data_3OMF # _model_server_result.job_id HYHoT503Yplt--xIcDNWlQ _model_server_result.datetime_utc '2024-12-21 13:53:11' _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 3omf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":115}' # _entry.id 3OMF # _exptl.entry_id 3OMF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 347.221 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'ADENOSINE 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 3OMF _cell.length_a 53.58 _cell.length_b 60.63 _cell.length_c 67.88 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3OMF _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _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 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 4_555 x,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 3 _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 metalc ? metalc1 A SG CYS 9 A CYS 5 1_555 B ZN ZN . A ZN 114 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.315 ? metalc ? metalc2 A SG CYS 12 A CYS 8 1_555 B ZN ZN . A ZN 114 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.246 ? metalc ? metalc3 A ND1 HIS 51 A HIS 47 1_555 B ZN ZN . A ZN 114 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.104 ? metalc ? metalc4 A ND1 HIS 101 A HIS 97 1_555 B ZN ZN . A ZN 114 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.106 ? # _chem_comp.formula 'C10 H14 N5 O7 P' _chem_comp.formula_weight 347.221 _chem_comp.id AMP _chem_comp.mon_nstd_flag . _chem_comp.name 'ADENOSINE MONOPHOSPHATE' _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 P O1P AMP doub 13 n n P O2P AMP sing 14 n n P O3P AMP sing 15 n n P O5' AMP sing 16 n n O2P HOP2 AMP sing 17 n n O3P HOP3 AMP sing 18 n n O5' C5' AMP sing 19 n n C5' C4' AMP sing 20 n n C5' "H5'1" AMP sing 21 n n C5' "H5'2" AMP sing 22 n n C4' O4' AMP sing 23 n n C4' C3' AMP sing 24 n n C4' H4' AMP sing 25 n n O4' C1' AMP sing 26 n n C3' O3' AMP sing 27 n n C3' C2' AMP sing 28 n n C3' H3' AMP sing 29 n n O3' HO3' AMP sing 30 n n C2' O2' AMP sing 31 n n C2' C1' AMP sing 32 n n C2' H2' AMP sing 33 n n O2' HO2' AMP sing 34 n n C1' N9 AMP sing 35 n n C1' H1' AMP sing 36 n n N9 C8 AMP sing 37 n y N9 C4 AMP sing 38 n y C8 N7 AMP doub 39 n y C8 H8 AMP sing 40 n n N7 C5 AMP sing 41 n y C5 C6 AMP sing 42 n y C5 C4 AMP doub 43 n y C6 N6 AMP sing 44 n n C6 N1 AMP doub 45 n y N6 HN61 AMP sing 46 n n N6 HN62 AMP sing 47 n n N1 C2 AMP sing 48 n y C2 N3 AMP doub 49 n y C2 H2 AMP sing 