data_7X9J # _model_server_result.job_id sq3Ygn5Yl44EmG_W3_nLqw _model_server_result.datetime_utc '2024-11-28 00:12:40' _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 7x9j # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":201}' # _entry.id 7X9J # _exptl.entry_id 7X9J _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 7X9J _cell.length_a 38.13 _cell.length_b 55.98 _cell.length_c 59.198 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7X9J _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 MN MN . A MN 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.267 ? metalc ? metalc2 A OE1 GLU 53 A GLU 53 1_555 F NA NA . A NA 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.6 ? metalc ? metalc3 A OE2 GLU 57 A GLU 57 1_555 E MN MN . A MN 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.502 ? metalc ? metalc4 A OE2 GLU 57 A GLU 57 1_555 F NA NA . A NA 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.685 ? metalc ? metalc5 C OP2 8OG . A 8OG 201 1_555 E MN MN . A MN 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.411 ? metalc ? metalc6 E MN MN . A MN 203 1_555 G O HOH . A HOH 309 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.447 ? metalc ? metalc7 E MN MN . A MN 203 1_555 G O HOH . A HOH 316 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.162 ? metalc ? metalc8 E MN MN . A MN 203 1_555 G O HOH . A HOH 398 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.503 ? metalc ? metalc9 F NA NA . A NA 204 1_555 G O HOH . A HOH 310 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.466 ? metalc ? metalc10 F NA NA . A NA 204 1_555 G O HOH . A HOH 311 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.719 ? metalc ? metalc11 F NA NA . A NA 204 1_555 G O HOH . A HOH 316 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? # _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 7X9J _atom_sites.fract_transf_matrix[1][1] 0.026226 _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] 0.017864 _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] 0.016892 _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 28 HOH HOH . G 7 HOH A 2 302 19 HOH HOH . G 7 HOH A 3 303 9 HOH HOH . G 7 HOH A 4 304 108 HOH HOH . G 7 HOH A 5 305 79 HOH HOH . G 7 HOH A 6 306 91 HOH HOH . G 7 HOH A 7 307 29 HOH HOH . G 7 HOH A 8 308 71 HOH HOH . G 7 HOH A 9 309 36 HOH HOH . G 7 HOH A 10 310 6 HOH HOH . G 7 HOH A 11 311 138 HOH HOH . G 7 HOH A 12 312 77 HOH HOH . G 7 HOH A 13 313 89 HOH HOH . G 7 HOH A 14 314 15 HOH HOH . G 7 HOH A 15 315 118 HOH HOH . G 7 HOH A 16 316 1 HOH HOH . G 7 HOH A 17 317 56 HOH HOH . G 7 HOH A 18 318 7 HOH HOH . G 7 HOH A 19 319 22 HOH HOH . G 7 HOH A 20 320 96 HOH HOH . G 7 HOH A 