data_1Y84 # _model_server_result.job_id rZ-RKK3O096_y_L8tEtzEg _model_server_result.datetime_utc '2024-11-12 21:12:56' _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 1y84 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":100}' # _entry.id 1Y84 # _exptl.entry_id 1Y84 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 202.34 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description SPERMINE _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 1Y84 _cell.length_a 24.097 _cell.length_b 43.071 _cell.length_c 46.26 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1Y84 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F _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 3 _struct_asym.id D _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 covale ? covale1 A O3' DA 5 A DA 5 1_555 A P EIT 6 A EIT 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.605 ? covale ? covale2 A O3' EIT 6 A EIT 6 1_555 A P DA 7 A DA 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.599 ? covale ? covale3 B O3' DA 5 B DA 15 1_555 B P EIT 6 B EIT 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.606 ? covale ? covale4 B O3' EIT 6 B EIT 16 1_555 B P DA 7 B DA 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.606 ? metalc ? metalc1 C MG MG . A MG 101 1_555 E O HOH . A HOH 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.13 ? metalc ? metalc2 C MG MG . A MG 101 1_555 E O HOH . A HOH 103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? metalc ? metalc3 C MG MG . A MG 101 1_555 E O HOH . A HOH 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? metalc ? metalc4 C MG MG . A MG 101 1_555 E O HOH . A HOH 106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? metalc ? metalc5 C MG MG . A MG 101 1_555 F O HOH . B HOH 105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.269 ? metalc ? metalc6 C MG MG . A MG 101 1_555 F O HOH . B HOH 107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.956 ? hydrog WATSON-CRICK hydrog1 A N1 DG 1 A DG 1 1_555 B N3 DC 10 B DC 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 A N2 DG 1 A DG 1 1_555 B O2 DC 10 B DC 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A O6 DG 1 A DG 1 1_555 B N4 DC 10 B DC 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 A N3 DC 2 A DC 2 1_555 B N1 DG 9 B DG 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 A N4 DC 2 A DC 2 1_555 B O6 DG 9 B DG 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A O2 DC 2 A DC 2 1_555 B N2 DG 9 B DG 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A N1 DG 3 A DG 3 1_555 B N3 DC 8 B DC 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A N2 DG 3 A DG 3 1_555 B O2 DC 8 B DC 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A O6 DG 3 A DG 3 1_555 B N4 DC 8 B DC 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 A N3 DT 4 A DT 4 1_555 B N1 DA 7 B DA 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 A O4 DT 4 A DT 4 1_555 B N6 DA 7 B DA 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 A N1 DA 5 A DA 5 1_555 B N3 EIT 6 B EIT 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 A N6 DA 5 A DA 5 1_555 B O4 EIT 6 B EIT 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 A N3 EIT 6 A EIT 6 1_555 B N1 DA 5 B DA 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 A O4 EIT 6 A EIT 6 1_555 B N6 DA 5 B DA 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 A N1 DA 7 A DA 7 1_555 B N3 DT 4 B DT 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 A N6 DA 7 A DA 7 1_555 B O4 DT 4 B DT 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 