data_5IPE # _model_server_result.job_id uTBoqf2Py5yHKJNCmdZkUg _model_server_result.datetime_utc '2025-03-27 22:05:37' _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 5ipe # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":201}' # _entry.id 5IPE # _exptl.entry_id 5IPE _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 379.286 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-S-phosphono-5'-thioguanosine" _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 94.72 _cell.angle_gamma 90 _cell.entry_id 5IPE _cell.length_a 78.27 _cell.length_b 46.311 _cell.length_c 63.963 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5IPE _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _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,E,F,G,H _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 H14 N5 O7 P S' _chem_comp.formula_weight 379.286 _chem_comp.id 6CG _chem_comp.mon_nstd_flag . _chem_comp.name "5'-S-phosphono-5'-thioguanosine" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'TrpGMPS hydrolysis product' # 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 O6 C6 6CG doub 1 n n N1 C6 6CG sing 2 n n N1 C2 6CG doub 3 n n C6 C5 6CG sing 4 n n N2 C2 6CG sing 5 n n C2 N3 6CG sing 6 n n C5 N7 6CG sing 7 n y C5 C4 6CG doub 8 n y N7 C8 6CG doub 9 n y N3 C4 6CG sing 10 n n C4 N9 6CG sing 11 n y C8 N9 6CG sing 12 n y N9 C1' 6CG sing 13 n n O2' C2' 6CG sing 14 n n C1' C2' 6CG sing 15 n n C1' O4' 6CG sing 16 n n C2' C3' 6CG sing 17 n n O4' C4' 6CG sing 18 n n C3' C4' 6CG sing 19 n n C3' O3' 6CG sing 20 n n C4' C5' 6CG sing 21 n n C5' S5' 6CG sing 22 n n S5' P 6CG sing 23 n n O1P P 6CG doub 24 n n P O3P 6CG sing 25 n n P O2P 6CG sing 26 n n N2 H1 6CG sing 27 n n N2 H2 6CG sing 28 n n N3 H3 6CG sing 29 n n C8 H4 6CG sing 30 n n C1' H5 6CG sing 31 n n C3' H6 6CG sing 32 n n C4' H7 6CG sing 33 n n C5' H8 6CG sing 34 n n C5' H9 6CG sing 35 n n C2' H10 6CG sing 36 n n O2' H11 6CG sing 37 n n O3' H12 6CG sing 38 n n O2P H13 6CG sing 39 n n O3P H14 6CG sing 40 n n # _atom_sites.entry_id 5IPE _atom_sites.fract_transf_matrix[1][1] 0.012776 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001054 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.021593 _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] 0.015687 _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 6CG A 1 201 1 6CG 801 . D 3 CL B 1 201 1 CL CL . E 4 EDO B 1 202 1 EDO EDO . F 4 EDO B 1 203 