50 n n N3 C4 AMP sing 51 n y # _atom_sites.entry_id 3OMF _atom_sites.fract_transf_matrix[1][1] 0.018664 _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] 0.016493 _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] 0.014732 _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 B 2 ZN A 1 114 1 ZN ZN . C 3 AMP A 1 115 1 AMP AMP . D 4 HOH A 1 116 2 HOH HOH . D 4 HOH A 2 117 3 HOH HOH . D 4 HOH A 3 118 4 HOH HOH . D 4 HOH A 4 119 119 HOH HOH . D 4 HOH A 5 120 120 HOH HOH . D 4 HOH A 6 121 121 HOH HOH . D 4 HOH A 7 122 5 HOH HOH . D 4 HOH A 8 123 123 HOH HOH . D 4 HOH A 9 124 124 HOH HOH . D 4 HOH A 10 125 125 HOH HOH . D 4 HOH A 11 126 126 HOH HOH . D 4 HOH A 12 127 127 HOH HOH . D 4 HOH A 13 128 128 HOH HOH . D 4 HOH A 14 129 129 HOH HOH . D 4 HOH A 15 130 130 HOH HOH . D 4 HOH A 16 131 131 HOH HOH . D 4 HOH A 17 132 132 HOH HOH . D 4 HOH A 18 133 133 HOH HOH . D 4 HOH A 19 134 134 HOH HOH . D 4 HOH A 20 135 135 HOH HOH . D 4 HOH A 21 136 136 HOH HOH . D 4 HOH A 22 137 137 HOH HOH . D 4 HOH A 23 138 6 HOH HOH . D 4 HOH A 24 139 139 HOH HOH . D 4 HOH A 25 140 140 HOH HOH . D 4 HOH A 26 141 141 HOH HOH . D 4 HOH A 27 142 142 HOH HOH . D 4 HOH A 28 143 143 HOH HOH . D 4 HOH A 29 144 144 HOH HOH . D 4 HOH A 30 145 145 HOH HOH . D 4 HOH A 31 146 146 HOH HOH . D 4 HOH A 32 147 7 HOH HOH . D 4 HOH A 33 148 148 HOH HOH . D 4 HOH A 34 149 149 HOH HOH . D 4 HOH A 35 150 150 HOH HOH . D 4 HOH A 36 151 151 HOH HOH . D 4 HOH A 37 152 152 HOH HOH . D 4 HOH A 38 153 153 HOH HOH . D 4 HOH A 39 154 154 HOH HOH . D 4 HOH A 40 155 155 HOH HOH . D 4 HOH A 41 156 156 HOH HOH . D 4 HOH A 42 157 8 HOH HOH . D 4 HOH A 43 158 158 HOH HOH . D 4 HOH A 44 159 159 HOH HOH . D 4 HOH A 45 160 160 HOH HOH . D 4 HOH A 46 161 161 HOH HOH . D 4 HOH A 47 162 162 HOH HOH . D 4 HOH A 48 163 163 HOH HOH . D 4 HOH A 49 164 164 HOH HOH . D 4 HOH A 50 165 165 HOH HOH . D 4 HOH A 51 166 166 HOH HOH . D 4 HOH A 52 167 167 HOH HOH . D 4 HOH A 53 168 9 HOH HOH . D 4 HOH A 54 169 169 HOH HOH . D 4 HOH A 55 170 170 HOH HOH . D 4 HOH A 56 171 10 HOH HOH . D 4 HOH A 57 172 11 HOH HOH . D 4 HOH A 58 173 173 HOH HOH . D 4 HOH A 59 174 174 HOH HOH . D 4 HOH A 60 175 175 HOH HOH . D 4 HOH A 61 176 176 HOH HOH . D 4 HOH A 62 177 177 HOH HOH . D 4 HOH A 63 178 178 HOH HOH . D 4 HOH A 64 179 179 HOH HOH . D 4 HOH A 65 180 12 HOH HOH . D 4 HOH A 66 181 181 HOH HOH . D 4 HOH A 67 182 182 HOH HOH . D 4 HOH A 68 183 183 HOH HOH . D 4 HOH A 69 184 184 HOH HOH . D 