data_7X9L # _model_server_result.job_id st8BaNcJPa5Yxdp8SbEWCg _model_server_result.datetime_utc '2024-11-24 01:14:56' _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 7x9l # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":201}' # _entry.id 7X9L # _exptl.entry_id 7X9L _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 363.221 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE" _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 7X9L _cell.length_a 38.531 _cell.length_b 56.106 _cell.length_c 59.369 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7X9L _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall 'P 2ac 2ab' _symmetry.space_group_name_H-M 'P 21 21 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,E,F,G _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 # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 2 _pdbx_entity_branch_link.entity_branch_list_num_1 1 _pdbx_entity_branch_link.entity_branch_list_num_2 2 _pdbx_entity_branch_link.comp_id_1 GLC _pdbx_entity_branch_link.comp_id_2 FRU _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O2 _pdbx_entity_branch_link.leaving_atom_id_2 HO2 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 2 n B GLC 1 B 1 GLC Y 1 SUC 2 n B FRU 2 B 2 FRU Y 1 SUC # 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 covale ? covale1 B C1 GLC . B GLC 1 1_555 B O2 FRU . B FRU 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.414 ? metalc ? metalc1 A O GLY 37 A GLY 37 1_555 E MN MN . A MN 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.182 ? metalc ? metalc2 A OE1 GLU 53 A GLU 53 1_555 F NA NA . A NA 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.569 ? metalc ? metalc3 A OE2 GLU 57 A GLU 57 1_555 E MN MN . A MN 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.287 ? metalc ? metalc4 A OE2 GLU 57 A GLU 57 1_555 F NA NA . A NA 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.616 ? metalc ? metalc5 C OP2 8OG . A 8OG 201 1_555 E MN MN . A MN 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.287 ? metalc ? metalc6 E MN MN . A MN 203 1_555 G O HOH . A HOH 312 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.173 ? metalc ? metalc7 E MN MN . A MN 203 1_555 G O HOH . A HOH 346 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.196 ? metalc ? metalc8 E MN MN . A MN 203 1_555 G O HOH . A HOH 388 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.279 ? metalc ? metalc9 F NA NA . A NA 204 1_555 G O HOH . A HOH 308 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.441 ? metalc ? metalc10 F NA NA . A NA 204 1_555 G O HOH . A HOH 312 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.288 ? metalc ? metalc11 F NA NA . A NA 204 1_555 G O HOH . A HOH 