1 EDO EDO . G 5 HOH A 1 301 58 HOH HOH . G 5 HOH A 2 302 118 HOH HOH . G 5 HOH A 3 303 226 HOH HOH . G 5 HOH A 4 304 191 HOH HOH . G 5 HOH A 5 305 136 HOH HOH . G 5 HOH A 6 306 197 HOH HOH . G 5 HOH A 7 307 96 HOH HOH . G 5 HOH A 8 308 27 HOH HOH . G 5 HOH A 9 309 114 HOH HOH . G 5 HOH A 10 310 64 HOH HOH . G 5 HOH A 11 311 47 HOH HOH . G 5 HOH A 12 312 53 HOH HOH . G 5 HOH A 13 313 8 HOH HOH . G 5 HOH A 14 314 19 HOH HOH . G 5 HOH A 15 315 20 HOH HOH . G 5 HOH A 16 316 6 HOH HOH . G 5 HOH A 17 317 42 HOH HOH . G 5 HOH A 18 318 142 HOH HOH . G 5 HOH A 19 319 181 HOH HOH . G 5 HOH A 20 320 216 HOH HOH . G 5 HOH A 21 321 122 HOH HOH . G 5 HOH A 22 322 13 HOH HOH . G 5 HOH A 23 323 179 HOH HOH . G 5 HOH A 24 324 3 HOH HOH . G 5 HOH A 25 325 50 HOH HOH . G 5 HOH A 26 326 206 HOH HOH . G 5 HOH A 27 327 99 HOH HOH . G 5 HOH A 28 328 172 HOH HOH . G 5 HOH A 29 329 88 HOH HOH . G 5 HOH A 30 330 26 HOH HOH . G 5 HOH A 31 331 31 HOH HOH . G 5 HOH A 32 332 160 HOH HOH . G 5 HOH A 33 333 132 HOH HOH . G 5 HOH A 34 334 33 HOH HOH . G 5 HOH A 35 335 174 HOH HOH . G 5 HOH A 36 336 7 HOH HOH . G 5 HOH A 37 337 61 HOH HOH . G 5 HOH A 38 338 56 HOH HOH . G 5 HOH A 39 339 182 HOH HOH . G 5 HOH A 40 340 98 HOH HOH . G 5 HOH A 41 341 185 HOH HOH . G 5 HOH A 42 342 242 HOH HOH . G 5 HOH A 43 343 29 HOH HOH . G 5 HOH A 44 344 166 HOH HOH . G 5 HOH A 45 345 84 HOH HOH . G 5 HOH A 46 346 168 HOH HOH . G 5 HOH A 47 347 10 HOH HOH . G 5 HOH A 48 348 130 HOH HOH . G 5 HOH A 49 349 106 HOH HOH . G 5 HOH A 50 350 23 HOH HOH . G 5 HOH A 51 351 77 HOH HOH . G 5 HOH A 52 352 54 HOH HOH . G 5 HOH A 53 353 57 HOH HOH . G 5 HOH A 54 354 104 HOH HOH . G 5 HOH A 55 355 11 HOH HOH . G 5 HOH A 56 356 186 HOH HOH . G 5 HOH A 57 357 36 HOH HOH . G 5 HOH A 58 358 225 HOH HOH . G 5 HOH A 59 359 83 HOH HOH . G 5 HOH A 60 360 131 HOH HOH . G 5 HOH A 61 361 201 HOH HOH . G 5 HOH A 62 362 214 HOH HOH . G 5 HOH A 63 363 90 HOH HOH . G 5 HOH A 64 364 141 HOH HOH . G 5 HOH A 65 365 4 HOH HOH . G 5 HOH A 66 366 75 HOH HOH . G 5 HOH A 67 367 229 HOH HOH . G 5 HOH A 68 368 2 HOH HOH . G 5 HOH A 69 369 137 HOH HOH . G 5 HOH A 70 370 178 HOH HOH . G 5 HOH A 71 371 212 HOH HOH . G 5 HOH A 72 372 62 HOH HOH . G 5 HOH A 73 373 116 HOH HOH . G 5 HOH A 74 374 176 HOH HOH . G 5 HOH A 75 375 34 HOH HOH . G 5 HOH A 76 376 97 HOH HOH . G 5 HOH A 77 377 108 HOH HOH . G 5 HOH A 78 378 145 HOH HOH . G 5 HOH A 79 379 25 HOH HOH . G 5 HOH A 80 380 