data_1RQ7 # _model_server_result.job_id xmh8BfunzM1CSlHp47yhKw _model_server_result.datetime_utc '2024-11-14 16:59:48' _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 1rq7 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":380}' # _entry.id 1RQ7 # _exptl.entry_id 1RQ7 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 2 _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 120 _cell.entry_id 1RQ7 _cell.length_a 88.619 _cell.length_b 88.619 _cell.length_c 179.196 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1RQ7 _symmetry.cell_setting ? _symmetry.Int_Tables_number 170 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65' # _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 _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 # _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 1RQ7 _atom_sites.fract_transf_matrix[1][1] 0.011284 _atom_sites.fract_transf_matrix[1][2] 0.006515 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01303 _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] 0.00558 _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 GDP A 1 380 100 GDP GDP . D 3 HOH A 1 381 101 HOH HOH . D 3 HOH A 2 382 105 HOH HOH . D 3 HOH A 3 383 108 HOH HOH . D 3 HOH A 4 384 111 HOH HOH . D 3 HOH A 5 385 112 HOH HOH . D 3 HOH A 6 386 115 HOH HOH . D 3 HOH A 7 387 116 HOH HOH . D 3 HOH A 8 388 118 HOH HOH . D 3 HOH A 9 389 121 HOH HOH . D 3 HOH A 10 390 122 HOH HOH . D 3 HOH A 11 391 126 HOH HOH . D 3 HOH A 12 392 127 HOH HOH . D 3 HOH A 13 393 133 HOH HOH . D 3 HOH A 14 394 134 HOH HOH . D 3 HOH A 15 395 135 HOH HOH . D 3 HOH A 16 396 140 HOH HOH . D 3 HOH A 17 397 141 HOH HOH . D 3 HOH A 18 398 142 HOH HOH . D 3 HOH A 19 399 143 HOH HOH . D 3 HOH A 20 400 146 HOH HOH . D 3 HOH A 21 401 147 HOH HOH . D 3 HOH A 22 402 152 HOH HOH . D 3 HOH A 23 403 157 HOH HOH . D 3 HOH A 24 404 161 HOH HOH . D 3 HOH A 25 405 163 HOH HOH . D 3 HOH A 26 406 167 HOH HOH . D 3 HOH A 27 407 175 HOH HOH . D 3 HOH A 28 408 180 HOH HOH . D 3 HOH A 29 409 182 HOH HOH . D 3 HOH A 30 410 183 HOH HOH . D 3 HOH A 31 411 184 HOH HOH . D 3 HOH A 32 412 185 HOH HOH . D 3 HOH A 33 413 188 HOH HOH . D 3 HOH A 34 414 189 HOH HOH . D 3 HOH A 35 415 190 HOH HOH . D 3 HOH A 36 416 191 HOH HOH . D 3 HOH A 37 417 192 HOH HOH . D 3 HOH A 38 418 193 HOH HOH . D 3 HOH A 39 419 195 HOH HOH . D 3 HOH A 40 420 196 HOH HOH . D 3 HOH A 41 421 199 HOH HOH . D 3 HOH A 42 422 201 HOH HOH . D 3 HOH A 43 423 202 HOH HOH . D 3 HOH A 44 424 207 HOH HOH . D 3 HOH A 45 425 208 HOH HOH . D 3 HOH A 46 426 217 HOH HOH . D 3 HOH A 47 427 219 HOH HOH . D 3 HOH A 48 428 220 HOH HOH . D 3 HOH A 49 429 221 HOH HOH . D 3 HOH A 50 430 224 HOH HOH . D 3 HOH A 51 431 225 HOH HOH . D 3 HOH A 52 432 226 HOH HOH . D 3 HOH A 53 433 227 HOH HOH . D 3 HOH A 54 434 228 HOH HOH . D 3 HOH A 55 435 230 HOH HOH . D 3 HOH A 56 436 232 HOH HOH . D 3 HOH A 57 437 234 HOH HOH . D 3 HOH A 58 438 235 HOH HOH . D 3 HOH A 59 439 238 HOH HOH . D 3 HOH A 60 440 241 HOH HOH . D 3 HOH A 61 441 244 HOH HOH . D 