data_3A6T # _model_server_result.job_id mV5KkX69HhgItS_yfuQy6A _model_server_result.datetime_utc '2024-10-11 15:15:47' _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 3a6t # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":134}' # _entry.id 3A6T # _exptl.entry_id 3A6T _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 363.221 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE" _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 3A6T _cell.length_a 37.972 _cell.length_b 56.007 _cell.length_c 59.369 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3A6T _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 PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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,E,F,G _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 5 _struct_asym.id F _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 2 _pdbx_entity_branch_link.entity_branch_list_num_1 1 _pdbx_entity_branch_link.entity_branch_list_num_2 2 _pdbx_entity_branch_link.comp_id_1 GLC _pdbx_entity_branch_link.comp_id_2 FRU _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O2 _pdbx_entity_branch_link.leaving_atom_id_2 HO2 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 2 n B GLC 1 B 1 GLC A 130 SUC 2 n B FRU 2 B 2 FRU A 130 SUC # _struct_conn.conn_type_id covale _struct_conn.details ? _struct_conn.id covale1 _struct_conn.ptnr1_label_asym_id B _struct_conn.ptnr1_label_atom_id C1 _struct_conn.ptnr1_label_comp_id GLC _struct_conn.ptnr1_label_seq_id . _struct_conn.ptnr1_auth_asym_id B _struct_conn.ptnr1_auth_comp_id GLC _struct_conn.ptnr1_auth_seq_id 1 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id B _struct_conn.ptnr2_label_atom_id O2 _struct_conn.ptnr2_label_comp_id FRU _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id B _struct_conn.ptnr2_auth_comp_id FRU _struct_conn.ptnr2_auth_seq_id 2 _struct_conn.ptnr2_symmetry 1_555 _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 1.456 _struct_conn.pdbx_value_order sing # _chem_comp.formula 'C10 H14 N5 O8 P' _chem_comp.formula_weight 363.221 _chem_comp.id 8OG _chem_comp.mon_nstd_flag n _chem_comp.name "8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE" _chem_comp.type 'dna linking' _chem_comp.pdbx_synonyms "8-OXO-7,8-DIHYDRO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE" # 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 OP3 P 8OG sing 1 n n OP3 HOP3 8OG sing 2 n n P OP1 8OG doub 3 n n P OP2 8OG sing 4 n n P O5' 8OG sing 5 n n OP2 HOP2 8OG sing 6 n n O5' C5' 8OG sing 7 n n C5' C4' 8OG sing 8 n n C5' H5' 8OG sing 9 n n C5' "H5''" 8OG sing 10 n n C4' O4' 8OG sing 11 n n C4' C3' 8OG sing 12 n n C4' H4' 8OG sing 13 n n O4' C1' 8OG sing 14 n n C3' O3' 8OG sing 15 n n C3' C2' 8OG sing 16 n n C3' H3' 8OG sing 17 n n O3' HO3' 8OG sing 18 n n C2' C1' 8OG sing 19 n n C2' H2' 8OG sing 20 n n C2' "H2''" 8OG sing 21 n n C1' N9 8OG sing 22 n n C1' H1' 8OG sing 23 n n N9 C8 8OG sing 24 n n N9 C4 8OG sing 25 n n C8 N7 8OG sing 26 n n C8 O8 8OG doub 27 n n N7 C5 8OG sing 28 n n N7 H7 8OG sing 29 n n C5 C6 8OG sing 30 n n C5 C4 8OG doub 31 n n C6 O6 8OG doub 32 n n C6 N1 8OG sing 33 n n N1 C2 8OG sing 34 n n N1 H1 8OG sing 35 n n C2 N2 8OG sing 36 n n C2 N3 8OG doub 37 n n N2 H21 8OG sing 38 n n N2 H22 8OG sing 39 n n N3 C4 8OG sing 40 n n # _atom_sites.entry_id 3A6T _atom_sites.fract_transf_matrix[1][1] 0.026335 _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] 0.017855 _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] 0.016844 _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 3 NA A 1 131 131 NA NA . D 4 SO4 A 1 132 132 SO4 SO4 . E 4 SO4 A 1 133 133 SO4 SO4 . F 5 8OG A 1 134 134 8OG 8OG . G 6 HOH A 1 135 135 HOH HOH . G 6 HOH A 2 136 136 HOH HOH . G 6 HOH A 3 137 137 HOH HOH . G 6 HOH A 4 138 138 HOH HOH . G 6 HOH A 5 139 139 HOH HOH . G 6 HOH A 6 140 140 HOH HOH . G 6 HOH A 7 141 141 HOH HOH . G 6 HOH A 8 142 142 HOH HOH . G 6 HOH A 9 143 143 HOH HOH . G 6 HOH A 10 144 144 HOH HOH . G 6 HOH A 11 145 145 HOH HOH . G 6 HOH A 12 146 146 HOH HOH . G 6 HOH A 13 147 147 HOH HOH . G 6 HOH A 14 148 148 HOH HOH . G 6 HOH A 15 149 149 HOH HOH . G 6 HOH A 16 150 150 HOH HOH . G 6 HOH A 17 151 151 HOH HOH . G 6 HOH A 18 152 152 HOH HOH . G 6 HOH A 19 153 153 HOH HOH . G 6 HOH A 20 154 154 HOH HOH . G 6 HOH A 21 155 155 HOH HOH . G 6 HOH A 22 156 156 HOH HOH . G 6 HOH A 23 157 157 HOH HOH . G 6 HOH A 24 158 158 HOH HOH . G 6 HOH A 25 159 159 HOH HOH . G 6 HOH A 26 160 160 HOH HOH . G 6 HOH A 27 161 161 HOH HOH . G 6 HOH A 28 162 162 HOH HOH . G 6 HOH A 29 163 163 HOH HOH . G 6 HOH A 30 164 164 HOH HOH . G 6 HOH A 31 165 165 HOH HOH . G 6 HOH A 32 166 166 HOH HOH . G 6 HOH A 33 167 167 HOH HOH . G 6 HOH A 34 168 168 HOH HOH . G 6 HOH A 35 169 169 HOH HOH . G 6 HOH A 36 170 170 HOH HOH . G 6 HOH A 37 171 171 HOH HOH . G 6 HOH A 38 172 172 HOH HOH . G 6 HOH A 39 173 173 HOH HOH . G 6 HOH A 40 174 174 HOH HOH . G 6 HOH A 41 175 175 HOH HOH . G 6 HOH A 42 176 176 HOH HOH . G 6 HOH A 43 177 177 HOH HOH . G 6 HOH A 44 178 178 HOH HOH . G 6 HOH A 45 179 179 HOH HOH . G 6 HOH A 46 180 180 HOH HOH . G 6 HOH A 47 181 181 HOH HOH . G 6 HOH A 48 182 182 HOH HOH . G 6 HOH A 49 183 183 HOH HOH . G 6 HOH A 50 184 184 HOH HOH . G 6 HOH A 51 185 185 HOH HOH . G 6 HOH A 52 186 186 HOH HOH . G 6 HOH A 53 187 187 HOH HOH . G 6 HOH A 54 188 188 HOH HOH . G 6 HOH A 55 189 189 HOH HOH . G 6 HOH A 56 190 190 HOH HOH . G 6 HOH A 57 191 191 HOH HOH . G 6 HOH A 58 192 192 HOH HOH . G 6 HOH A 59 193 193 HOH HOH . G 6 HOH A 60 194 194 HOH HOH . G 6 HOH A 61 195 195 HOH HOH . G 6 HOH A 62 196 196 HOH HOH . G 6 HOH A 63 197 197 HOH HOH . G 6 HOH A 64 198 198 HOH HOH . G 6 HOH A 65 199 199 HOH HOH . G 6 HOH A 66 200 200 HOH HOH . G 6 HOH A 67 201 201 HOH HOH . G 6 HOH A 68 202 202 HOH HOH . G 6 HOH A 69 203 203 HOH HOH . G 6 HOH A 70 204 204 HOH HOH . G 6 HOH A 71 205 205 HOH HOH . G 6 HOH A 72 206 206 HOH HOH . G 6 HOH A 73 207 207 HOH HOH . G 6 HOH A 74 208 208 HOH HOH . G 6 HOH A 75 209 209 HOH HOH . G 6 HOH A 76 210 210 HOH HOH . G 6 HOH A 77 211 211 HOH HOH . G 6 HOH A 78 212 212 HOH HOH . G 6 HOH A 79 213 213 HOH HOH . G 6 HOH A 80 214 214 HOH HOH . G 6 HOH A 81 215 215 HOH HOH . G 6 HOH A 82 216 216 HOH HOH . G 6 HOH A 83 217 217 HOH HOH . G 6 HOH A 84 218 218 HOH HOH . G 6 HOH A 85 219 219 HOH HOH . G 6 HOH A 86 220 220 HOH HOH . G 6 HOH A 87 221 221 HOH HOH . G 6 HOH A 88 222 222 HOH HOH . G 6 HOH A 89 223 223 HOH HOH . G 6 HOH A 90 224 224 HOH HOH . G 6 HOH A 91 225 225 HOH HOH . G 6 HOH A 92 226 226 HOH HOH . G 6 HOH A 93 227 227 HOH HOH . G 6 HOH A 94 228 228 HOH HOH . G 6 HOH A 95 229 