data_1Z0I # _model_server_result.job_id Qa09N9TaKAKB3tb5AJcIeQ _model_server_result.datetime_utc '2024-11-14 19:54:33' _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 1z0i # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":200}' # _entry.id 1Z0I # _exptl.entry_id 1Z0I _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-DIPHOSPHATE" _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 1Z0I _cell.length_a 36.295 _cell.length_b 88.861 _cell.length_c 118.03 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1Z0I _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 ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_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 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 OG1 THR 20 A THR 33 1_555 B MG MG . A MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.143 ? metalc ? metalc2 C O3B GDP . A GDP 200 1_555 B MG MG . A MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.283 ? metalc ? metalc3 B MG MG . A MG 201 1_555 D O HOH . A HOH 217 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.506 ? metalc ? metalc4 B MG MG . A MG 201 1_555 D O HOH . A HOH 222 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.926 ? metalc ? metalc5 B MG MG . A MG 201 1_555 D O HOH . A HOH 228 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.413 ? metalc ? metalc6 B MG MG . A MG 201 1_555 D O HOH . A HOH 229 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.202 ? # _chem_comp.formula 'C10 H15 N5 O11 P2' _chem_comp.formula_weight 443.201 _chem_comp.id GDP _chem_comp.mon_nstd_flag n _chem_comp.name "GUANOSINE-5'-DIPHOSPHATE" _chem_comp.type 'rna linking' _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 PB O1B GDP doub 83 n n PB O2B GDP sing 84 n n PB O3B GDP sing 85 n n PB O3A GDP sing 86 n n O2B HOB2 GDP sing 87 n n O3B HOB3 GDP sing 88 n n O3A PA GDP sing 89 n n PA O1A GDP doub 90 n n PA O2A GDP sing 91 n n PA O5' GDP sing 92 n n O2A HOA2 GDP sing 93 n n O5' C5' GDP sing 94 n n C5' C4' GDP sing 95 n n C5' H5' GDP sing 96 n n C5' "H5''" GDP sing 97 n n C4' O4' GDP sing 98 n n C4' C3' GDP sing 99 n n C4' H4' GDP sing 100 n n O4' C1' GDP sing 101 n n C3' O3' GDP sing 102 n n C3' C2' GDP sing 103 n n C3' H3' GDP sing 104 n n O3' HO3' GDP sing 105 n n C2' O2' GDP sing 106 n n C2' C1' GDP sing 107 n n C2' H2' GDP sing 108 n n O2' HO2' GDP sing 109 n n C1' N9 GDP sing 110 n n C1' H1' GDP sing 111 n n N9 C8 GDP sing 112 n y N9 C4 GDP sing 113 n y C8 N7 GDP doub 114 n y C8 H8 GDP sing 115 n n N7 C5 GDP sing 116 n y C5 C6 GDP sing 117 n n C5 C4 GDP doub 118 n y C6 O6 GDP doub 119 n n C6 N1 GDP sing 120 n n N1 C2 GDP sing 121 n n N1 HN1 GDP sing 122 n n C2 N2 GDP sing 123 n n C2 N3 GDP doub 124 n n N2 HN21 GDP sing 125 n n N2 HN22 GDP sing 126 n n N3 C4 GDP sing 127 n n # _atom_sites.entry_id 1Z0I _atom_sites.fract_transf_matrix[1][1] 0.027552 _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] 0.011254 _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] 0.008472 _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 MG A 1 201 201 MG MG . C 3 GDP A 1 200 200 GDP GDP . D 4 HOH A 1 202 1 HOH HOH . D 4 HOH A 2 203 2 HOH HOH . D 4 HOH A 3 204 3 HOH HOH . D 4 HOH A 4 205 4 HOH HOH . D 4 HOH A 5 206 5 HOH HOH . D 4 HOH A 6 207 7 HOH HOH . D 4 HOH A 