4 HOH A 70 185 185 HOH HOH . D 4 HOH A 71 186 186 HOH HOH . D 4 HOH A 72 187 187 HOH HOH . D 4 HOH A 73 188 188 HOH HOH . D 4 HOH A 74 189 189 HOH HOH . D 4 HOH A 75 190 190 HOH HOH . D 4 HOH A 76 191 191 HOH HOH . D 4 HOH A 77 192 192 HOH HOH . D 4 HOH A 78 193 193 HOH HOH . D 4 HOH A 79 194 194 HOH HOH . D 4 HOH A 80 195 14 HOH HOH . D 4 HOH A 81 196 15 HOH HOH . D 4 HOH A 82 197 16 HOH HOH . D 4 HOH A 83 198 17 HOH HOH . D 4 HOH A 84 199 18 HOH HOH . D 4 HOH A 85 200 19 HOH HOH . D 4 HOH A 86 201 20 HOH HOH . D 4 HOH A 87 202 21 HOH HOH . D 4 HOH A 88 203 22 HOH HOH . D 4 HOH A 89 204 24 HOH HOH . D 4 HOH A 90 205 25 HOH HOH . D 4 HOH A 91 206 26 HOH HOH . D 4 HOH A 92 207 27 HOH HOH . D 4 HOH A 93 208 28 HOH HOH . D 4 HOH A 94 209 29 HOH HOH . D 4 HOH A 95 210 30 HOH HOH . D 4 HOH A 96 211 31 HOH HOH . D 4 HOH A 97 212 32 HOH HOH . D 4 HOH A 98 213 33 HOH HOH . D 4 HOH A 99 214 34 HOH HOH . D 4 HOH A 100 215 35 HOH HOH . D 4 HOH A 101 216 36 HOH HOH . D 4 HOH A 102 217 37 HOH HOH . D 4 HOH A 103 218 39 HOH HOH . D 4 HOH A 104 219 40 HOH HOH . D 4 HOH A 105 220 41 HOH HOH . D 4 HOH A 106 221 42 HOH HOH . D 4 HOH A 107 222 43 HOH HOH . D 4 HOH A 108 223 44 HOH HOH . D 4 HOH A 109 224 46 HOH HOH . D 4 HOH A 110 225 48 HOH HOH . D 4 HOH A 111 226 49 HOH HOH . D 4 HOH A 112 227 50 HOH HOH . D 4 HOH A 113 228 51 HOH HOH . D 4 HOH A 114 229 52 HOH HOH . D 4 HOH A 115 230 53 HOH HOH . D 4 HOH A 116 231 55 HOH HOH . D 4 HOH A 117 232 56 HOH HOH . D 4 HOH A 118 233 57 HOH HOH . D 4 HOH A 119 234 59 HOH HOH . D 4 HOH A 120 235 60 HOH HOH . D 4 HOH A 121 236 61 HOH HOH . D 4 HOH A 122 237 62 HOH HOH . D 4 HOH A 123 238 63 HOH HOH . D 4 HOH A 124 239 64 HOH HOH . D 4 HOH A 125 240 65 HOH HOH . D 4 HOH A 126 241 66 HOH HOH . D 4 HOH A 127 242 67 HOH HOH . D 4 HOH A 128 243 68 HOH HOH . D 4 HOH A 129 244 69 HOH HOH . D 4 HOH A 130 245 70 HOH HOH . D 4 HOH A 131 246 71 HOH HOH . D 4 HOH A 132 247 72 HOH HOH . D 4 HOH A 133 248 73 HOH HOH . D 4 HOH A 134 249 74 HOH HOH . D 4 HOH A 135 250 75 HOH HOH . D 4 HOH A 136 251 76 HOH HOH . D 4 HOH A 137 252 77 HOH HOH . D 4 HOH A 138 253 78 HOH HOH . D 4 HOH A 139 254 81 HOH HOH . D 4 HOH A 140 255 84 HOH HOH . D 4 HOH A 141 256 86 HOH HOH . D 4 HOH A 142 257 88 HOH HOH . D 4 HOH A 143 258 89 HOH HOH . D 4 HOH A 144 259 91 HOH HOH . D 4 HOH A 145 260 92 HOH HOH . D 4 HOH A 146 261 94 HOH HOH . D 4 HOH A 147 262 95 HOH HOH . D 4 HOH A 148 263 96 HOH HOH . D 4 HOH A 149 264 97 HOH