229 HOH HOH . G 6 HOH A 96 230 230 HOH HOH . G 6 HOH A 97 231 231 HOH HOH . G 6 HOH A 98 232 232 HOH HOH . G 6 HOH A 99 233 233 HOH HOH . G 6 HOH A 100 234 234 HOH HOH . G 6 HOH A 101 235 235 HOH HOH . G 6 HOH A 102 236 236 HOH HOH . G 6 HOH A 103 237 237 HOH HOH . G 6 HOH A 104 238 238 HOH HOH . G 6 HOH A 105 239 239 HOH HOH . G 6 HOH A 106 240 240 HOH HOH . G 6 HOH A 107 241 241 HOH HOH . G 6 HOH A 108 242 242 HOH HOH . G 6 HOH A 109 243 243 HOH HOH . G 6 HOH A 110 244 244 HOH HOH . G 6 HOH A 111 245 245 HOH HOH . G 6 HOH A 112 246 246 HOH HOH . G 6 HOH A 113 247 247 HOH HOH . G 6 HOH A 114 248 248 HOH HOH . G 6 HOH A 115 249 249 HOH HOH . G 6 HOH A 116 250 250 HOH HOH . G 6 HOH A 117 251 251 HOH HOH . G 6 HOH A 118 252 252 HOH HOH . G 6 HOH A 119 253 253 HOH HOH . G 6 HOH A 120 254 254 HOH HOH . G 6 HOH A 121 255 255 HOH HOH . G 6 HOH A 122 256 256 HOH HOH . G 6 HOH A 123 257 257 HOH HOH . G 6 HOH A 124 258 258 HOH HOH . G 6 HOH A 125 259 259 HOH HOH . G 6 HOH A 126 260 260 HOH HOH . G 6 HOH A 127 261 261 HOH HOH . G 6 HOH A 128 262 262 HOH HOH . G 6 HOH A 129 263 263 HOH HOH . G 6 HOH A 130 264 264 HOH HOH . G 6 HOH A 131 265 265 HOH HOH . G 6 HOH A 132 266 266 HOH HOH . G 6 HOH A 133 267 267 HOH HOH . G 6 HOH A 134 268 268 HOH HOH . G 6 HOH A 135 269 269 HOH HOH . G 6 HOH A 136 270 270 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 O OP3 8OG . . . F 5 -11.528 0.538 23.417 1 22.69 ? OP3 8OG 134 A 1 HETATM 2 P P 8OG . . . F 5 -10.075 0.826 23.477 1 22.32 ? P 8OG 134 A 1 HETATM 3 O OP1 8OG . . . F 5 -9.892 1.988 24.375 1 20.7 ? OP1 8OG 134 A 1 HETATM 4 O OP2 8OG . . . F 5 -9.593 0.935 22.086 1 21.67 ? OP2 8OG 134 A 1 HETATM 5 O O5' 8OG . . . F 5 -9.379 -0.463 24.137 1 18.97 ? O5' 8OG 134 A 1 HETATM 6 C C5' 8OG . . . F 5 -8.049 -0.402 24.669 1 14.13 ? C5' 8OG 134 A 1 HETATM 7 C C4' 8OG . . . F 5 -7.953 -1.144 26.007 1 11.53 ? C4' 8OG 134 A 1 HETATM 8 O O4' 8OG . . . F 5 -6.584 -1.49 26.307 1 11.33 ? O4' 8OG 134 A 1 HETATM 9 C C3' 8OG . . . F 5 -8.457 -0.303 27.175 1 11.11 ? C3' 8OG 134 A 1 HETATM 10 O O3' 8OG . . . F 5 -9.188 -1.133 28.093 1 10.19 ? O3' 8OG 134 A 1 HETATM 11 C C2' 8OG . . . F 5 -7.213 0.258 27.786 1 10.38 ? C2' 8OG 134 A 1 HETATM 12 C C1' 8OG . . . F 5 -6.18 -0.832 27.525 1 10.92 ? C1' 8OG 134 A 1 HETATM 13 N N9 8OG . . . F 5 -4.82 -0.256 27.38 1 10.85 ? N9 8OG 134 A 1 HETATM 14 C C8 8OG . . . F 5 -3.815 -0.428 28.299 1 11.14 ? C8 8OG 134 A 1 HETATM 15 N N7 8OG . . . F 5 -2.715 0.14 28.014 1 9.94 ? N7 8OG 134 A 1 HETATM 16 C C5 8OG . . . F 5 -2.93 0.776 26.787 1 10.43 ? C5 8OG 134 A 1 HETATM 17 C C6 8OG . . . F 5 -2.081 1.577 25.957 1 10.83 ? C6 8OG 134 A 1 HETATM 18 O O6 8OG . . . F 5 -0.913 1.894 26.152 1 10.84 ? O6 8OG 134 A 1 HETATM 19 N N1 8OG . . . F 5 -2.743 2.011 24.788 1 9.76 ? N1 8OG 134 A 1 HETATM 20 C C2 8OG . . . F 5 -4.068 1.719 24.449 1 10.18 ? C2 8OG 134 A 1 HETATM 21 N N2 8OG . . . F 5 -4.522 2.216 23.295 1 9.39 ? N2 8OG 134 A 1 HETATM 22 N N3 8OG . . . F 5 -4.879 0.969 25.23 1 9.31 ? N3 8OG 134 A 1 HETATM 23 C C4 8OG . . . F 5 -4.258 0.531 26.376 1 11.35 ? C4 8OG 134 A 1 HETATM 24 O O8 8OG . . . F 5 -4.032 -1.102 29.322 1 10.67 ? O8 8OG 134 A 1 # _model_server_stats.io_time_ms 30 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 314 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 24 #