7 208 8 HOH HOH . D 4 HOH A 8 209 9 HOH HOH . D 4 HOH A 9 210 10 HOH HOH . D 4 HOH A 10 211 11 HOH HOH . D 4 HOH A 11 212 13 HOH HOH . D 4 HOH A 12 213 15 HOH HOH . D 4 HOH A 13 214 17 HOH HOH . D 4 HOH A 14 215 18 HOH HOH . D 4 HOH A 15 216 20 HOH HOH . D 4 HOH A 16 217 21 HOH HOH . D 4 HOH A 17 218 23 HOH HOH . D 4 HOH A 18 219 24 HOH HOH . D 4 HOH A 19 220 25 HOH HOH . D 4 HOH A 20 221 26 HOH HOH . D 4 HOH A 21 222 27 HOH HOH . D 4 HOH A 22 223 29 HOH HOH . D 4 HOH A 23 224 30 HOH HOH . D 4 HOH A 24 225 31 HOH HOH . D 4 HOH A 25 226 32 HOH HOH . D 4 HOH A 26 227 33 HOH HOH . D 4 HOH A 27 228 34 HOH HOH . D 4 HOH A 28 229 35 HOH HOH . D 4 HOH A 29 230 36 HOH HOH . D 4 HOH A 30 231 38 HOH HOH . D 4 HOH A 31 232 39 HOH HOH . D 4 HOH A 32 233 41 HOH HOH . D 4 HOH A 33 234 42 HOH HOH . D 4 HOH A 34 235 43 HOH HOH . D 4 HOH A 35 236 44 HOH HOH . D 4 HOH A 36 237 45 HOH HOH . D 4 HOH A 37 238 46 HOH HOH . D 4 HOH A 38 239 47 HOH HOH . D 4 HOH A 39 240 48 HOH HOH . D 4 HOH A 40 241 49 HOH HOH . D 4 HOH A 41 242 50 HOH HOH . D 4 HOH A 42 243 52 HOH HOH . D 4 HOH A 43 244 53 HOH HOH . D 4 HOH A 44 245 54 HOH HOH . D 4 HOH A 45 246 56 HOH HOH . D 4 HOH A 46 247 57 HOH HOH . D 4 HOH A 47 248 58 HOH HOH . D 4 HOH A 48 249 59 HOH HOH . D 4 HOH A 49 250 60 HOH HOH . D 4 HOH A 50 251 62 HOH HOH . D 4 HOH A 51 252 63 HOH HOH . D 4 HOH A 52 253 64 HOH HOH . D 4 HOH A 53 254 65 HOH HOH . D 4 HOH A 54 255 66 HOH HOH . D 4 HOH A 55 256 67 HOH HOH . D 4 HOH A 56 257 68 HOH HOH . D 4 HOH A 57 258 69 HOH HOH . D 4 HOH A 58 259 70 HOH HOH . D 4 HOH A 59 260 73 HOH HOH . D 4 HOH A 60 261 74 HOH HOH . D 4 HOH A 61 262 75 HOH HOH . D 4 HOH A 62 263 76 HOH HOH . D 4 HOH A 63 264 78 HOH HOH . D 4 HOH A 64 265 79 HOH HOH . D 4 HOH A 65 266 80 HOH HOH . D 4 HOH A 66 267 81 HOH HOH . D 4 HOH A 67 268 82 HOH HOH . D 4 HOH A 68 269 83 HOH HOH . D 4 HOH A 69 270 84 HOH HOH . D 4 HOH A 70 271 85 HOH HOH . D 4 HOH A 71 272 86 HOH HOH . D 4 HOH A 72 273 87 HOH HOH . D 4 HOH A 73 274 89 HOH HOH . D 4 HOH A 74 275 90 HOH HOH . D 4 HOH A 75 276 91 HOH HOH . D 4 HOH A 76 277 94 HOH HOH . D 4 HOH A 77 278 96 HOH HOH . D 4 HOH A 78 279 97 HOH HOH . D 4 HOH A 79 280 98 HOH HOH . D 4 HOH A 80 281 99 HOH HOH . D 4 HOH A 81 282 100 HOH HOH . D 4 HOH A 82 283 101 HOH HOH . D 4 HOH A 83 284 102 HOH HOH . D 4 HOH A 84 285 103 HOH HOH . D 4 HOH A 85 286 104 HOH HOH . D 4 HOH A 86 287 105 HOH HOH . D 4 HOH A 87 288 107 HOH HOH . D 4 HOH A 88 289 108 HOH HOH . D 4 HOH A 89 290 109 HOH HOH . D 4 HOH A 90 291 111 HOH HOH . D 4 HOH A 91 292 113 HOH HOH . D 4 HOH A 92 293 114 HOH HOH . D 4 HOH A 93 294 115 HOH HOH . D 4 HOH A 94 295 116 HOH HOH . D 4 HOH A 95 296 117 HOH HOH . D 4 HOH A 96 297 118 HOH HOH . D 4 HOH A 97 298 120 HOH HOH . D 4 HOH A 98 299 123 HOH HOH . D 4 HOH A 99 300 124 HOH HOH . D 4 HOH A 100 301 126 HOH HOH . D 4 HOH A 101 302 127 HOH HOH . D 4 HOH A 102 303 128 HOH HOH . D 4 HOH A 103 304 129 HOH HOH . D 4 HOH A 104 305 130 HOH HOH . D 4 HOH A 105 306 131 HOH HOH . D 4 HOH A 106 307 133 HOH HOH . D 4 HOH A 107 308 134 HOH HOH . D 4 HOH A 108 309 135 HOH HOH . D 4 HOH A 109 310 138 HOH HOH . D 4 HOH A 110 311 139 HOH HOH . D 4 HOH A 111 312 140 HOH HOH . D 4 HOH A 112 313 141 HOH HOH . D 4 HOH A 113 314 142 HOH HOH . D 4 HOH A 114 315 143 HOH HOH . D 