A N3 DC 8 A DC 8 1_555 B N1 DG 3 B DG 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 A N4 DC 8 A DC 8 1_555 B O6 DG 3 B DG 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 A O2 DC 8 A DC 8 1_555 B N2 DG 3 B DG 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 A N1 DG 9 A DG 9 1_555 B N3 DC 2 B DC 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 A N2 DG 9 A DG 9 1_555 B O2 DC 2 B DC 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 A O6 DG 9 A DG 9 1_555 B N4 DC 2 B DC 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 A N3 DC 10 A DC 10 1_555 B N1 DG 1 B DG 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 A N4 DC 10 A DC 10 1_555 B O6 DG 1 B DG 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 A O2 DC 10 A DC 10 1_555 B N2 DG 1 B DG 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C10 H26 N4' _chem_comp.formula_weight 202.34 _chem_comp.id SPM _chem_comp.mon_nstd_flag . _chem_comp.name SPERMINE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 N1 C2 SPM sing 204 n n N1 HN11 SPM sing 205 n n N1 HN12 SPM sing 206 n n C2 C3 SPM sing 207 n n C2 H21 SPM sing 208 n n C2 H22 SPM sing 209 n n C3 C4 SPM sing 210 n n C3 H31 SPM sing 211 n n C3 H32 SPM sing 212 n n C4 N5 SPM sing 213 n n C4 H41 SPM sing 214 n n C4 H42 SPM sing 215 n n N5 C6 SPM sing 216 n n N5 HN5 SPM sing 217 n n C6 C7 SPM sing 218 n n C6 H61 SPM sing 219 n n C6 H62 SPM sing 220 n n C7 C8 SPM sing 221 n n C7 H71 SPM sing 222 n n C7 H72 SPM sing 223 n n C8 C9 SPM sing 224 n n C8 H81 SPM sing 225 n n C8 H82 SPM sing 226 n n C9 N10 SPM sing 227 n n C9 H91 SPM sing 228 n n C9 H92 SPM sing 229 n n N10 C11 SPM sing 230 n n N10 HN0 SPM sing 231 n n C11 C12 SPM sing 232 n n C11 H111 SPM sing 233 n n C11 H112 SPM sing 234 n n C12 C13 SPM sing 235 n n C12 H121 SPM sing 236 n n C12 H122 SPM sing 237 n n C13 N14 SPM sing 238 n n C13 H131 SPM sing 239 n n C13 H132 SPM sing 240 n n N14 HN41 SPM sing 241 n n N14 HN42 SPM sing 242 n n # _atom_sites.entry_id 1Y84 _atom_sites.fract_transf_matrix[1][1] 0.041499 _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] 0.023217 _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] 0.021617 _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 MG A 1 101 101 MG MG . D 3 SPM B 1 100 100 SPM SPM . E 4 HOH A 1 102 102 HOH HOH . E 4 HOH A 2 103 103 HOH HOH . E 4 HOH A 3 104 104 HOH HOH . E 4 HOH A 4 106 106 HOH HOH . E 4 HOH A 5 109 109 HOH HOH . E 4 HOH A 6 112 112 HOH HOH . E 4 HOH A 7 113 113 HOH HOH . E 4 HOH A 8 115 115 HOH HOH . E 4 HOH A 9 117 117 HOH HOH . E 4 HOH A 10 118 118 HOH HOH . E 4 HOH A 11 119 119 HOH HOH . E 4 HOH A 12 122 122 HOH HOH . E 4 HOH A 13 126 126 HOH HOH . E 4 HOH A 14 127 127 HOH HOH . E 4 HOH A 15 128 128 HOH HOH . E 4 HOH A 16 129 129 HOH HOH . E 4 HOH A 17 130 130 HOH HOH . E 4 HOH A 18 131 131 HOH HOH . E 4 HOH A 19 132 132 HOH HOH . E 4 HOH A 20 134 134 HOH HOH . E 4 HOH A 21 135 135 HOH HOH . E 4 HOH A 22 138 138 HOH HOH . E 4 HOH A 23 139 139 HOH HOH . E 4 HOH A 24 141 141 HOH HOH . E 4 HOH A 25 143 143 HOH HOH . E 4 HOH A 26 148 148 HOH HOH . E 4 HOH A 27 149 149 HOH HOH . E 4 HOH A 28 150 150 HOH HOH . E 4 HOH A 29 151 151 HOH HOH . E 4 HOH A 30 159 159 HOH HOH . E 4 HOH A 31 161 161 HOH HOH . E 4 HOH A 32 164 164 HOH HOH . E 4 HOH A 33 165 165 HOH HOH . E 4 HOH A 34 166 166 HOH HOH . E 4 HOH A 35 167 167 HOH HOH . E 4 HOH A 36 168 168 HOH HOH . E 4 HOH A 37 169 169 HOH HOH . E 4 HOH A 38 170 170 HOH HOH . E 4 HOH A 39 173 173 HOH HOH . E 4 HOH A 40 174 174 HOH HOH . E 4 HOH A 41 