data_3Q4P # _model_server_result.job_id b---ub0ce4AuQQ9a-GzyBg _model_server_result.datetime_utc '2024-10-23 02:18:27' _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 3q4p # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":247}' # _entry.id 3Q4P # _exptl.entry_id 3Q4P _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 459.243 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "7N-METHYL-8-HYDROGUANOSINE-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 3Q4P _cell.length_a 129.848 _cell.length_b 129.848 _cell.length_c 39.717 _cell.Z_PDB 9 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3Q4P _symmetry.cell_setting ? _symmetry.Int_Tables_number 146 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 B _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 ND2 _struct_conn.ptnr1_label_comp_id ASN _struct_conn.ptnr1_label_seq_id 227 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id ASN _struct_conn.ptnr1_auth_seq_id 227 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id E _struct_conn.ptnr2_label_atom_id C1 _struct_conn.ptnr2_label_comp_id NAG _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id NAG _struct_conn.ptnr2_auth_seq_id 250 _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 1.449 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C11 H19 N5 O11 P2' _chem_comp.formula_weight 459.243 _chem_comp.id M7G _chem_comp.mon_nstd_flag . _chem_comp.name "7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE" _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 PA O1A M7G doub 218 n n PA O2A M7G sing 219 n n PA O3A M7G sing 220 n n PA O5' M7G sing 221 n n O2A HOA2 M7G sing 222 n n O3A PB M7G sing 223 n n O5' C5' M7G sing 224 n n PB O1B M7G doub 225 n n PB O2B M7G sing 226 n n PB O3B M7G sing 227 n n O2B HOB2 M7G sing 228 n n O3B HOB3 M7G sing 229 n n C5' C4' M7G sing 230 n n C5' "H5'1" M7G sing 231 n n C5' "H5'2" M7G sing 232 n n C4' O4' M7G sing 233 n n C4' C3' M7G sing 234 n n C4' H4' M7G sing 235 n n O4' C1' M7G sing 236 n n C3' O3' M7G sing 237 n n C3' C2' M7G sing 238 n n C3' H3' M7G sing 239 n n O3' HO3' M7G sing 240 n n C2' O2' M7G sing 241 n n C2' C1' M7G sing 242 n n C2' H2' M7G sing 243 n n O2' HO2' M7G sing 244 n n C1' N9 M7G sing 245 n n C1' H1' M7G sing 246 n n N9 C8 M7G sing 247 n n N9 C4 M7G sing 248 n n C8 N7 M7G sing 249 n n C8 H81 M7G sing 250 n n C8 H82 M7G sing 251 n n N7 CM7 M7G sing 252 n n N7 C5 M7G sing 253 n n CM7 HM71 M7G sing 254 n n CM7 HM72 M7G sing 255 n n CM7 HM73 M7G sing 256 n n C5 C6 M7G sing 257 n n C5 C4 M7G doub 258 n n C6 O6 M7G doub 259 n n C6 N1 M7G sing 260 n n N1 C2 M7G sing 261 n n N1 HN1 M7G sing 262 n n C2 N2 M7G sing 263 n n C2 N3 M7G doub 264 n n N2 HN21 M7G sing 265 n n N2 HN22 M7G sing 266 n n N3 C4 M7G sing 267 n n # _atom_sites.entry_id 3Q4P _atom_sites.fract_transf_matrix[1][1] 0.007701 _atom_sites.fract_transf_matrix[1][2] 0.004446 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008893 _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] 0.025178 _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 M7G A 1 247 1 M7G M7G . C 3 PEG A 1 248 1 PEG PEG . D 4 GOL A 1 249 2 GOL GOL . E 5 NAG A 1 250 3 NAG NAG . F 6 HOH A 1 251 1 HOH HOH . F 6 HOH A 2 252 2 HOH HOH . F 6 HOH A 3 253 4 HOH HOH . F 6 HOH A 4 254 6 HOH HOH . F 6 HOH A 5 255 7 HOH HOH . F 6 HOH A 6 256 8 HOH HOH . F 6 HOH A 7 257 9 HOH HOH . F 6 HOH A 8 258 10 HOH HOH . F 6 HOH A 9 259 11 HOH HOH . F 6 HOH A 10 260 12 HOH HOH . F 6 HOH A 11 261 13 HOH HOH . F 6 HOH A 12 262 14 HOH HOH . F 6 HOH A 13 263 15 HOH HOH . F 6 HOH A 14 264 16 HOH HOH . F 6 HOH A 15 265 17 HOH HOH . F 6 HOH A 16 266 18 HOH HOH . F 6 HOH A 17 267 19 HOH HOH . F 6 HOH A 18 268 20 HOH HOH . F 6 HOH A 19 269 21 HOH HOH . F 6 HOH A 20 270 22 HOH HOH . F 6 HOH A 21 271 23 HOH HOH . F 6 HOH A 22 272 24 HOH HOH . F 6 HOH A 23 273 25 HOH HOH . F 6 HOH A 24 274 26 HOH HOH . F 6 HOH A 25 275 27 HOH HOH . F 6 HOH A 26 276 28 HOH HOH . F 6 HOH A 27 277 29 HOH HOH . F 6 HOH A 28 278 30 HOH HOH . F 6 HOH A 29 279 31 HOH HOH . F 6 HOH A 30 280 32 HOH HOH . F 6 HOH A 31 281 33 HOH HOH . F 6 HOH A 32 282 34 HOH HOH . F 6 HOH A 33 283 35 HOH HOH . F 6 HOH A 34 284 36 HOH HOH . F 6 HOH A 35 285 37 HOH HOH . F 6 HOH A 36 286 38 HOH HOH . F 6 HOH A 37 287 39 HOH HOH . F 6 HOH A 38 288 40 HOH HOH . F 6 HOH A 39 289 41 HOH HOH . F 6 HOH A 40 290 42 HOH HOH . F 6 HOH A 41 291 43 HOH HOH . F 6 HOH A 42 292 44 HOH HOH . F 6 HOH A 43 293 45 HOH HOH . F 6 HOH A 44 294 46 HOH HOH . F 6 HOH A 45 295 47 HOH HOH . F 6 HOH A 46 296 48 HOH HOH . F 6 HOH A 47 297 49 HOH HOH . F 6 HOH A 48 298 50 HOH HOH . F 6 HOH A 49 299 51 HOH HOH . F 6 HOH A 50 300 52 HOH HOH . F 6 HOH A 51 301 53 HOH HOH . F 6 HOH A 52 302 54 HOH HOH . F 6 HOH A 53 303 55 HOH HOH . F 6 HOH A 54 304 56 HOH HOH . F 6 HOH A 55 305 57 HOH HOH . F 6 HOH A 56 306 58 HOH HOH . F 6 HOH A 57 307 59 HOH HOH . F 6 HOH A 58 308 60 HOH HOH . F 6 HOH A 59 309 61 HOH HOH . F 6 HOH A 60 310 62 HOH HOH . F 6 HOH A 61 311 63 HOH HOH . F 6 HOH A 62 312 64 HOH HOH . F 6 HOH A 63 313 65 HOH HOH . F 6 HOH A 64 314 66 HOH HOH . F 6 HOH A 65 315 67 HOH HOH . F 6 HOH A 66 316 68 HOH HOH . F 6 HOH A 67 317 69 HOH HOH . F 6 HOH A 68 318 70 HOH HOH . F 6 HOH A 69 319 71 HOH HOH . F 6 HOH A 70 320 72 HOH HOH . F 6 HOH A 71 321 73 HOH HOH . F 6 HOH A 72 322 74 HOH HOH . F 6 HOH A 73 323 75 HOH HOH . F 6 HOH A 74 324 76 HOH HOH . F 6 HOH A 75 325 77 HOH HOH . F 6 HOH A 76 326 78 HOH HOH . F 6 HOH A 77 327 79 HOH HOH . F 6 HOH A 78 328 80 HOH HOH . F 6 HOH A 79 329 81 HOH HOH . F 6 HOH A 80 330 82 HOH HOH . F 6 HOH A 81 331 83 HOH HOH . F 