348 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.683 ? # _chem_comp.formula 'C10 H14 N5 O8 P' _chem_comp.formula_weight 363.221 _chem_comp.id 8OG _chem_comp.mon_nstd_flag n _chem_comp.name "8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE" _chem_comp.type 'dna linking' _chem_comp.pdbx_synonyms "8-OXO-7,8-DIHYDRO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE" # 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 OP3 P 8OG sing 1 n n OP3 HOP3 8OG sing 2 n n P OP1 8OG doub 3 n n P OP2 8OG sing 4 n n P O5' 8OG sing 5 n n OP2 HOP2 8OG sing 6 n n O5' C5' 8OG sing 7 n n C5' C4' 8OG sing 8 n n C5' H5' 8OG sing 9 n n C5' "H5''" 8OG sing 10 n n C4' O4' 8OG sing 11 n n C4' C3' 8OG sing 12 n n C4' H4' 8OG sing 13 n n O4' C1' 8OG sing 14 n n C3' O3' 8OG sing 15 n n C3' C2' 8OG sing 16 n n C3' H3' 8OG sing 17 n n O3' HO3' 8OG sing 18 n n C2' C1' 8OG sing 19 n n C2' H2' 8OG sing 20 n n C2' "H2''" 8OG sing 21 n n C1' N9 8OG sing 22 n n C1' H1' 8OG sing 23 n n N9 C8 8OG sing 24 n n N9 C4 8OG sing 25 n n C8 N7 8OG sing 26 n n C8 O8 8OG doub 27 n n N7 C5 8OG sing 28 n n N7 H7 8OG sing 29 n n C5 C6 8OG sing 30 n n C5 C4 8OG doub 31 n n C6 O6 8OG doub 32 n n C6 N1 8OG sing 33 n n N1 C2 8OG sing 34 n n N1 H1 8OG sing 35 n n C2 N2 8OG sing 36 n n C2 N3 8OG doub 37 n n N2 H21 8OG sing 38 n n N2 H22 8OG sing 39 n n N3 C4 8OG sing 40 n n # _atom_sites.entry_id 7X9L _atom_sites.fract_transf_matrix[1][1] 0.025953 _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] 0.017823 _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] 0.016844 _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 3 8OG A 1 201 25 8OG 8OG . D 4 SO4 A 1 202 1 SO4 SO4 . E 5 MN A 1 203 1 MN MN . F 6 NA A 1 204 2 NA NA . G 7 HOH A 1 301 19 HOH HOH . G 7 HOH A 2 302 22 HOH HOH . G 7 HOH A 3 303 126 HOH HOH . G 7 HOH A 4 304 113 HOH HOH . G 7 HOH A 5 305 75 HOH HOH . G 7 HOH A 6 306 82 HOH HOH . G 7 HOH A 7 307 31 HOH HOH . G 7 HOH A 8 308 16 HOH HOH . G 7 HOH A 9 309 91 HOH HOH . G 7 HOH A 10 310 15 HOH HOH . G 7 HOH A 11 311 51 HOH HOH . G 7 HOH A 12 312 18 HOH HOH . G 7 HOH A 13 313 129 HOH HOH . G 7 HOH A 14 314 77 HOH HOH . G 7 HOH A 15 315 155 HOH HOH . G 7 HOH A 16 316 23 HOH HOH . G 7 HOH A 17 317 21 HOH HOH . G 7 HOH A 18 318 37 HOH HOH . G 7 HOH A 19 319 10 HOH HOH . G 7 HOH A 20 320 30 HOH HOH . G 7 HOH A 21 321 4 HOH HOH . G 7 HOH A 22 322 6 HOH HOH . G 7 HOH A 23 323 2 HOH HOH . G 7 HOH A 24 324 34 HOH HOH . G 7 HOH A 25 325 108 HOH HOH . G 7 HOH A 26 326 33 HOH HOH . G 7 HOH A 27 327 73 HOH HOH . G 7 HOH A 28 328 43 HOH HOH . G 7 HOH A 29 329 65 HOH HOH . G 7 HOH A 30 330 71 HOH HOH . G 7 HOH A 31 331 7 HOH HOH . G 7 HOH A 32 332 114 HOH HOH . G 7 HOH A 33 333 120 HOH