21 321 42 HOH HOH . G 7 HOH A 22 322 84 HOH HOH . G 7 HOH A 23 323 26 HOH HOH . G 7 HOH A 24 324 81 HOH HOH . G 7 HOH A 25 325 11 HOH HOH . G 7 HOH A 26 326 24 HOH HOH . G 7 HOH A 27 327 16 HOH HOH . G 7 HOH A 28 328 101 HOH HOH . G 7 HOH A 29 329 5 HOH HOH . G 7 HOH A 30 330 33 HOH HOH . G 7 HOH A 31 331 69 HOH HOH . G 7 HOH A 32 332 13 HOH HOH . G 7 HOH A 33 333 3 HOH HOH . G 7 HOH A 34 334 117 HOH HOH . G 7 HOH A 35 335 70 HOH HOH . G 7 HOH A 36 336 75 HOH HOH . G 7 HOH A 37 337 4 HOH HOH . G 7 HOH A 38 338 39 HOH HOH . G 7 HOH A 39 339 10 HOH HOH . G 7 HOH A 40 340 34 HOH HOH . G 7 HOH A 41 341 2 HOH HOH . G 7 HOH A 42 342 106 HOH HOH . G 7 HOH A 43 343 23 HOH HOH . G 7 HOH A 44 344 18 HOH HOH . G 7 HOH A 45 345 110 HOH HOH . G 7 HOH A 46 346 67 HOH HOH . G 7 HOH A 47 347 14 HOH HOH . G 7 HOH A 48 348 20 HOH HOH . G 7 HOH A 49 349 58 HOH HOH . G 7 HOH A 50 350 80 HOH HOH . G 7 HOH A 51 351 25 HOH HOH . G 7 HOH A 52 352 64 HOH HOH . G 7 HOH A 53 353 66 HOH HOH . G 7 HOH A 54 354 104 HOH HOH . G 7 HOH A 55 355 63 HOH HOH . G 7 HOH A 56 356 30 HOH HOH . G 7 HOH A 57 357 139 HOH HOH . G 7 HOH A 58 358 8 HOH HOH . G 7 HOH A 59 359 46 HOH HOH . G 7 HOH A 60 360 105 HOH HOH . G 7 HOH A 61 361 98 HOH HOH . G 7 HOH A 62 362 38 HOH HOH . G 7 HOH A 63 363 78 HOH HOH . G 7 HOH A 64 364 57 HOH HOH . G 7 HOH A 65 365 43 HOH HOH . G 7 HOH A 66 366 129 HOH HOH . G 7 HOH A 67 367 41 HOH HOH . G 7 HOH A 68 368 128 HOH HOH . G 7 HOH A 69 369 21 HOH HOH . G 7 HOH A 70 370 86 HOH HOH . G 7 HOH A 71 371 40 HOH HOH . G 7 HOH A 72 372 76 HOH HOH . G 7 HOH A 73 373 32 HOH HOH . G 7 HOH A 74 374 49 HOH HOH . G 7 HOH A 75 375 37 HOH HOH . G 7 HOH A 76 376 90 HOH HOH . G 7 HOH A 77 377 51 HOH HOH . G 7 HOH A 78 378 115 HOH HOH . G 7 HOH A 79 379 88 HOH HOH . G 7 HOH A 80 380 31 HOH HOH . G 7 HOH A 81 381 135 HOH HOH . G 7 HOH A 82 382 107 HOH HOH . G 7 HOH A 83 383 47 HOH HOH . G 7 HOH A 84 384 83 HOH HOH . G 7 HOH A 85 385 82 HOH HOH . G 7 HOH A 86 386 72 HOH HOH . G 7 HOH A 87 387 112 HOH HOH . G 7 HOH A 88 388 17 HOH HOH . G 7 HOH A 89 389 45 HOH HOH . G 7 HOH A 90 390 27 HOH HOH . G 7 HOH A 91 391 12 HOH HOH . G 7 HOH A 92 392 48 HOH HOH . G 7 HOH A 93 393 68 HOH HOH . G 7 HOH A 94 394 61 HOH HOH . G 7 HOH A 95 395 132 HOH HOH . G 7 HOH A 96 396 87 HOH HOH . G 7 HOH A 97 397 100 HOH HOH . G 7 HOH A 98 398 114 HOH HOH . G 7 HOH A 99 399 102 HOH HOH . G 7 HOH A 100 400 50 HOH HOH . G 7 HOH A 101 401 52 HOH HOH . G 7 HOH A 102 402 62 HOH HOH . G 7 HOH A 103 403 119 HOH HOH . G 7 HOH A 104 404 44 HOH HOH . G 7 HOH A 105 405 74 HOH HOH . G 7 HOH A 106 406 97 HOH HOH . G 7 HOH A 107 407 85 HOH HOH . G 7 HOH A 108 408 120 HOH HOH . G 7 HOH A 109 409 130 HOH