6 HOH A 82 332 84 HOH HOH . F 6 HOH A 83 333 85 HOH HOH . F 6 HOH A 84 334 86 HOH HOH . F 6 HOH A 85 335 87 HOH HOH . F 6 HOH A 86 336 88 HOH HOH . F 6 HOH A 87 337 89 HOH HOH . F 6 HOH A 88 338 90 HOH HOH . F 6 HOH A 89 339 91 HOH HOH . F 6 HOH A 90 340 92 HOH HOH . F 6 HOH A 91 341 93 HOH HOH . F 6 HOH A 92 342 94 HOH HOH . F 6 HOH A 93 343 95 HOH HOH . F 6 HOH A 94 344 96 HOH HOH . F 6 HOH A 95 345 97 HOH HOH . F 6 HOH A 96 346 98 HOH HOH . F 6 HOH A 97 347 99 HOH HOH . F 6 HOH A 98 348 100 HOH HOH . F 6 HOH A 99 349 101 HOH HOH . F 6 HOH A 100 350 102 HOH HOH . F 6 HOH A 101 351 103 HOH HOH . F 6 HOH A 102 352 104 HOH HOH . F 6 HOH A 103 353 105 HOH HOH . F 6 HOH A 104 354 106 HOH HOH . F 6 HOH A 105 355 107 HOH HOH . F 6 HOH A 106 356 108 HOH HOH . F 6 HOH A 107 357 109 HOH HOH . F 6 HOH A 108 358 110 HOH HOH . F 6 HOH A 109 359 111 HOH HOH . F 6 HOH A 110 360 112 HOH HOH . F 6 HOH A 111 361 113 HOH HOH . F 6 HOH A 112 362 114 HOH HOH . F 6 HOH A 113 363 115 HOH HOH . F 6 HOH A 114 364 116 HOH HOH . F 6 HOH A 115 365 117 HOH HOH . F 6 HOH A 116 366 118 HOH HOH . F 6 HOH A 117 367 119 HOH HOH . F 6 HOH A 118 368 120 HOH HOH . F 6 HOH A 119 369 121 HOH HOH . F 6 HOH A 120 370 122 HOH HOH . F 6 HOH A 121 371 123 HOH HOH . F 6 HOH A 122 372 124 HOH HOH . F 6 HOH A 123 373 125 HOH HOH . F 6 HOH A 124 374 126 HOH HOH . F 6 HOH A 125 375 127 HOH HOH . F 6 HOH A 126 376 128 HOH HOH . F 6 HOH A 127 377 129 HOH HOH . F 6 HOH A 128 378 130 HOH HOH . F 6 HOH A 129 379 131 HOH HOH . F 6 HOH A 130 380 132 HOH HOH . F 6 HOH A 131 381 133 HOH HOH . F 6 HOH A 132 382 134 HOH HOH . F 6 HOH A 133 383 135 HOH HOH . F 6 HOH A 134 384 136 HOH HOH . F 6 HOH A 135 385 138 HOH HOH . F 6 HOH A 136 386 139 HOH HOH . F 6 HOH A 137 387 140 HOH HOH . F 6 HOH A 138 388 141 HOH HOH . F 6 HOH A 139 389 142 HOH HOH . F 6 HOH A 140 390 143 HOH HOH . F 6 HOH A 141 391 144 HOH HOH . F 6 HOH A 142 392 145 HOH HOH . F 6 HOH A 143 393 146 HOH HOH . F 6 HOH A 144 394 147 HOH HOH . F 6 HOH A 145 395 148 HOH HOH . F 6 HOH A 146 396 149 HOH HOH . F 6 HOH A 147 397 150 HOH HOH . F 6 HOH A 148 398 151 HOH HOH . F 6 HOH A 149 399 152 HOH HOH . F 6 HOH A 150 400 153 HOH HOH . F 6 HOH A 151 401 154 HOH HOH . F 6 HOH A 152 402 155 HOH HOH . F 6 HOH A 153 403 156 HOH HOH . F 6 HOH A 154 404 157 HOH HOH . F 6 HOH A 155 405 158 HOH HOH . F 6 HOH A 156 406 159 HOH HOH . F 6 HOH A 157 407 160 HOH HOH . F 6 HOH A 158 408 161 HOH HOH . F 6 HOH A 159 409 162 HOH HOH . F 6 HOH A 160 410 163 HOH HOH . F 6 HOH A 161 411 164 HOH HOH . F 6 HOH A 162 412 165 HOH HOH . F 6 HOH A 163 413 166 HOH HOH . F 6 HOH A 164 414 167 HOH HOH . F 6 HOH A 165 415 168 HOH HOH . F 6 HOH A 166 416 169 HOH HOH . F 6 HOH A 167 417 170 HOH HOH . F 6 HOH A 168 418 171 HOH HOH . F 6 HOH A 169 419 172 HOH HOH . F 6 HOH A 170 