3 HOH A 62 442 245 HOH HOH . D 3 HOH A 63 443 246 HOH HOH . D 3 HOH A 64 444 247 HOH HOH . D 3 HOH A 65 445 249 HOH HOH . D 3 HOH A 66 446 251 HOH HOH . D 3 HOH A 67 447 253 HOH HOH . D 3 HOH A 68 448 256 HOH HOH . D 3 HOH A 69 449 257 HOH HOH . D 3 HOH A 70 450 260 HOH HOH . D 3 HOH A 71 451 262 HOH HOH . D 3 HOH A 72 452 263 HOH HOH . D 3 HOH A 73 453 264 HOH HOH . D 3 HOH A 74 454 265 HOH HOH . D 3 HOH A 75 455 267 HOH HOH . D 3 HOH A 76 456 268 HOH HOH . D 3 HOH A 77 457 272 HOH HOH . D 3 HOH A 78 458 273 HOH HOH . D 3 HOH A 79 459 276 HOH HOH . D 3 HOH A 80 460 278 HOH HOH . D 3 HOH A 81 461 279 HOH HOH . D 3 HOH A 82 462 280 HOH HOH . D 3 HOH A 83 463 281 HOH HOH . E 3 HOH B 1 380 102 HOH HOH . E 3 HOH B 2 381 103 HOH HOH . E 3 HOH B 3 382 104 HOH HOH . E 3 HOH B 4 383 106 HOH HOH . E 3 HOH B 5 384 107 HOH HOH . E 3 HOH B 6 385 109 HOH HOH . E 3 HOH B 7 386 110 HOH HOH . E 3 HOH B 8 387 113 HOH HOH . E 3 HOH B 9 388 114 HOH HOH . E 3 HOH B 10 389 117 HOH HOH . E 3 HOH B 11 390 119 HOH HOH . E 3 HOH B 12 391 120 HOH HOH . E 3 HOH B 13 392 123 HOH HOH . E 3 HOH B 14 393 124 HOH HOH . E 3 HOH B 15 394 125 HOH HOH . E 3 HOH B 16 395 128 HOH HOH . E 3 HOH B 17 396 129 HOH HOH . E 3 HOH B 18 397 130 HOH HOH . E 3 HOH B 19 398 131 HOH HOH . E 3 HOH B 20 399 132 HOH HOH . E 3 HOH B 21 400 136 HOH HOH . E 3 HOH B 22 401 137 HOH HOH . E 3 HOH B 23 402 138 HOH HOH . E 3 HOH B 24 403 139 HOH HOH . E 3 HOH B 25 404 144 HOH HOH . E 3 HOH B 26 405 145 HOH HOH . E 3 HOH B 27 406 148 HOH HOH . E 3 HOH B 28 407 149 HOH HOH . E 3 HOH B 29 408 150 HOH HOH . E 3 HOH B 30 409 151 HOH HOH . E 3 HOH B 31 410 153 HOH HOH . E 3 HOH B 32 411 154 HOH HOH . E 3 HOH B 33 412 155 HOH HOH . E 3 HOH B 34 413 156 HOH HOH . E 3 HOH B 35 414 158 HOH HOH . E 3 HOH B 36 415 159 HOH HOH . E 3 HOH B 37 416 160 HOH HOH . E 3 HOH B 38 417 162 HOH HOH . E 3 HOH B 39 418 164 HOH HOH . E 3 HOH B 40 419 165 HOH HOH . E 3 HOH B 41 420 166 HOH HOH . E 3 HOH B 42 421 168 HOH HOH . E 3 HOH B 43 422 169 HOH HOH . E 3 HOH B 44 423 170 HOH HOH . E 3 HOH B 45 424 171 HOH HOH . E 3 HOH B 46 425 172 HOH HOH . E 3 HOH B 47 426 173 HOH HOH . E 3 HOH B 48 427 174 HOH HOH . E 3 HOH B 49 428 176 HOH HOH . E 3 HOH B 50 429 177 HOH HOH . E 3 HOH B 51 430 178 HOH HOH . E 3 HOH B 52 431 179 HOH HOH . E 3 HOH B 53 432 181 HOH HOH . E 3 HOH B 54 433 186 HOH HOH . E 3 HOH B 55 434 187 HOH HOH . E 3 HOH B 56 435 194 HOH HOH . E 3 HOH B 57 436 197 HOH HOH . E 3 HOH B 58 437 198 HOH HOH . E 3 HOH B 59 438 200 HOH HOH . E 3 HOH B 60 439 203 HOH HOH . E 3 HOH B 61 440 205 HOH HOH . E 3 HOH B 62 441 206 HOH HOH . E 3 HOH B 63 442 209 HOH HOH . E 3 HOH B 64 443 210 HOH HOH . E 3 HOH B 65 444 211 HOH HOH . E 3 HOH B 66 445 212 HOH HOH . E 3 HOH B 67 446 213 HOH HOH . E 3 HOH B 68 447 214 HOH HOH . E 3 HOH B 69 448 215 HOH HOH . E 3 HOH B 70 449 216 HOH HOH . E 3 HOH B 71 450 218 HOH HOH . E 3 HOH B 72 451 222 HOH HOH . E 3 HOH B 73 452 223 HOH HOH . E 3 HOH B 74 453 229 HOH HOH . E 3 HOH B 75 454 231 HOH HOH . E 3 HOH B 76 