HOH . G 7 HOH A 110 410 121 HOH HOH . G 7 HOH A 111 411 123 HOH HOH . G 7 HOH A 112 412 54 HOH HOH . G 7 HOH A 113 413 65 HOH HOH . G 7 HOH A 114 414 137 HOH HOH . G 7 HOH A 115 415 94 HOH HOH . G 7 HOH A 116 416 92 HOH HOH . G 7 HOH A 117 417 111 HOH HOH . G 7 HOH A 118 418 60 HOH HOH . G 7 HOH A 119 419 122 HOH HOH . G 7 HOH A 120 420 93 HOH HOH . G 7 HOH A 121 421 131 HOH HOH . G 7 HOH A 122 422 35 HOH HOH . G 7 HOH A 123 423 125 HOH HOH . G 7 HOH A 124 424 116 HOH HOH . G 7 HOH A 125 425 136 HOH HOH . G 7 HOH A 126 426 113 HOH HOH . G 7 HOH A 127 427 103 HOH HOH . G 7 HOH A 128 428 127 HOH HOH . G 7 HOH A 129 429 73 HOH HOH . G 7 HOH A 130 430 95 HOH HOH . G 7 HOH A 131 431 99 HOH HOH . G 7 HOH A 132 432 134 HOH HOH . G 7 HOH A 133 433 53 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 -10.111 2.051 24.25 1 18.94 ? OP3 8OG 201 A 1 HETATM 2 P P 8OG . . . C 3 -9.417 1.238 23.199 1 22.07 ? P 8OG 201 A 1 HETATM 3 O OP1 8OG . . . C 3 -10.225 0.864 21.992 1 27.43 ? OP1 8OG 201 A 1 HETATM 4 O OP2 8OG . . . C 3 -8.054 1.832 22.907 1 22.21 ? OP2 8OG 201 A 1 HETATM 5 O O5' 8OG . . . C 3 -9.096 -0.169 23.912 1 15.23 ? O5' 8OG 201 A 1 HETATM 6 C C5' 8OG . . . C 3 -7.817 -0.306 24.523 1 6.57 ? C5' 8OG 201 A 1 HETATM 7 C C4' 8OG . . . C 3 -7.904 -1.06 25.852 1 7.17 ? C4' 8OG 201 A 1 HETATM 8 O O4' 8OG . . . C 3 -6.571 -1.424 26.194 1 9.95 ? O4' 8OG 201 A 1 HETATM 9 C C3' 8OG . . . C 3 -8.417 -0.21 27.001 1 9.24 ? C3' 8OG 201 A 1 HETATM 10 O O3' 8OG . . . C 3 -9.045 -1.078 27.961 1 7.37 ? O3' 8OG 201 A 1 HETATM 11 C C2' 8OG . . . C 3 -7.156 0.331 27.645 1 8.54 ? C2' 8OG 201 A 1 HETATM 12 C C1' 8OG . . . C 3 -6.173 -0.815 27.42 1 7.8 ? C1' 8OG 201 A 1 HETATM 13 N N9 8OG . . . C 3 -4.8 -0.268 27.351 1 7.07 ? N9 8OG 201 A 1 HETATM 14 C C8 8OG . . . C 3 -3.821 -0.427 28.235 1 9.62 ? C8 8OG 201 A 1 HETATM 15 N N7 8OG . . . C 3 -2.67 0.185 27.921 1 7.88 ? N7 8OG 201 A 1 HETATM 16 C C5 8OG . . . C 3 -2.948 0.791 26.738 1 5.67 ? C5 8OG 201 A 1 HETATM 17 C C6 8OG . . . C 3 -2.196 1.584 25.883 1 9.06 ? C6 8OG 201 A 1 HETATM 18 O O6 8OG . . . C 3 -1.006 1.859 26.171 1 8.41 ? O6 8OG 201 A 1 HETATM 19 N N1 8OG . . . C 3 -2.756 2.048 24.751 1 6.82 ? N1 8OG 201 A 1 HETATM 20 C C2 8OG . . . C 3 -4.03 1.755 24.426 1 5.93 ? C2 8OG 201 A 1 HETATM 21 N N2 8OG . . . C 3 -4.578 2.213 23.277 1 7.64 ? N2 8OG 201 A 1 HETATM 22 N N3 8OG . . . C 3 -4.787 0.988 25.227 1 5.6 ? N3 8OG 201 A 1 HETATM 23 C C4 8OG . . . C 3 -4.27 0.498 26.385 1 7.8 ? C4 8OG 201 A 1 HETATM 24 O O8 8OG . . . C 3 -3.971 -1.121 29.306 1 7.9 ? O8 8OG 201 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 290 _model_server_stats.encode_time_ms 46 _model_server_stats.element_count 24 #