420 173 HOH HOH . F 6 HOH A 171 421 174 HOH HOH . F 6 HOH A 172 422 175 HOH HOH . F 6 HOH A 173 423 176 HOH HOH . F 6 HOH A 174 424 177 HOH HOH . F 6 HOH A 175 425 178 HOH HOH . F 6 HOH A 176 426 179 HOH HOH . F 6 HOH A 177 427 180 HOH HOH . F 6 HOH A 178 428 181 HOH HOH . F 6 HOH A 179 429 182 HOH HOH . F 6 HOH A 180 430 183 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 PA M7G . . . B 2 -6.015 -21.242 -22.049 0.5 32.18 ? PA M7G 247 A 1 HETATM 2 O O1A M7G . . . B 2 -7.222 -22.065 -22.238 0.5 33.19 ? O1A M7G 247 A 1 HETATM 3 O O2A M7G . . . B 2 -5.705 -20.086 -22.892 0.5 36.86 ? O2A M7G 247 A 1 HETATM 4 O O3A M7G . . . B 2 -4.807 -22.283 -21.896 0.5 37.33 ? O3A M7G 247 A 1 HETATM 5 O O5' M7G . . . B 2 -5.965 -20.671 -20.645 0.5 30.33 ? O5' M7G 247 A 1 HETATM 6 P PB M7G . . . B 2 -4.177 -23.306 -22.945 0.5 36.17 ? PB M7G 247 A 1 HETATM 7 O O1B M7G . . . B 2 -4.381 -22.736 -24.292 0.5 38.3 ? O1B M7G 247 A 1 HETATM 8 O O2B M7G . . . B 2 -2.778 -23.218 -22.562 0.5 36.13 ? O2B M7G 247 A 1 HETATM 9 O O3B M7G . . . B 2 -4.872 -24.579 -22.652 0.5 37.66 ? O3B M7G 247 A 1 HETATM 10 C C5' M7G . . . B 2 -5.942 -21.587 -19.649 0.5 33.41 ? C5' M7G 247 A 1 HETATM 11 C C4' M7G . . . B 2 -4.803 -21.354 -18.695 0.5 32.75 ? C4' M7G 247 A 1 HETATM 12 O O4' M7G . . . B 2 -5.562 -21.57 -17.556 0.5 31.25 ? O4' M7G 247 A 1 HETATM 13 C C3' M7G . . . B 2 -4.028 -22.657 -18.811 0.5 32.33 ? C3' M7G 247 A 1 HETATM 14 O O3' M7G . . . B 2 -3.306 -23.02 -17.626 0.5 40.92 ? O3' M7G 247 A 1 HETATM 15 C C2' M7G . . . B 2 -5.189 -23.581 -18.792 0.5 33.4 ? C2' M7G 247 A 1 HETATM 16 O O2' M7G . . . B 2 -4.714 -24.816 -18.301 0.5 35.65 ? O2' M7G 247 A 1 HETATM 17 C C1' M7G . . . B 2 -6.027 -22.874 -17.756 0.5 31.18 ? C1' M7G 247 A 1 HETATM 18 N N9 M7G . . . B 2 -7.404 -22.848 -18.17 0.5 35.09 ? N9 M7G 247 A 1 HETATM 19 C C8 M7G . . . B 2 -7.66 -23.511 -19.425 0.5 38.88 ? C8 M7G 247 A 1 HETATM 20 N N7 M7G . . . B 2 -9.083 -23.285 -19.379 0.5 38.99 ? N7 M7G 247 A 1 HETATM 21 C CM7 M7G . . . B 2 -9.232 -23.465 -20.836 0.5 41.54 ? CM7 M7G 247 A 1 HETATM 22 C C5 M7G . . . B 2 -9.537 -22.636 -18.306 0.5 37.16 ? C5 M7G 247 A 1 HETATM 23 C C6 M7G . . . B 2 -10.85 -22.222 -17.838 0.5 38.45 ? C6 M7G 247 A 1 HETATM 24 O O6 M7G . . . B 2 -11.866 -22.457 -18.506 0.5 39.58 ? O6 M7G 247 A 1 HETATM 25 N N1 M7G . . . B 2 -10.869 -21.592 -16.659 0.5 37.15 ? N1 M7G 247 A 1 HETATM 26 C C2 M7G . . . B 2 -9.763 -21.349 -15.94 0.5 33.1 ? C2 M7G 247 A 1 HETATM 27 N N2 M7G . . . B 2 -9.836 -20.723 -14.778 0.5 31.97 ? N2 M7G 247 A 1 HETATM 28 N N3 M7G . . . B 2 -8.548 -21.718 -16.313 0.5 35.57 ? N3 M7G 247 A 1 HETATM 29 C C4 M7G . . . B 2 -8.392 -22.354 -17.476 0.5 36.12 ? C4 M7G 247 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 308 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 29 #