data_5IPD # _model_server_result.job_id 6Odh4SIoa2JOZlJOQT6tGA _model_server_result.datetime_utc '2024-10-22 00:38:08' _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 5ipd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":201}' # _entry.id 5IPD # _exptl.entry_id 5IPD _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 94.78 _cell.angle_gamma 90 _cell.entry_id 5IPD _cell.length_a 78.445 _cell.length_b 46.241 _cell.length_c 64.218 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5IPD _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 _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 # _struct_conn.conn_type_id covale _struct_conn.details ? _struct_conn.id covale1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id NE2 _struct_conn.ptnr1_label_comp_id HIS _struct_conn.ptnr1_label_seq_id 115 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id HIS _struct_conn.ptnr1_auth_seq_id 112 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id C _struct_conn.ptnr2_label_atom_id P _struct_conn.ptnr2_label_comp_id 6CG _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id 6CG _struct_conn.ptnr2_auth_seq_id 201 _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 1.687 _struct_conn.pdbx_value_order ? # _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 5IPD _atom_sites.fract_transf_matrix[1][1] 0.012748 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001066 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.021626 _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] 0.015626 _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 1 201 312 6CG 6CG . D 3 HOH A 1 301 201 HOH HOH . D 3 HOH A 2 302 202 HOH HOH . D 3 HOH A 3 303 203 HOH HOH . D 3 HOH A 4 304 204 HOH HOH . D 3 HOH A 5 305 205 HOH HOH . D 3 HOH A 6 306 206 HOH HOH . D 3 HOH A 7 307 207 HOH HOH . D 3 HOH A 8 308 208 HOH HOH . D 3 HOH A 9 309 209 HOH HOH . D 3 HOH A 10 310 210 HOH HOH . D 3 HOH A 11 311 211 HOH HOH . D 3 HOH A 12 312 212 HOH HOH . D 3 HOH A 13 313 213 HOH HOH . D 3 HOH A 14 314 214 HOH HOH . D 3 HOH A 15 315 215 HOH HOH . D 3 HOH A 16 316 216 HOH HOH . D 3 HOH A 17 317 217 HOH HOH . D 3 HOH A 18 318 218 HOH HOH . D 3 HOH A 19 319 219 HOH HOH . D 3 HOH A 20 320 220 HOH HOH . D 3 HOH A 21 321 221 HOH HOH . D 3 HOH A 22 322 222 HOH HOH . D 3 HOH A 23 323 223 HOH HOH . D 3 HOH A 24 324 224 HOH HOH . D 3 HOH A 25 325 225 HOH HOH . D 3 HOH A 26 326 226 HOH HOH . D 3 HOH A 27 327 227 HOH HOH . D 3 HOH A 28 328 228 HOH HOH . D 3 HOH A 29 329 229 HOH HOH . D 3 HOH A 30 330 230 HOH HOH . D 3 HOH A 31 331 231 HOH HOH . D 3 HOH A 32 332 232 HOH HOH . D 3 HOH A 33 333 233 HOH HOH . D 3 HOH A 34 334 234 HOH HOH . D 3 HOH A 35 335 235 HOH HOH . D 3 HOH A 36 336 236 HOH HOH . D 3 HOH A 37 337 237 HOH HOH . D 3 HOH A 38 338 238 HOH HOH . D 3 HOH A 39 339 239 HOH HOH . D 3 HOH A 40 340 240 HOH HOH . D 3 HOH A 41 341 241 HOH HOH . D 3 HOH A 42 342 242 HOH HOH . D 3 HOH A 43 343 243 HOH HOH . D 3 HOH A 44 344 244 HOH HOH . D 3 HOH A 45 345 245 HOH HOH . D 3 HOH A 46 346 246 HOH HOH . D 3 HOH A 47 347 247 HOH HOH . D 3 HOH A 48 348 248 HOH HOH . D 3 HOH A 49 349 249 HOH HOH . D 3 HOH A 50 350 250 HOH HOH . D 3 HOH A 51 351 251 HOH HOH . D 3 HOH A 52 352 252 HOH HOH . D 3 HOH A 53 353 253 HOH HOH . D 3 HOH A 54 354 254 HOH HOH . D 3 HOH A 55 355 255 HOH HOH . D 3 HOH A 56 356 256 HOH HOH . D 3 HOH A 57 357 257 HOH HOH . D 3 HOH A 58 358 258 HOH HOH . D 3 HOH A 59 359 259 HOH HOH . D 3 HOH A 60 360 260 HOH HOH . D 3 HOH A 61 361 261 HOH HOH . D 3 HOH A 62 362 262 HOH HOH . D 3 HOH A 63 363 263 HOH HOH . D 3 HOH A 64 364 264 HOH HOH . D 3 HOH A 65 365 265 HOH HOH . D 3 HOH A 66 366 266 HOH HOH . D 3 HOH A 67 367 267 HOH HOH . D 3 HOH A 68 368 268 HOH HOH . D 3 HOH A 69 369 269 HOH HOH . D 3 HOH A 70 370 270 HOH HOH . D 3 HOH A 71 371 271 HOH HOH . D 3 HOH A 72 372 272 HOH HOH . D 3 HOH A 73 373 273 HOH HOH . D 3 HOH A 74 374 274 HOH HOH . D 3 HOH A 75 375 275 HOH HOH . D 3 HOH A 76 376 276 HOH HOH . D 3 HOH A 77 377 277 HOH HOH . D 3 HOH A 78 378 278 HOH HOH . D 3 HOH A 79 379 279 HOH HOH . D 3 HOH A 80 380 280 HOH HOH . D 3 HOH A 81 381 281 HOH HOH . D 3 HOH A 82 382 282 HOH HOH . D 3 HOH A 83 383 283 HOH HOH . D 3 HOH A 84 384 284 HOH HOH . D 3 HOH A 85 385 285 HOH HOH . D 3 HOH A 86 386 286 HOH HOH . D 3 HOH A 87 387 287 HOH HOH . D 3 HOH A 88 388 288 HOH HOH . D 3 HOH A 89 389 289 HOH HOH . D 3 HOH A 90 390 290 HOH HOH . D 3 HOH A 91 391 291 HOH HOH . D 3 HOH A 92 392 292 HOH HOH . E 3 HOH B 1 201 201 HOH HOH . E 3 HOH B 2 202 202 HOH HOH . E 3 HOH B 3 203 203 HOH HOH . E 3 HOH B 4 204 204 HOH HOH . E 3 HOH B 5 205 205 HOH HOH . E 3 HOH B 6 206 206 HOH HOH . E 3 HOH B 7 207 207 HOH HOH . E 3 HOH B 8 208 208 HOH HOH . E 3 HOH B 9 209 209 HOH HOH . E 3 HOH B 10 210 210 HOH HOH . E 3 HOH B 11 211 211 HOH HOH . E 3 HOH B 12 212 212 HOH HOH . E 3 HOH B 13 213 213 HOH HOH . E 3 HOH B 14 214 214 HOH HOH . E 3 HOH B 15 215 215 HOH HOH . E 3 HOH B 16 216 216 HOH HOH . E 3 HOH B 17 217 217 HOH HOH . E 3 HOH B 18 218 218 HOH HOH . E 3 HOH B 19 219 219 HOH HOH . E 3 HOH B 20 220 220 HOH HOH . E 3 HOH B 21 221 221 HOH HOH . E 3 HOH B 22 222 222 HOH HOH . E 3 HOH B 23 223 223 HOH HOH . E 3 HOH B 24 224 224 HOH HOH . E 3 HOH B 25 225 225 HOH HOH . E 3 HOH B 26 226 226 HOH HOH . E 3 HOH B 27 227 227 HOH HOH . E 3 HOH B 28 228 228 HOH HOH . E 3 HOH B 29 229 229 HOH HOH . E 3 HOH B 30 230 230 HOH HOH . E 3 HOH B 31 231 231 HOH HOH . E 3 HOH B 32 232 232 HOH HOH . E 3 HOH B 33 233 233 HOH HOH . E 3 HOH B 34 234 234 HOH HOH . E 3 HOH B 35 235 235 HOH HOH . E 3 HOH B 36 236 236 HOH HOH . E 3 HOH B 37 237 237 HOH HOH . E 3 HOH B 38 238 238 HOH HOH . E 3 HOH B 39 239 239 HOH HOH . E 3 HOH B 40 240 240 HOH HOH . E 3 HOH B 41 241 241 HOH HOH . E 3 HOH B 42 242 242 HOH HOH . E 3 HOH B 43 243 243 HOH HOH . E 3 HOH B 44 244 244 HOH HOH . E 3 HOH B 45 245 245 HOH HOH . E 3 HOH B 46 246 246 HOH HOH . E 3 HOH B 47 247 247 HOH HOH . E 3 HOH B 48 248 248 HOH HOH . E 3 HOH B 49 249 249 HOH HOH . E 3 HOH B 50 250 250 HOH HOH . E 3 HOH B 51 251 251 HOH HOH . E 3 HOH B 52 252 252 HOH HOH . E 3 HOH B 53 253 253 HOH HOH . E 3 HOH B 54 254 254 HOH HOH . E 3 HOH B 55 255 255 HOH HOH . E 3 HOH B 56 256 256 HOH HOH . E 3 HOH B 57 257 257 HOH HOH . E 3 HOH B 58 258 258 HOH HOH . E 3 HOH B 59 259 259 HOH HOH . E 3 HOH B 60 260 260 HOH HOH . E 3 HOH B 61 261 261 HOH HOH . E 3 HOH B 62 262 262 HOH HOH . E 3 HOH B 63 263 263 HOH HOH . E 3 HOH B 64 264 264 HOH HOH . E 3 HOH B 65 265 265 HOH HOH . E 3 HOH B 66 266 266 HOH HOH . E 3 HOH B 67 267 267 HOH HOH . E 3 HOH B 68 268 268 HOH HOH . E 3 HOH B 69 269 269 HOH HOH . E 3 HOH B 70 270 270 HOH HOH . E 3 HOH B 71 271 271 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 -26.936 5.053 -33.218 1 12.32 ? C2 6CG 201 A 1 HETATM 2 C C4 6CG . . . C 2 -28.891 5.281 -31.939 1 12.6 ? C4 6CG 201 A 1 HETATM 3 C C5 6CG . . . C 2 -29.699 4.99 -33.048 1 17.08 ? C5 6CG 201 A 1 HETATM 4 C C6 6CG . . . C 2 -29.018 4.738 -34.28 1 17.14 ? C6 6CG 201 A 1 HETATM 5 N N1 6CG . . . C 2 -27.662 4.791 -34.299 1 13.15 ? N1 6CG 201 A 1 HETATM 6 N N2 6CG . . . C 2 -25.518 5.084 -33.336 1 11.21 ? N2 6CG 201 A 1 HETATM 7 N N3 6CG . . . C 2 -27.517 5.303 -32.042 1 12.42 ? N3 6CG 201 A 1 HETATM 8 C C8 6CG . . . C 2 -31.022 5.341 -31.32 1 13.63 ? C8 6CG 201 A 1 HETATM 9 C C1' 6CG . . . C 2 -29.33 5.833 -29.553 1 14.56 ? C1' 6CG 201 A 1 HETATM 10 C C3' 6CG . . . C 2 -30.061 6.399 -27.495 1 16.02 ? C3' 6CG 201 A 1 HETATM 11 C C4' 6CG . . . C 2 -29.738 5.142 -27.335 1 13.05 ? C4' 6CG 201 A 1 HETATM 12 C C5' 6CG . . . C 2 -30.881 4.327 -26.669 1 14.36 ? C5' 6CG 201 A 1 HETATM 13 O O6 6CG . . . C 2 -29.765 4.455 -35.436 1 15.28 ? O6 6CG 201 A 1 HETATM 14 N N7 6CG . . . C 2 -31.026 5.037 -32.634 1 16.11 ? N7 6CG 201 A 1 HETATM 15 N N9 6CG . . . C 2 -29.759 5.499 -30.885 1 14.48 ? N9 6CG 201 A 1 HETATM 16 O O4' 6CG . . . C 2 -29.603 4.527 -28.705 1 15.66 ? O4' 6CG 201 A 1 HETATM 17 C C2' 6CG . . . C 2 -30.07 6.698 -29.005 1 13.65 ? C2' 6CG 201 A 1 HETATM 18 O O2' 6CG . . . C 2 -29.616 8.061 -29.303 1 14.63 ? O2' 6CG 201 A 1 HETATM 19 O O3' 6CG . . . C 2 -29.149 7.267 -26.783 1 13.71 ? O3' 6CG 201 A 1 HETATM 20 S S5' 6CG . . . C 2 -30.692 4.763 -24.959 1 15.86 ? S5' 6CG 201 A 1 HETATM 21 P P 6CG . . . C 2 -31.215 3.098 -23.871 1 13.51 ? P 6CG 201 A 1 HETATM 22 O O2P 6CG . . . C 2 -30.874 3.498 -22.384 1 14.66 ? O2P 6CG 201 A 1 HETATM 23 O O3P 6CG . . . C 2 -32.74 2.732 -24.081 1 13.1 ? O3P 6CG 201 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 289 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 23 #