HOH . G 7 HOH A 34 334 68 HOH HOH . G 7 HOH A 35 335 98 HOH HOH . G 7 HOH A 36 336 49 HOH HOH . G 7 HOH A 37 337 3 HOH HOH . G 7 HOH A 38 338 35 HOH HOH . G 7 HOH A 39 339 1 HOH HOH . G 7 HOH A 40 340 53 HOH HOH . G 7 HOH A 41 341 81 HOH HOH . G 7 HOH A 42 342 151 HOH HOH . G 7 HOH A 43 343 8 HOH HOH . G 7 HOH A 44 344 24 HOH HOH . G 7 HOH A 45 345 25 HOH HOH . G 7 HOH A 46 346 20 HOH HOH . G 7 HOH A 47 347 11 HOH HOH . G 7 HOH A 48 348 86 HOH HOH . G 7 HOH A 49 349 12 HOH HOH . G 7 HOH A 50 350 88 HOH HOH . G 7 HOH A 51 351 61 HOH HOH . G 7 HOH A 52 352 13 HOH HOH . G 7 HOH A 53 353 101 HOH HOH . G 7 HOH A 54 354 14 HOH HOH . G 7 HOH A 55 355 78 HOH HOH . G 7 HOH A 56 356 69 HOH HOH . G 7 HOH A 57 357 139 HOH HOH . G 7 HOH A 58 358 36 HOH HOH . G 7 HOH A 59 359 41 HOH HOH . G 7 HOH A 60 360 148 HOH HOH . G 7 HOH A 61 361 27 HOH HOH . G 7 HOH A 62 362 89 HOH HOH . G 7 HOH A 63 363 17 HOH HOH . G 7 HOH A 64 364 54 HOH HOH . G 7 HOH A 65 365 119 HOH HOH . G 7 HOH A 66 366 111 HOH HOH . G 7 HOH A 67 367 32 HOH HOH . G 7 HOH A 68 368 79 HOH HOH . G 7 HOH A 69 369 74 HOH HOH . G 7 HOH A 70 370 144 HOH HOH . G 7 HOH A 71 371 64 HOH HOH . G 7 HOH A 72 372 57 HOH HOH . G 7 HOH A 73 373 112 HOH HOH . G 7 HOH A 74 374 142 HOH HOH . G 7 HOH A 75 375 137 HOH HOH . G 7 HOH A 76 376 109 HOH HOH . G 7 HOH A 77 377 70 HOH HOH . G 7 HOH A 78 378 55 HOH HOH . G 7 HOH A 79 379 104 HOH HOH . G 7 HOH A 80 380 52 HOH HOH . G 7 HOH A 81 381 40 HOH HOH . G 7 HOH A 82 382 132 HOH HOH . G 7 HOH A 83 383 39 HOH HOH . G 7 HOH A 84 384 152 HOH HOH . G 7 HOH A 85 385 60 HOH HOH . G 7 HOH A 86 386 63 HOH HOH . G 7 HOH A 87 387 76 HOH HOH . G 7 HOH A 88 388 72 HOH HOH . G 7 HOH A 89 389 94 HOH HOH . G 7 HOH A 90 390 83 HOH HOH . G 7 HOH A 91 391 143 HOH HOH . G 7 HOH A 92 392 38 HOH HOH . G 7 HOH A 93 393 9 HOH HOH . G 7 HOH A 94 394 127 HOH HOH . G 7 HOH A 95 395 44 HOH HOH . G 7 HOH A 96 396 56 HOH HOH . G 7 HOH A 97 397 95 HOH HOH . G 7 HOH A 98 398 46 HOH HOH . G 7 HOH A 99 399 29 HOH HOH . G 7 HOH A 100 400 5 HOH HOH . G 7 HOH A 101 401 66 HOH HOH . G 7 HOH A 102 402 28 HOH HOH . G 7 HOH A 103 403 85 HOH HOH . G 7 HOH A 104 404 103 HOH HOH . G 7 HOH A 105 405 107 HOH HOH . G 7 HOH A 106 406 154 HOH HOH . G 7 HOH A 107 407 135 HOH HOH . G 7 HOH A 108 408 117 HOH HOH . G 7 HOH A 109 409 134 HOH HOH . G 7 HOH A 110 410 130 HOH HOH . G 7 HOH A 111 411 67 HOH HOH . G 7 HOH A 112 412 48 HOH HOH . G 7 HOH A 113 413 131 HOH HOH . G 7 HOH A 114 414 118 HOH HOH . G 7 HOH A 115 415 87 HOH HOH . G 7 HOH A 116 416 133 HOH HOH . G 7 HOH A 117 417 47 HOH HOH . G 7 HOH A 118 418 140 HOH HOH . G 7 HOH A 119 419 150 HOH HOH . G 7 HOH A 120 420 136 HOH HOH . G 7 HOH A 121 421 141 HOH HOH . G 7 HOH A 122 