 29 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_16_PAIR hydrog35 A O2 U 19 A U 20 1_555 B N3 U 5 B U 29 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog36 A N3 C 20 A C 21 1_555 B N1 G 4 B G 28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog37 A N4 C 20 A C 21 1_555 B O6 G 4 B G 28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog38 A O2 C 20 A C 21 1_555 B N2 G 4 B G 28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog39 A N1 G 21 A G 22 1_555 B N3 C 3 B C 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog40 A N2 G 21 A G 22 1_555 B O2 C 3 B C 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog41 A O6 G 21 A G 22 1_555 B N4 C 3 B C 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog42 A N3 C 22 A C 23 1_555 B N1 G 2 B G 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog43 A N4 C 22 A C 23 1_555 B O6 G 2 B G 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog44 A O2 C 22 A C 23 1_555 B N2 G 2 B G 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C20 H40 N4 O10' _chem_comp.formula_weight 496.552 _chem_comp.id GET _chem_comp.mon_nstd_flag . _chem_comp.name GENETICIN _chem_comp.type non-polymer _chem_comp.pdbx_synonyms G418 # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag C11 O11 GET sing 116 n n C11 C21 GET sing 117 n n C11 O51 GET sing 118 n n C11 H111 GET sing 119 n n O11 C42 GET sing 120 n n C21 N21 GET sing 121 n n C21 C31 GET sing 122 n n C21 H21 GET sing 123 n n N21 H211 GET sing 124 n n N21 H212 GET sing 125 n n C31 O31 GET sing 126 n n C31 C41 GET sing 127 n n C31 H311 GET sing 128 n n O31 H31 GET sing 129 n n C41 O41 GET sing 130 n n C41 C51 GET sing 131 n n C41 H411 GET sing 132 n n O41 H41 GET sing 133 n n C51 O51 GET sing 134 n n C51 C61 GET sing 135 n n C51 H511 GET sing 136 n n C61 O61 GET sing 137 n n C61 C71 GET sing 138 n n C61 H611 GET sing 139 n n O61 H61 GET sing 140 n n C71 H711 GET sing 141 n n C71 H712 GET sing 142 n n C71 H713 GET sing 143 n n C12 N12 GET sing 144 n n C12 C22 GET sing 145 n n C12 C62 GET sing 146 n n C12 H12 GET sing 147 n n N12 H121 GET sing 148 n n N12 H122 GET sing 149 n n C22 C32 GET sing 150 n n C22 H221 GET sing 151 n n C22 H222 GET sing 152 n n C32 N32 GET sing 153 n n C32 C42 GET sing 154 n n C32 H32 GET sing 155 n n N32 H321 GET sing 156 n n N32 H322 GET sing 157 n n C42 C52 GET sing 158 n n C42 H421 GET sing 159 n n C52 O52 GET sing 160 n n C52 C62 GET sing 161 n n C52 H521 GET sing 162 n n O52 H52 GET sing 163 n n C62 O62 GET sing 164 n n C62 H621 GET sing 165 n n O62 C13 GET sing 166 n n C13 C23 GET sing 167 n n C13 O53 GET sing 168 n n C13 H131 GET sing 169 n n C23 O23 GET sing 170 n n C23 C33 GET sing 171 n n C23 H231 GET sing 172 n n O23 H23 GET sing 173 n n C33 N33 GET sing 174 n n C33 C43 GET sing 175 n n C33 H331 GET sing 176 n n N33 C93 GET sing 177 n n N33 H33 GET sing 178 n n C93 H931 GET sing 179 n n C93 H932 GET sing 180 n n C93 H933 GET sing 181 n n C43 O43 GET sing 182 n n C43 C83 GET sing 183 n n C43 C53 GET sing 184 n n O43 H43 GET sing 185 n n C83 H831 GET sing 186 n n C83 H832 GET sing 187 n n C83 H833 GET sing 188 n n C53 O53 GET sing 189 n n C53 H531 GET sing 190 n n C53 H532 GET sing 191 n n # _atom_sites.entry_id 