HOH . D 4 HOH A 150 265 98 HOH HOH . D 4 HOH A 151 266 99 HOH HOH . D 4 HOH A 152 267 101 HOH HOH . D 4 HOH A 153 268 102 HOH HOH . D 4 HOH A 154 269 103 HOH HOH . D 4 HOH A 155 270 104 HOH HOH . D 4 HOH A 156 271 105 HOH HOH . D 4 HOH A 157 272 106 HOH HOH . D 4 HOH A 158 273 107 HOH HOH . D 4 HOH A 159 274 108 HOH HOH . D 4 HOH A 160 275 109 HOH HOH . D 4 HOH A 161 276 110 HOH HOH . D 4 HOH A 162 277 111 HOH HOH . D 4 HOH A 163 278 113 HOH HOH . D 4 HOH A 164 279 114 HOH HOH . D 4 HOH A 165 280 115 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 P P AMP . . . C 3 1.704 2.345 -10.285 1 17.61 ? P AMP 115 A 1 HETATM 2 O O1P AMP . . . C 3 2.458 2.054 -11.563 1 17.64 ? O1P AMP 115 A 1 HETATM 3 O O2P AMP . . . C 3 0.285 1.854 -10.272 1 21.67 ? O2P AMP 115 A 1 HETATM 4 O O3P AMP . . . C 3 2.449 1.974 -9.011 1 17.61 ? O3P AMP 115 A 1 HETATM 5 O O5' AMP . . . C 3 1.647 3.92 -10.059 1 21.69 ? O5' AMP 115 A 1 HETATM 6 C C5' AMP . . . C 3 1.684 4.838 -11.138 1 20.09 ? C5' AMP 115 A 1 HETATM 7 C C4' AMP . . . C 3 1.287 6.151 -10.53 1 18.7 ? C4' AMP 115 A 1 HETATM 8 O O4' AMP . . . C 3 1.779 7.173 -11.376 1 17.61 ? O4' AMP 115 A 1 HETATM 9 C C3' AMP . . . C 3 -0.224 6.318 -10.388 1 17.54 ? C3' AMP 115 A 1 HETATM 10 O O3' AMP . . . C 3 -0.556 6.686 -9.044 1 17.52 ? O3' AMP 115 A 1 HETATM 11 C C2' AMP . . . C 3 -0.549 7.421 -11.385 1 17.92 ? C2' AMP 115 A 1 HETATM 12 O O2' AMP . . . C 3 -1.634 8.259 -10.967 1 17.51 ? O2' AMP 115 A 1 HETATM 13 C C1' AMP . . . C 3 0.776 8.179 -11.434 1 18.01 ? C1' AMP 115 A 1 HETATM 14 N N9 AMP . . . C 3 1.024 8.951 -12.663 1 18.89 ? N9 AMP 115 A 1 HETATM 15 C C8 AMP . . . C 3 0.87 8.461 -13.909 1 19.7 ? C8 AMP 115 A 1 HETATM 16 N N7 AMP . . . C 3 1.198 9.393 -14.83 1 18.93 ? N7 AMP 115 A 1 HETATM 17 C C5 AMP . . . C 3 1.577 10.486 -14.156 1 18.48 ? C5 AMP 115 A 1 HETATM 18 C C6 AMP . . . C 3 2.026 11.813 -14.538 1 17.54 ? C6 AMP 115 A 1 HETATM 19 N N6 AMP . . . C 3 2.141 12.13 -15.851 1 18.88 ? N6 AMP 115 A 1 HETATM 20 N N1 AMP . . . C 3 2.339 12.672 -13.529 1 18.16 ? N1 AMP 115 A 1 HETATM 21 C C2 AMP . . . C 3 2.231 12.353 -12.225 1 18.61 ? C2 AMP 115 A 1 HETATM 22 N N3 AMP . . . C 3 1.798 11.156 -11.803 1 17.74 ? N3 AMP 115 A 1 HETATM 23 C C4 AMP . . . C 3 1.471 10.196 -12.713 1 18.6 ? C4 AMP 115 A 1 # _model_server_stats.io_time_ms 72 _model_server_stats.parse_time_ms 23 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 864 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 23 #