175 175 HOH HOH . E 4 HOH A 42 176 176 HOH HOH . E 4 HOH A 43 180 180 HOH HOH . E 4 HOH A 44 182 182 HOH HOH . E 4 HOH A 45 183 183 HOH HOH . E 4 HOH A 46 184 184 HOH HOH . E 4 HOH A 47 189 189 HOH HOH . E 4 HOH A 48 191 191 HOH HOH . E 4 HOH A 49 192 192 HOH HOH . E 4 HOH A 50 193 193 HOH HOH . E 4 HOH A 51 194 194 HOH HOH . E 4 HOH A 52 196 196 HOH HOH . E 4 HOH A 53 197 197 HOH HOH . E 4 HOH A 54 205 205 HOH HOH . E 4 HOH A 55 207 207 HOH HOH . E 4 HOH A 56 210 210 HOH HOH . E 4 HOH A 57 214 214 HOH HOH . E 4 HOH A 58 215 215 HOH HOH . F 4 HOH B 1 105 105 HOH HOH . F 4 HOH B 2 107 107 HOH HOH . F 4 HOH B 3 108 108 HOH HOH . F 4 HOH B 4 110 110 HOH HOH . F 4 HOH B 5 111 111 HOH HOH . F 4 HOH B 6 114 114 HOH HOH . F 4 HOH B 7 116 116 HOH HOH . F 4 HOH B 8 120 120 HOH HOH . F 4 HOH B 9 121 121 HOH HOH . F 4 HOH B 10 123 123 HOH HOH . F 4 HOH B 11 124 124 HOH HOH . F 4 HOH B 12 125 125 HOH HOH . F 4 HOH B 13 133 133 HOH HOH . F 4 HOH B 14 136 136 HOH HOH . F 4 HOH B 15 137 137 HOH HOH . F 4 HOH B 16 140 140 HOH HOH . F 4 HOH B 17 142 142 HOH HOH . F 4 HOH B 18 144 144 HOH HOH . F 4 HOH B 19 145 145 HOH HOH . F 4 HOH B 20 146 146 HOH HOH . F 4 HOH B 21 147 147 HOH HOH . F 4 HOH B 22 152 152 HOH HOH . F 4 HOH B 23 153 153 HOH HOH . F 4 HOH B 24 154 154 HOH HOH . F 4 HOH B 25 155 155 HOH HOH . F 4 HOH B 26 156 156 HOH HOH . F 4 HOH B 27 157 157 HOH HOH . F 4 HOH B 28 158 158 HOH HOH . F 4 HOH B 29 160 160 HOH HOH . F 4 HOH B 30 162 162 HOH HOH . F 4 HOH B 31 163 163 HOH HOH . F 4 HOH B 32 171 171 HOH HOH . F 4 HOH B 33 172 172 HOH HOH . F 4 HOH B 34 177 177 HOH HOH . F 4 HOH B 35 178 178 HOH HOH . F 4 HOH B 36 179 179 HOH HOH . F 4 HOH B 37 181 181 HOH HOH . F 4 HOH B 38 185 185 HOH HOH . F 4 HOH B 39 186 186 HOH HOH . F 4 HOH B 40 187 187 HOH HOH . F 4 HOH B 41 188 188 HOH HOH . F 4 HOH B 42 190 190 HOH HOH . F 4 HOH B 43 195 195 HOH HOH . F 4 HOH B 44 198 198 HOH HOH . F 4 HOH B 45 199 199 HOH HOH . F 4 HOH B 46 200 200 HOH HOH . F 4 HOH B 47 201 201 HOH HOH . F 4 HOH B 48 202 202 HOH HOH . F 4 HOH B 49 203 203 HOH HOH . F 4 HOH B 50 204 204 HOH HOH . F 4 HOH B 51 206 206 HOH HOH . F 4 HOH B 52 208 208 HOH HOH . F 4 HOH B 53 209 209 HOH HOH . F 4 HOH B 54 211 211 HOH HOH . F 4 HOH B 55 212 212 HOH HOH . F 4 HOH B 56 213 213 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 N N1 SPM . . . D 3 -3.135 5.01 23.029 1 16.1 ? N1 SPM 100 B 1 HETATM 2 C C2 SPM . . . D 3 -2.938 3.836 23.921 1 16.77 ? C2 SPM 100 B 1 HETATM 3 C C3 SPM . . . D 3 -1.926 2.913 23.282 1 16.12 ? C3 SPM 100 B 1 HETATM 4 C C4 SPM . . . D 3 -1.559 1.757 24.162 1 19.26 ? C4 SPM 100 B 1 HETATM 5 N N5 SPM . . . D 3 -0.527 0.964 23.514 1 18.92 ? N5 SPM 100 B 1 HETATM 6 C C6 SPM . . . D 3 -0.229 -0.218 24.306 1 23.59 ? C6 SPM 100 B 1 HETATM 7 C C7 SPM . . . D 3 0.209 -1.37 23.423 1 27.25 ? C7 SPM 100 B 1 HETATM 8 C C8 SPM . . . D 3 0.14 -2.728 24.123 1 31.01 ? C8 SPM 100 B 1 HETATM 9 C C9 SPM . . . D 3 -1.269 -3.053 24.675 1 34.12 ? C9 SPM 100 B 1 HETATM 10 N N10 SPM . . . D 3 -1.474 -2.58 26.055 1 37.26 ? N10 SPM 100 B 1 HETATM 11 C C11 SPM . . . D 3 -2.086 -3.636 26.87 1 37.35 ? C11 SPM 100 B 1 HETATM 12 C C12 SPM . . . D 3 -1.839 -3.504 28.38 1 37.24 ? C12 SPM 100 B 1 HETATM 13 C C13 SPM . . . D 3 -2.298 -4.78 29.088 1 37.97 ? C13 SPM 100 B 1 HETATM 14 N N14 SPM . . . D 3 -2.024 -4.799 30.555 1 39.42 ? N14 SPM 100 B 1 # _model_server_stats.io_time_ms 56 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 1 _model_server_stats.query_time_ms 315 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 14 #