5Z71 _atom_sites.fract_transf_matrix[1][1] 0.032337 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011098 _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] 0.021413 _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 C 2 GET B 1 201 201 GET GET . D 3 HOH B 1 301 102 HOH HOH . D 3 HOH B 2 302 104 HOH HOH . D 3 HOH B 3 303 103 HOH HOH . D 3 HOH B 4 304 101 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 C C11 GET . . . C 2 -18.41 17.175 11.881 1 55.12 ? C11 GET 201 B 1 HETATM 2 O O11 GET . . . C 2 -18.825 17.414 13.227 1 63.65 ? O11 GET 201 B 1 HETATM 3 C C21 GET . . . C 2 -16.901 16.829 11.96 1 53.93 ? C21 GET 201 B 1 HETATM 4 N N21 GET . . . C 2 -16.685 15.657 12.817 1 53.32 ? N21 GET 201 B 1 HETATM 5 C C31 GET . . . C 2 -16.103 18.042 12.501 1 56.67 ? C31 GET 201 B 1 HETATM 6 O O31 GET . . . C 2 -14.701 17.712 12.587 1 53.15 ? O31 GET 201 B 1 HETATM 7 C C41 GET . . . C 2 -16.358 19.263 11.554 1 55.54 ? C41 GET 201 B 1 HETATM 8 O O41 GET . . . C 2 -15.635 20.407 12.009 1 61.45 ? O41 GET 201 B 1 HETATM 9 C C51 GET . . . C 2 -17.889 19.582 11.51 1 53.45 ? C51 GET 201 B 1 HETATM 10 O O51 GET . . . C 2 -18.645 18.378 11.037 1 58.87 ? O51 GET 201 B 1 HETATM 11 C C61 GET . . . C 2 -18.173 20.799 10.572 1 55.5 ? C61 GET 201 B 1 HETATM 12 O O61 GET . . . C 2 -19.553 21.118 10.545 1 59.83 ? O61 GET 201 B 1 HETATM 13 C C71 GET . . . C 2 -17.719 20.524 9.128 1 58.59 ? C71 GET 201 B 1 HETATM 14 C C12 GET . . . C 2 -22.185 16.145 15.558 1 63.3 ? C12 GET 201 B 1 HETATM 15 N N12 GET . . . C 2 -23.545 15.795 15.948 1 54.38 ? N12 GET 201 B 1 HETATM 16 C C22 GET . . . C 2 -22.167 17.621 15.036 1 60.59 ? C22 GET 201 B 1 HETATM 17 C C32 GET . . . C 2 -20.696 17.979 14.632 1 61.25 ? C32 GET 201 B 1 HETATM 18 N N32 GET . . . C 2 -20.617 19.37 14.121 1 58.73 ? N32 GET 201 B 1 HETATM 19 C C42 GET . . . C 2 -20.187 17.015 13.536 1 59.07 ? C42 GET 201 B 1 HETATM 20 C C52 GET . . . C 2 -20.254 15.561 14.073 1 62.29 ? C52 GET 201 B 1 HETATM 21 O O52 GET . . . C 2 -19.783 14.682 13.06 1 69.23 ? O52 GET 201 B 1 HETATM 22 C C62 GET . . . C 2 -21.712 15.173 14.431 1 65.98 ? C62 GET 201 B 1 HETATM 23 O O62 GET . . . C 2 -21.714 13.839 14.927 1 65.42 ? O62 GET 201 B 1 HETATM 24 C C13 GET . . . C 2 -22.681 12.975 14.332 1 61.45 ? C13 GET 201 B 1 HETATM 25 C C23 GET . . . C 2 -22.933 11.902 15.42 1 59.73 ? C23 GET 201 B 1 HETATM 26 O O23 GET . . . C 2 -23.484 12.506 16.573 1 66.69 ? O23 GET 201 B 1 HETATM 27 C C33 GET . . . C 2 -21.574 11.21 15.755 1 60.3 ? C33 GET 201 B 1 HETATM 28 N N33 GET . . . C 2 -21.764 10.195 16.819 1 64.02 ? N33 GET 201 B 1 HETATM 29 C C93 GET . . . C 2 -21.241 10.773 18.087 1 63.52 ? C93 GET 201 B 1 HETATM 30 C C43 GET . . . C 2 -21.012 10.554 14.46 1 58.29 ? C43 GET 201 B 1 HETATM 31 O O43 GET . . . C 2 -21.931 9.598 13.984 1 64.69 ? O43 GET 201 B 1 HETATM 32 C C83 GET . . . C 2 -19.681 9.848 14.698 1 55.37 ? C83 GET 201 B 1 HETATM 33 C C53 GET . . . C 2 -20.831 11.654 13.393 1 60.97 ? C53 GET 201 B 1 HETATM 34 O O53 GET . . . C 2 -22.108 12.353 13.141 1 60.68 ? O53 GET 201 B 1 # _model_server_stats.io_time_ms 67 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 293 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 34 #