455 233 HOH HOH . E 3 HOH B 77 456 236 HOH HOH . E 3 HOH B 78 457 237 HOH HOH . E 3 HOH B 79 458 239 HOH HOH . E 3 HOH B 80 459 240 HOH HOH . E 3 HOH B 81 460 242 HOH HOH . E 3 HOH B 82 461 243 HOH HOH . E 3 HOH B 83 462 248 HOH HOH . E 3 HOH B 84 463 250 HOH HOH . E 3 HOH B 85 464 252 HOH HOH . E 3 HOH B 86 465 254 HOH HOH . E 3 HOH B 87 466 255 HOH HOH . E 3 HOH B 88 467 258 HOH HOH . E 3 HOH B 89 468 259 HOH HOH . E 3 HOH B 90 469 261 HOH HOH . E 3 HOH B 91 470 266 HOH HOH . E 3 HOH B 92 471 269 HOH HOH . E 3 HOH B 93 472 270 HOH HOH . E 3 HOH B 94 473 271 HOH HOH . E 3 HOH B 95 474 274 HOH HOH . E 3 HOH B 96 475 275 HOH HOH . E 3 HOH B 97 476 277 HOH HOH . E 3 HOH B 98 477 282 HOH HOH . E 3 HOH B 99 478 283 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 2 -6.78 40.888 3.288 1 27.81 ? PB GDP 380 A 1 HETATM 2 O O1B GDP . . . C 2 -5.357 40.509 3.456 1 25.86 ? O1B GDP 380 A 1 HETATM 3 O O2B GDP . . . C 2 -7.293 41.96 4.236 1 24.53 ? O2B GDP 380 A 1 HETATM 4 O O3B GDP . . . C 2 -7.113 41.281 1.784 1 28.29 ? O3B GDP 380 A 1 HETATM 5 O O3A GDP . . . C 2 -7.609 39.562 3.631 1 25.77 ? O3A GDP 380 A 1 HETATM 6 P PA GDP . . . C 2 -8.094 39.051 5.054 1 24.77 ? PA GDP 380 A 1 HETATM 7 O O1A GDP . . . C 2 -7.015 39.195 6.084 1 22.89 ? O1A GDP 380 A 1 HETATM 8 O O2A GDP . . . C 2 -9.497 39.604 5.427 1 24.12 ? O2A GDP 380 A 1 HETATM 9 O O5' GDP . . . C 2 -8.198 37.544 4.662 1 23.71 ? O5' GDP 380 A 1 HETATM 10 C C5' GDP . . . C 2 -7.055 36.741 4.456 1 25.95 ? C5' GDP 380 A 1 HETATM 11 C C4' GDP . . . C 2 -7.251 35.444 5.247 1 27.2 ? C4' GDP 380 A 1 HETATM 12 O O4' GDP . . . C 2 -7.309 35.746 6.641 1 25.08 ? O4' GDP 380 A 1 HETATM 13 C C3' GDP . . . C 2 -8.569 34.704 4.955 1 23.76 ? C3' GDP 380 A 1 HETATM 14 O O3' GDP . . . C 2 -8.509 33.912 3.777 1 25.44 ? O3' GDP 380 A 1 HETATM 15 C C2' GDP . . . C 2 -8.785 33.92 6.228 1 23.86 ? C2' GDP 380 A 1 HETATM 16 O O2' GDP . . . C 2 -8.083 32.688 6.283 1 23.7 ? O2' GDP 380 A 1 HETATM 17 C C1' GDP . . . C 2 -8.184 34.829 7.276 1 24.51 ? C1' GDP 380 A 1 HETATM 18 N N9 GDP . . . C 2 -9.196 35.592 8.024 1 24.22 ? N9 GDP 380 A 1 HETATM 19 C C8 GDP . . . C 2 -10.376 36.163 7.592 1 22.63 ? C8 GDP 380 A 1 HETATM 20 N N7 GDP . . . C 2 -10.961 36.817 8.62 1 22.57 ? N7 GDP 380 A 1 HETATM 21 C C5 GDP . . . C 2 -10.161 36.618 9.721 1 23.59 ? C5 GDP 380 A 1 HETATM 22 C C6 GDP . . . C 2 -10.25 37.002 11.054 1 22.41 ? C6 GDP 380 A 1 HETATM 23 O O6 GDP . . . C 2 -11.191 37.658 11.483 1 22.19 ? O6 GDP 380 A 1 HETATM 24 N N1 GDP . . . C 2 -9.26 36.639 11.939 1 24.1 ? N1 GDP 380 A 1 HETATM 25 C C2 GDP . . . C 2 -8.184 35.908 11.509 1 25.15 ? C2 GDP 380 A 1 HETATM 26 N N2 GDP . . . C 2 -7.198 35.632 12.345 1 22.81 ? N2 GDP 380 A 1 HETATM 27 N N3 GDP . . . C 2 -8.124 35.5 10.197 1 25.2 ? N3 GDP 380 A 1 HETATM 28 C C4 GDP . . . C 2 -9.076 35.861 9.339 1 22.03 ? C4 GDP 380 A 1 # _model_server_stats.io_time_ms 65 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 290 _model_server_stats.encode_time_ms 38 _model_server_stats.element_count 28 #