128 HOH HOH . G 5 HOH A 81 381 48 HOH HOH . G 5 HOH A 82 382 80 HOH HOH . G 5 HOH A 83 383 79 HOH HOH . G 5 HOH A 84 384 76 HOH HOH . G 5 HOH A 85 385 92 HOH HOH . G 5 HOH A 86 386 51 HOH HOH . G 5 HOH A 87 387 117 HOH HOH . G 5 HOH A 88 388 24 HOH HOH . G 5 HOH A 89 389 169 HOH HOH . G 5 HOH A 90 390 170 HOH HOH . G 5 HOH A 91 391 208 HOH HOH . G 5 HOH A 92 392 60 HOH HOH . G 5 HOH A 93 393 249 HOH HOH . G 5 HOH A 94 394 41 HOH HOH . G 5 HOH A 95 395 193 HOH HOH . G 5 HOH A 96 396 220 HOH HOH . G 5 HOH A 97 397 159 HOH HOH . G 5 HOH A 98 398 241 HOH HOH . G 5 HOH A 99 399 115 HOH HOH . G 5 HOH A 100 400 246 HOH HOH . G 5 HOH A 101 401 112 HOH HOH . G 5 HOH A 102 402 73 HOH HOH . G 5 HOH A 103 403 211 HOH HOH . G 5 HOH A 104 404 1 HOH HOH . G 5 HOH A 105 405 52 HOH HOH . G 5 HOH A 106 406 194 HOH HOH . G 5 HOH A 107 407 244 HOH HOH . G 5 HOH A 108 408 188 HOH HOH . G 5 HOH A 109 409 217 HOH HOH . G 5 HOH A 110 410 237 HOH HOH . G 5 HOH A 111 411 222 HOH HOH . G 5 HOH A 112 412 175 HOH HOH . G 5 HOH A 113 413 144 HOH HOH . G 5 HOH A 114 414 143 HOH HOH . G 5 HOH A 115 415 192 HOH HOH . G 5 HOH A 116 416 152 HOH HOH . G 5 HOH A 117 417 133 HOH HOH . G 5 HOH A 118 418 161 HOH HOH . G 5 HOH A 119 419 219 HOH HOH . G 5 HOH A 120 420 205 HOH HOH . G 5 HOH A 121 421 124 HOH HOH . G 5 HOH A 122 422 200 HOH HOH . G 5 HOH A 123 423 63 HOH HOH . G 5 HOH A 124 424 162 HOH HOH . G 5 HOH A 125 425 85 HOH HOH . G 5 HOH A 126 426 163 HOH HOH . G 5 HOH A 127 427 120 HOH HOH . G 5 HOH A 128 428 202 HOH HOH . G 5 HOH A 129 429 195 HOH HOH . G 5 HOH A 130 430 121 HOH HOH . G 5 HOH A 131 431 87 HOH HOH . G 5 HOH A 132 432 67 HOH HOH . G 5 HOH A 133 433 173 HOH HOH . G 5 HOH A 134 434 180 HOH HOH . G 5 HOH A 135 435 95 HOH HOH . G 5 HOH A 136 436 215 HOH HOH . G 5 HOH A 137 437 213 HOH HOH . H 5 HOH B 1 301 245 HOH HOH . H 5 HOH B 2 302 236 HOH HOH . H 5 HOH B 3 303 113 HOH HOH . H 5 HOH B 4 304 65 HOH HOH . H 5 HOH B 5 305 55 HOH HOH . H 5 HOH B 6 306 243 HOH HOH . H 5 HOH B 7 307 5 HOH HOH . H 5 HOH B 8 308 37 HOH HOH . H 5 HOH B 9 309 248 HOH HOH . H 5 HOH B 10 310 154 HOH HOH . H 5 HOH B 11 311 30 HOH HOH . H 5 HOH B 12 312 72 HOH HOH . H 5 HOH B 13 313 38 HOH HOH . H 5 HOH B 14 314 70 HOH HOH . H 5 HOH B 15 315 59 HOH HOH . H 5 HOH B 16 316 221 HOH HOH . H 5 HOH B 17 317 235 HOH HOH . H 5 HOH B 18 318 22 HOH HOH . H 5 HOH B 19 319 232 HOH HOH . H 5 HOH B 20 320 69 HOH HOH . H 5 HOH B 21 321 71 