data_7X9O # _model_server_result.job_id DYap0q_ssanZCVvt-7XidQ _model_server_result.datetime_utc '2024-11-24 03:51:26' _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 7x9o # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":201}' # _entry.id 7X9O # _exptl.entry_id 7X9O _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 7X9O _cell.length_a 38.449 _cell.length_b 56.014 _cell.length_c 59.126 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7X9O _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 ? ? ? ? ? ? ? ? ? ? ? ? 1.415 ? metalc ? metalc1 A O GLY 37 A GLY 37 1_555 E MG MG . A MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? metalc ? metalc2 A OE1 GLU 53 A GLU 53 1_555 F MG MG . A MG 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.429 ? metalc ? metalc3 A OE2 GLU 57 A GLU 57 1_555 E MG MG . A MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.089 ? metalc ? metalc4 A OE2 GLU 57 A GLU 57 1_555 F MG MG . A MG 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.313 ? metalc ? metalc5 C OP2 8OG . A 8OG 201 1_555 E MG MG . A MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.091 ? metalc ? metalc6 E MG MG . A MG 203 1_555 G O HOH . A HOH 343 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? metalc ? metalc7 E MG MG . A MG 203 1_555 G O HOH . A HOH 356 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? metalc ? metalc8 E MG MG . A MG 203 1_555 G O HOH . A HOH 386 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.175 ? metalc ? metalc9 F MG MG . A MG 204 1_555 G O HOH . A HOH 311 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.158 ? metalc ? metalc10 F MG MG . A MG 204 1_555 G O HOH . A HOH 343 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? metalc ? metalc11 F MG MG . A MG 204 1_555 G O HOH . A HOH 348 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.253 ? # _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 7X9O _atom_sites.fract_transf_matrix[1][1] 0.026008 _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] 0.017853 _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] 0.016913 _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 MG A 1 203 1 MG MG . F 5 MG A 1 204 2 MG MG . G 6 HOH A 1 301 78 HOH HOH . G 6 HOH A 2 302 56 HOH HOH . G 6 HOH A 3 303 44 HOH HOH . G 6 HOH A 4 304 62 HOH HOH . G 6 HOH A 5 305 119 HOH HOH . G 6 HOH A 6 306 157 HOH HOH . G 6 HOH A 7 307 66 HOH HOH . G 6 HOH A 8 308 36 HOH HOH . G 6 HOH A 9 309 126 HOH HOH . G 6 HOH A 10 310 136 HOH HOH . G 6 HOH A 11 311 57 HOH HOH . G 6 HOH A 12 312 38 HOH HOH . G 6 HOH A 13 313 93 HOH HOH . G 6 HOH A 14 314 100 HOH HOH . G 6 HOH A 15 315 45 HOH HOH . G 6 HOH A 16 316 15 HOH HOH . G 6 HOH A 17 317 146 HOH HOH . G 6 HOH A 18 318 101 HOH HOH . G 6 HOH A 19 319 10 HOH HOH . G 6 HOH A 20 320 35 HOH HOH . G 6 HOH A 21 321 46 HOH HOH . G 6 HOH A 22 322 111 HOH HOH . G 6 HOH A 23 323 34 HOH HOH . G 6 HOH A 24 324 68 