422 93 HOH HOH . G 7 HOH A 123 423 84 HOH HOH . G 7 HOH A 124 424 145 HOH HOH . G 7 HOH A 125 425 110 HOH HOH . G 7 HOH A 126 426 116 HOH HOH . G 7 HOH A 127 427 102 HOH HOH . G 7 HOH A 128 428 105 HOH HOH . G 7 HOH A 129 429 62 HOH HOH . G 7 HOH A 130 430 115 HOH HOH . G 7 HOH A 131 431 80 HOH HOH . G 7 HOH A 132 432 128 HOH HOH . G 7 HOH A 133 433 42 HOH HOH . G 7 HOH A 134 434 153 HOH HOH . G 7 HOH A 135 435 106 HOH HOH . G 7 HOH A 136 436 125 HOH HOH . G 7 HOH A 137 437 58 HOH HOH . G 7 HOH A 138 438 149 HOH HOH . G 7 HOH A 139 439 99 HOH HOH . G 7 HOH A 140 440 90 HOH HOH . G 7 HOH A 141 441 97 HOH HOH . G 7 HOH A 142 442 45 HOH HOH . G 7 HOH A 143 443 96 HOH HOH . G 7 HOH A 144 444 100 HOH HOH . G 7 HOH A 145 445 124 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 O OP3 8OG . . . C 3 -10.058 2.134 24.351 1 12.71 ? OP3 8OG 201 A 1 HETATM 2 P P 8OG . . . C 3 -9.347 1.365 23.27 1 18.91 ? P 8OG 201 A 1 HETATM 3 O OP1 8OG . . . C 3 -10.174 0.992 22.077 1 18.76 ? OP1 8OG 201 A 1 HETATM 4 O OP2 8OG . . . C 3 -8.014 2.027 22.905 1 17.21 ? OP2 8OG 201 A 1 HETATM 5 O O5' 8OG . . . C 3 -8.997 -0.051 23.97 1 16.03 ? O5' 8OG 201 A 1 HETATM 6 C C5' 8OG . . . C 3 -7.731 -0.214 24.614 1 10.83 ? C5' 8OG 201 A 1 HETATM 7 C C4' 8OG . . . C 3 -7.845 -1.023 25.911 1 7.24 ? C4' 8OG 201 A 1 HETATM 8 O O4' 8OG . . . C 3 -6.528 -1.398 26.321 1 8.9 ? O4' 8OG 201 A 1 HETATM 9 C C3' 8OG . . . C 3 -8.413 -0.213 27.055 1 9.76 ? C3' 8OG 201 A 1 HETATM 10 O O3' 8OG . . . C 3 -9.041 -1.105 27.985 1 9.2 ? O3' 8OG 201 A 1 HETATM 11 C C2' 8OG . . . C 3 -7.184 0.344 27.746 1 5.81 ? C2' 8OG 201 A 1 HETATM 12 C C1' 8OG . . . C 3 -6.172 -0.778 27.549 1 8.63 ? C1' 8OG 201 A 1 HETATM 13 N N9 8OG . . . C 3 -4.797 -0.219 27.48 1 7.91 ? N9 8OG 201 A 1 HETATM 14 C C8 8OG . . . C 3 -3.813 -0.392 28.352 1 8.32 ? C8 8OG 201 A 1 HETATM 15 N N7 8OG . . . C 3 -2.661 0.226 28.048 1 5.91 ? N7 8OG 201 A 1 HETATM 16 C C5 8OG . . . C 3 -2.936 0.835 26.855 1 4.8 ? C5 8OG 201 A 1 HETATM 17 C C6 8OG . . . C 3 -2.191 1.634 25.986 1 7.34 ? C6 8OG 201 A 1 HETATM 18 O O6 8OG . . . C 3 -0.985 1.948 26.235 1 6.76 ? O6 8OG 201 A 1 HETATM 19 N N1 8OG . . . C 3 -2.775 2.08 24.853 1 4.68 ? N1 8OG 201 A 1 HETATM 20 C C2 8OG . . . C 3 -4.048 1.777 24.557 1 3.62 ? C2 8OG 201 A 1 HETATM 21 N N2 8OG . . . C 3 -4.614 2.232 23.414 1 6.05 ? N2 8OG 201 A 1 HETATM 22 N N3 8OG . . . C 3 -4.795 1.017 25.373 1 6.46 ? N3 8OG 201 A 1 HETATM 23 C C4 8OG . . . C 3 -4.265 0.534 26.52 1 7.87 ? C4 8OG 201 A 1 HETATM 24 O O8 8OG . . . C 3 -3.975 -1.073 29.421 1 6.24 ? O8 8OG 201 A 1 # _model_server_stats.io_time_ms 57 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 344 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 24 #