HOH HOH . H 5 HOH B 22 322 35 HOH HOH . H 5 HOH B 23 323 18 HOH HOH . H 5 HOH B 24 324 28 HOH HOH . H 5 HOH B 25 325 14 HOH HOH . H 5 HOH B 26 326 218 HOH HOH . H 5 HOH B 27 327 135 HOH HOH . H 5 HOH B 28 328 157 HOH HOH . H 5 HOH B 29 329 139 HOH HOH . H 5 HOH B 30 330 224 HOH HOH . H 5 HOH B 31 331 119 HOH HOH . H 5 HOH B 32 332 223 HOH HOH . H 5 HOH B 33 333 9 HOH HOH . H 5 HOH B 34 334 140 HOH HOH . H 5 HOH B 35 335 227 HOH HOH . H 5 HOH B 36 336 44 HOH HOH . H 5 HOH B 37 337 12 HOH HOH . H 5 HOH B 38 338 101 HOH HOH . H 5 HOH B 39 339 233 HOH HOH . H 5 HOH B 40 340 16 HOH HOH . H 5 HOH B 41 341 209 HOH HOH . H 5 HOH B 42 342 93 HOH HOH . H 5 HOH B 43 343 40 HOH HOH . H 5 HOH B 44 344 49 HOH HOH . H 5 HOH B 45 345 39 HOH HOH . H 5 HOH B 46 346 158 HOH HOH . H 5 HOH B 47 347 103 HOH HOH . H 5 HOH B 48 348 155 HOH HOH . H 5 HOH B 49 349 126 HOH HOH . H 5 HOH B 50 350 68 HOH HOH . H 5 HOH B 51 351 91 HOH HOH . H 5 HOH B 52 352 89 HOH HOH . H 5 HOH B 53 353 150 HOH HOH . H 5 HOH B 54 354 183 HOH HOH . H 5 HOH B 55 355 32 HOH HOH . H 5 HOH B 56 356 129 HOH HOH . H 5 HOH B 57 357 149 HOH HOH . H 5 HOH B 58 358 43 HOH HOH . H 5 HOH B 59 359 123 HOH HOH . H 5 HOH B 60 360 239 HOH HOH . H 5 HOH B 61 361 15 HOH HOH . H 5 HOH B 62 362 231 HOH HOH . H 5 HOH B 63 363 146 HOH HOH . H 5 HOH B 64 364 105 HOH HOH . H 5 HOH B 65 365 127 HOH HOH . H 5 HOH B 66 366 78 HOH HOH . H 5 HOH B 67 367 46 HOH HOH . H 5 HOH B 68 368 190 HOH HOH . H 5 HOH B 69 369 74 HOH HOH . H 5 HOH B 70 370 204 HOH HOH . H 5 HOH B 71 371 45 HOH HOH . H 5 HOH B 72 372 177 HOH HOH . H 5 HOH B 73 373 86 HOH HOH . H 5 HOH B 74 374 109 HOH HOH . H 5 HOH B 75 375 107 HOH HOH . H 5 HOH B 76 376 187 HOH HOH . H 5 HOH B 77 377 21 HOH HOH . H 5 HOH B 78 378 171 HOH HOH . H 5 HOH B 79 379 151 HOH HOH . H 5 HOH B 80 380 66 HOH HOH . H 5 HOH B 81 381 100 HOH HOH . H 5 HOH B 82 382 240 HOH HOH . H 5 HOH B 83 383 199 HOH HOH . H 5 HOH B 84 384 138 HOH HOH . H 5 HOH B 85 385 228 HOH HOH . H 5 HOH B 86 386 238 HOH HOH . H 5 HOH B 87 387 147 HOH HOH . H 5 HOH B 88 388 125 HOH HOH . H 5 HOH B 89 389 148 HOH HOH . H 5 HOH B 90 390 210 HOH HOH . H 5 HOH B 91 391 156 HOH HOH . H 5 HOH B 92 392 196 HOH HOH . H 5 HOH B 93 393 134 HOH HOH . H 5 HOH B 94 394 167 HOH HOH . H 5 HOH B 95 395 94 HOH HOH . H 5 HOH B 96 396 82 HOH HOH . H 5 HOH B 97 397 230 HOH HOH . H 5 HOH B 98 398 110 HOH HOH . H 5 HOH B 99 399 184 HOH HOH . H 5 HOH B 100 400 