HOH HOH . G 6 HOH A 25 325 19 HOH HOH . G 6 HOH A 26 326 91 HOH HOH . G 6 HOH A 27 327 137 HOH HOH . G 6 HOH A 28 328 163 HOH HOH . G 6 HOH A 29 329 4 HOH HOH . G 6 HOH A 30 330 23 HOH HOH . G 6 HOH A 31 331 12 HOH HOH . G 6 HOH A 32 332 33 HOH HOH . G 6 HOH A 33 333 24 HOH HOH . G 6 HOH A 34 334 1 HOH HOH . G 6 HOH A 35 335 9 HOH HOH . G 6 HOH A 36 336 26 HOH HOH . G 6 HOH A 37 337 173 HOH HOH . G 6 HOH A 38 338 20 HOH HOH . G 6 HOH A 39 339 25 HOH HOH . G 6 HOH A 40 340 155 HOH HOH . G 6 HOH A 41 341 37 HOH HOH . G 6 HOH A 42 342 102 HOH HOH . G 6 HOH A 43 343 7 HOH HOH . G 6 HOH A 44 344 82 HOH HOH . G 6 HOH A 45 345 96 HOH HOH . G 6 HOH A 46 346 28 HOH HOH . G 6 HOH A 47 347 3 HOH HOH . G 6 HOH A 48 348 49 HOH HOH . G 6 HOH A 49 349 73 HOH HOH . G 6 HOH A 50 350 140 HOH HOH . G 6 HOH A 51 351 128 HOH HOH . G 6 HOH A 52 352 130 HOH HOH . G 6 HOH A 53 353 95 HOH HOH . G 6 HOH A 54 354 86 HOH HOH . G 6 HOH A 55 355 172 HOH HOH . G 6 HOH A 56 356 2 HOH HOH . G 6 HOH A 57 357 171 HOH HOH . G 6 HOH A 58 358 18 HOH HOH . G 6 HOH A 59 359 166 HOH HOH . G 6 HOH A 60 360 106 HOH HOH . G 6 HOH A 61 361 8 HOH HOH . G 6 HOH A 62 362 90 HOH HOH . G 6 HOH A 63 363 30 HOH HOH . G 6 HOH A 64 364 92 HOH HOH . G 6 HOH A 65 365 40 HOH HOH . G 6 HOH A 66 366 89 HOH HOH . G 6 HOH A 67 367 32 HOH HOH . G 6 HOH A 68 368 58 HOH HOH . G 6 HOH A 69 369 17 HOH HOH . G 6 HOH A 70 370 164 HOH HOH . G 6 HOH A 71 371 75 HOH HOH . G 6 HOH A 72 372 6 HOH HOH . G 6 HOH A 73 373 13 HOH HOH . G 6 HOH A 74 374 48 HOH HOH . G 6 HOH A 75 375 74 HOH HOH . G 6 HOH A 76 376 71 HOH HOH . G 6 HOH A 77 377 141 HOH HOH . G 6 HOH A 78 378 53 HOH HOH . G 6 HOH A 79 379 105 HOH HOH . G 6 HOH A 80 380 21 HOH HOH . G 6 HOH A 81 381 153 HOH HOH . G 6 HOH A 82 382 79 HOH HOH . G 6 HOH A 83 383 132 HOH HOH . G 6 HOH A 84 384 43 HOH HOH . G 6 HOH A 85 385 80 HOH HOH . G 6 HOH A 86 386 14 HOH HOH . G 6 HOH A 87 387 41 HOH HOH . G 6 HOH A 88 388 61 HOH HOH . G 6 HOH A 89 389 97 HOH HOH . G 6 HOH A 90 390 81 HOH HOH . G 6 HOH A 91 391 123 HOH HOH . G 6 HOH A 92 392 42 HOH HOH . G 6 HOH A 93 393 143 HOH HOH . G 6 HOH A 94 394 147 HOH HOH . G 6 HOH A 95 395 144 HOH HOH . G 6 HOH A 96 396 27 HOH HOH . G 6 HOH A 97 397 133 HOH HOH . G 6 HOH A 98 398 116 HOH HOH . G 6 HOH A 99 399 99 HOH HOH . G 6 HOH A 100 400 47 HOH HOH . G 6 HOH A 101 401 110 HOH HOH . G 6 HOH A 102 402 170 HOH HOH . G 6 HOH A 103 403 148 HOH HOH . G 6 HOH A 104 404 69 HOH HOH . G 6 HOH A 105 405 16 HOH HOH . G 6 HOH A 106 406 70 HOH HOH . G 6 HOH A 107 407 64 HOH HOH . G 6 HOH A 108 408 54 HOH HOH . G 6 HOH A 109 409 85 HOH HOH . G 6 HOH A 110 410 52 HOH HOH . G 6 HOH A 111 411 50 HOH HOH . G 6 HOH A 112 412 22 HOH HOH . G 6 HOH A 113 413 5 HOH HOH . G 6 HOH A 114 414 107 HOH HOH . G 6 HOH A 115 415 125 HOH HOH . G 6 HOH A 116 416 39 HOH HOH . G 6 HOH A 117 417 104 HOH HOH . G 6 HOH A 118 418 124 HOH HOH . G 6 HOH A 119 419 29 HOH HOH . G 6 