4 HOH A 115 316 145 HOH HOH . D 4 HOH A 116 317 146 HOH HOH . D 4 HOH A 117 318 147 HOH HOH . D 4 HOH A 118 319 148 HOH HOH . D 4 HOH A 119 320 149 HOH HOH . D 4 HOH A 120 321 151 HOH HOH . D 4 HOH A 121 322 153 HOH HOH . D 4 HOH A 122 323 157 HOH HOH . D 4 HOH A 123 324 161 HOH HOH . D 4 HOH A 124 325 162 HOH HOH . D 4 HOH A 125 326 163 HOH HOH . D 4 HOH A 126 327 164 HOH HOH . D 4 HOH A 127 328 166 HOH HOH . D 4 HOH A 128 329 167 HOH HOH . D 4 HOH A 129 330 168 HOH HOH . D 4 HOH A 130 331 169 HOH HOH . D 4 HOH A 131 332 172 HOH HOH . D 4 HOH A 132 333 174 HOH HOH . D 4 HOH A 133 334 175 HOH HOH . D 4 HOH A 134 335 176 HOH HOH . D 4 HOH A 135 336 177 HOH HOH . D 4 HOH A 136 337 179 HOH HOH . D 4 HOH A 137 338 180 HOH HOH . D 4 HOH A 138 339 182 HOH HOH . D 4 HOH A 139 340 184 HOH HOH . D 4 HOH A 140 341 185 HOH HOH . D 4 HOH A 141 342 186 HOH HOH . D 4 HOH A 142 343 188 HOH HOH . D 4 HOH A 143 344 189 HOH HOH . D 4 HOH A 144 345 191 HOH HOH . D 4 HOH A 145 346 192 HOH HOH . D 4 HOH A 146 347 193 HOH HOH . D 4 HOH A 147 348 194 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 PB GDP . . . C 3 12.335 27.487 7.131 1 16.12 ? PB GDP 200 A 1 HETATM 2 O O1B GDP . . . C 3 12.84 26.065 7.297 1 17.37 ? O1B GDP 200 A 1 HETATM 3 O O2B GDP . . . C 3 11.295 27.72 8.185 1 14.02 ? O2B GDP 200 A 1 HETATM 4 O O3B GDP . . . C 3 13.476 28.47 7.282 1 14.84 ? O3B GDP 200 A 1 HETATM 5 O O3A GDP . . . C 3 11.68 27.603 5.642 1 17.17 ? O3A GDP 200 A 1 HETATM 6 P PA GDP . . . C 3 12.417 28.195 4.328 1 17.48 ? PA GDP 200 A 1 HETATM 7 O O1A GDP . . . C 3 12.526 29.722 4.353 1 19.13 ? O1A GDP 200 A 1 HETATM 8 O O2A GDP . . . C 3 13.763 27.632 4.042 1 18.86 ? O2A GDP 200 A 1 HETATM 9 O O5' GDP . . . C 3 11.409 27.821 3.144 1 18.68 ? O5' GDP 200 A 1 HETATM 10 C C5' GDP . . . C 3 11.084 26.493 2.765 1 20.48 ? C5' GDP 200 A 1 HETATM 11 C C4' GDP . . . C 3 10.577 26.497 1.312 1 21.65 ? C4' GDP 200 A 1 HETATM 12 O O4' GDP . . . C 3 9.287 27.106 1.161 1 22.09 ? O4' GDP 200 A 1 HETATM 13 C C3' GDP . . . C 3 11.496 27.244 0.371 1 21.18 ? C3' GDP 200 A 1 HETATM 14 O O3' GDP . . . C 3 11.371 26.595 -0.88 1 20.53 ? O3' GDP 200 A 1 HETATM 15 C C2' GDP . . . C 3 10.861 28.597 0.196 1 22.83 ? C2' GDP 200 A 1 HETATM 16 O O2' GDP . . . C 3 11.274 29.212 -1.04 1 24.14 ? O2' GDP 200 A 1 HETATM 17 C C1' GDP . . . C 3 9.385 28.225 0.258 1 23 ? C1' GDP 200 A 1 HETATM 18 N N9 GDP . . . C 3 8.541 29.353 0.718 1 22.86 ? N9 GDP 200 A 1 HETATM 19 C C8 GDP . . . C 3 8.802 30.167 1.755 1 23.48 ? C8 GDP 200 A 1 HETATM 20 N N7 GDP . . . C 3 7.835 31.107 1.904 1 23.51 ? N7 GDP 200 A 1 HETATM 21 C C5 GDP . . . C 3 6.913 30.883 0.96 1 22.85 ? C5 GDP 200 A 1 HETATM 22 C C6 GDP . . . C 3 5.638 31.52 0.576 1 22.79 ? C6 GDP 200 A 1 HETATM 23 O O6 GDP . . . C 3 5.197 32.509 1.204 1 22.35 ? O6 GDP 200 A 1 HETATM 24 N N1 GDP . . . C 3 4.976 30.991 -0.464 1 23.99 ? N1 GDP 200 A 1 HETATM 25 C C2 GDP . . . C 3 5.442 29.926 -1.173 1 23.82 ? C2 GDP 200 A 1 HETATM 26 N N2 GDP . . . C 3 4.691 29.491 -2.216 1 22.83 ? N2 GDP 200 A 1 HETATM 27 N N3 GDP . . . C 3 6.617 29.289 -0.881 1 22.26 ? N3 GDP 200 A 1 HETATM 28 C C4 GDP . . . C 3 7.375 29.722 0.169 1 23.65 ? C4 GDP 200 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 351 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 28 #