234 HOH HOH . H 5 HOH B 101 401 153 HOH HOH . H 5 HOH B 102 402 17 HOH HOH . H 5 HOH B 103 403 102 HOH HOH . H 5 HOH B 104 404 111 HOH HOH . H 5 HOH B 105 405 165 HOH HOH . H 5 HOH B 106 406 203 HOH HOH . H 5 HOH B 107 407 189 HOH HOH . H 5 HOH B 108 408 247 HOH HOH . H 5 HOH B 109 409 207 HOH HOH . H 5 HOH B 110 410 164 HOH HOH . H 5 HOH B 111 411 81 HOH HOH . H 5 HOH B 112 412 198 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 C C2 6CG . . . C 2 -26.892 5.067 -32.854 1 8.21 ? C2 6CG 201 A 1 HETATM 2 C C4 6CG . . . C 2 -28.767 5.218 -31.467 1 8.85 ? C4 6CG 201 A 1 HETATM 3 C C5 6CG . . . C 2 -29.634 4.877 -32.599 1 11.66 ? C5 6CG 201 A 1 HETATM 4 C C6 6CG . . . C 2 -28.973 4.64 -33.895 1 11.01 ? C6 6CG 201 A 1 HETATM 5 N N1 6CG . . . C 2 -27.64 4.757 -33.931 1 9.63 ? N1 6CG 201 A 1 HETATM 6 N N2 6CG . . . C 2 -25.55 5.16 -33.001 1 8.65 ? N2 6CG 201 A 1 HETATM 7 N N3 6CG . . . C 2 -27.429 5.31 -31.635 1 8.96 ? N3 6CG 201 A 1 HETATM 8 C C8 6CG . . . C 2 -30.853 5.173 -30.823 1 12.89 ? C8 6CG 201 A 1 HETATM 9 C C1' 6CG . . . C 2 -29.145 5.76 -29.076 1 12.43 ? C1' 6CG 201 A 1 HETATM 10 C C3' 6CG . . . C 2 -30.013 6.821 -27.13 1 10.71 ? C3' 6CG 201 A 1 HETATM 11 C C4' 6CG . . . C 2 -29.985 5.316 -26.932 1 12.63 ? C4' 6CG 201 A 1 HETATM 12 C C5' 6CG . . . C 2 -31.394 4.766 -26.74 1 21.73 ? C5' 6CG 201 A 1 HETATM 13 O O6 6CG . . . C 2 -29.644 4.352 -34.921 1 13.34 ? O6 6CG 201 A 1 HETATM 14 N N7 6CG . . . C 2 -30.901 4.865 -32.14 1 14.15 ? N7 6CG 201 A 1 HETATM 15 N N9 6CG . . . C 2 -29.579 5.384 -30.433 1 10.95 ? N9 6CG 201 A 1 HETATM 16 O O4' 6CG . . . C 2 -29.441 4.741 -28.13 1 12.93 ? O4' 6CG 201 A 1 HETATM 17 C C2' 6CG . . . C 2 -29.975 6.959 -28.646 1 10.08 ? C2' 6CG 201 A 1 HETATM 18 O O2' 6CG . . . C 2 -29.415 8.201 -29.092 1 11.02 ? O2' 6CG 201 A 1 HETATM 19 O O3' 6CG . . . C 2 -28.878 7.42 -26.479 1 10.13 ? O3' 6CG 201 A 1 HETATM 20 S S5' 6CG . . . C 2 -32.201 5.463 -25.329 1 28.74 ? S5' 6CG 201 A 1 HETATM 21 P P 6CG . . . C 2 -31.935 4.152 -23.767 1 20.65 ? P 6CG 201 A 1 HETATM 22 O O1P 6CG . . . C 2 -32.665 2.85 -24.055 1 15.62 ? O1P 6CG 201 A 1 HETATM 23 O O2P 6CG . . . C 2 -32.493 4.904 -22.58 1 30.26 ? O2P 6CG 201 A 1 HETATM 24 O O3P 6CG . . . C 2 -30.445 3.942 -23.661 1 22.45 ? O3P 6CG 201 A 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 35 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 528 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 24 #