HOH A 120 420 88 HOH HOH . G 6 HOH A 121 421 103 HOH HOH . G 6 HOH A 122 422 167 HOH HOH . G 6 HOH A 123 423 63 HOH HOH . G 6 HOH A 124 424 159 HOH HOH . G 6 HOH A 125 425 94 HOH HOH . G 6 HOH A 126 426 139 HOH HOH . G 6 HOH A 127 427 117 HOH HOH . G 6 HOH A 128 428 129 HOH HOH . G 6 HOH A 129 429 84 HOH HOH . G 6 HOH A 130 430 120 HOH HOH . G 6 HOH A 131 431 118 HOH HOH . G 6 HOH A 132 432 31 HOH HOH . G 6 HOH A 133 433 161 HOH HOH . G 6 HOH A 134 434 115 HOH HOH . G 6 HOH A 135 435 134 HOH HOH . G 6 HOH A 136 436 162 HOH HOH . G 6 HOH A 137 437 158 HOH HOH . G 6 HOH A 138 438 108 HOH HOH . G 6 HOH A 139 439 145 HOH HOH . G 6 HOH A 140 440 72 HOH HOH . G 6 HOH A 141 441 131 HOH HOH . G 6 HOH A 142 442 98 HOH HOH . G 6 HOH A 143 443 122 HOH HOH . G 6 HOH A 144 444 156 HOH HOH . G 6 HOH A 145 445 150 HOH HOH . G 6 HOH A 146 446 142 HOH HOH . G 6 HOH A 147 447 59 HOH HOH . G 6 HOH A 148 448 83 HOH HOH . G 6 HOH A 149 449 149 HOH HOH . G 6 HOH A 150 450 65 HOH HOH . G 6 HOH A 151 451 160 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 -9.92 2.133 24.188 1 13.8 ? OP3 8OG 201 A 1 HETATM 2 P P 8OG . . . C 3 -9.147 1.452 23.1 1 13.13 ? P 8OG 201 A 1 HETATM 3 O OP1 8OG . . . C 3 -10.019 1.046 21.936 1 15.14 ? OP1 8OG 201 A 1 HETATM 4 O OP2 8OG . . . C 3 -7.88 2.191 22.685 1 13.32 ? OP2 8OG 201 A 1 HETATM 5 O O5' 8OG . . . C 3 -8.682 0.023 23.696 1 13.35 ? O5' 8OG 201 A 1 HETATM 6 C C5' 8OG . . . C 3 -7.505 -0.089 24.481 1 10.9 ? C5' 8OG 201 A 1 HETATM 7 C C4' 8OG . . . C 3 -7.726 -0.939 25.741 1 9.55 ? C4' 8OG 201 A 1 HETATM 8 O O4' 8OG . . . C 3 -6.442 -1.334 26.183 1 9.31 ? O4' 8OG 201 A 1 HETATM 9 C C3' 8OG . . . C 3 -8.326 -0.163 26.907 1 10.16 ? C3' 8OG 201 A 1 HETATM 10 O O3' 8OG . . . C 3 -8.974 -1.104 27.779 1 11.98 ? O3' 8OG 201 A 1 HETATM 11 C C2' 8OG . . . C 3 -7.127 0.372 27.658 1 9.72 ? C2' 8OG 201 A 1 HETATM 12 C C1' 8OG . . . C 3 -6.127 -0.761 27.446 1 9.69 ? C1' 8OG 201 A 1 HETATM 13 N N9 8OG . . . C 3 -4.75 -0.228 27.428 1 9.25 ? N9 8OG 201 A 1 HETATM 14 C C8 8OG . . . C 3 -3.791 -0.426 28.325 1 8.41 ? C8 8OG 201 A 1 HETATM 15 N N7 8OG . . . C 3 -2.623 0.178 28.036 1 8.02 ? N7 8OG 201 A 1 HETATM 16 C C5 8OG . . . C 3 -2.875 0.806 26.843 1 6.85 ? C5 8OG 201 A 1 HETATM 17 C C6 8OG . . . C 3 -2.122 1.61 25.978 1 7.44 ? C6 8OG 201 A 1 HETATM 18 O O6 8OG . . . C 3 -0.929 1.936 26.222 1 8.09 ? O6 8OG 201 A 1 HETATM 19 N N1 8OG . . . C 3 -2.699 2.061 24.845 1 6.46 ? N1 8OG 201 A 1 HETATM 20 C C2 8OG . . . C 3 -3.969 1.776 24.529 1 7.3 ? C2 8OG 201 A 1 HETATM 21 N N2 8OG . . . C 3 -4.507 2.231 23.371 1 8.76 ? N2 8OG 201 A 1 HETATM 22 N N3 8OG . . . C 3 -4.724 1.01 25.331 1 8.84 ? N3 8OG 201 A 1 HETATM 23 C C4 8OG . . . C 3 -4.197 0.534 26.481 1 7.83 ? C4 8OG 201 A 1 HETATM 24 O O8 8OG . . . C 3 -3.996 -1.13 29.395 1 8.09 ? O8 8OG 201 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 238 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 24 #