data_7WW9 # _model_server_result.job_id uCgt2a8RktG6zqs0krQ9bA _model_server_result.datetime_utc '2024-11-27 23:14:14' _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 7ww9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":202}' # _entry.id 7WW9 # _exptl.entry_id 7WW9 _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 7WW9 _cell.length_a 37.962 _cell.length_b 55.906 _cell.length_c 59.12 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7WW9 _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,H,I _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 # 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 metalc ? metalc1 A O GLY 37 A GLY 37 1_555 E MN MN . A MN 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.178 ? metalc ? metalc2 A OE2 GLU 53 A GLU 53 1_555 F MN MN . A MN 205 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.652 ? metalc ? metalc3 A OE1 GLU 53 A GLU 53 1_555 G MN MN . A MN 206 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.553 ? metalc ? metalc4 A OE1 GLU 53 A GLU 53 1_555 H NA NA . A NA 207 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.44 ? metalc ? metalc5 A OE2 GLU 57 A GLU 57 1_555 E MN MN . A MN 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.169 ? metalc ? metalc6 A OE2 GLU 57 A GLU 57 1_555 G MN MN . A MN 206 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.422 ? metalc ? metalc7 A OE2 GLU 57 A GLU 57 1_555 H NA NA . A NA 207 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.521 ? metalc ? metalc8 B O2B 8DG . A 8DG 201 1_555 E MN MN . A MN 204 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.142 ? metalc ? metalc9 B O1A 8DG . A 8DG 201 1_555 E MN MN . A MN 204 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.13 ? metalc ? metalc10 B O2G 8DG . A 8DG 201 1_555 F MN MN . A MN 205 1_555 ? A ? ? A ? ? ? ? ? ? ? 2.401 ? metalc ? metalc11 B O1B 8DG . A 8DG 201 1_555 F MN MN . A MN 205 1_555 ? A ? ? A ? ? ? ? ? ? ? 2.217 ? metalc ? metalc12 B O2B 8DG . A 8DG 201 1_555 G MN MN . A MN 206 1_555 ? A ? ? A ? ? ? ? ? ? ? 2.447 ? metalc ? metalc13 C OP2 8OG . A 8OG 202 1_555 E MN MN . A MN 204 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.177 ? metalc ? metalc14 E MN MN . A MN 204 1_555 I O HOH . A HOH 341 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.191 ? metalc ? metalc15 E MN MN . A MN 204 1_555 I O HOH . A HOH 398 1_555 ? ? ? ? C ? ? ? ? ? ? ? 2.105 ? metalc ? metalc16 E MN MN . A MN 204 1_555 I O HOH . A HOH 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.339 ? metalc ? metalc17 F MN MN . A MN 205 1_555 I O HOH . A HOH 326 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.453 ? metalc ? metalc18 F MN MN . A MN 205 1_555 I O HOH . A HOH 374 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.261 ? metalc ? metalc19 G MN MN . A MN 206 1_555 I O HOH . A HOH 308 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.318 ? metalc ? metalc20 G MN MN . A MN 206 1_555 I O HOH . A HOH 359 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.612 ? metalc ? metalc21 H NA NA . A NA 207 1_555 I O HOH . A HOH 308 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.429 ? metalc ? metalc22 H NA NA . A NA 207 1_555 I O HOH . A HOH 359 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.762 ? # _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 51 n n OP3 HOP3 8OG sing 52 n n P OP1 8OG doub 53 n n P OP2 8OG sing 54 n n P O5' 8OG sing 55 n n OP2 HOP2 8OG sing 56 n n O5' C5' 8OG sing 57 n n C5' C4' 8OG sing 58 n n C5' H5' 8OG sing 59 n n C5' "H5''" 8OG sing 60 n n C4' O4' 8OG sing 61 n n C4' C3' 8OG sing 62 n n C4' H4' 8OG sing 63 n n O4' C1' 8OG sing 64 n n C3' O3' 8OG sing 65 n n C3' C2' 8OG sing 66 n n C3' H3' 8OG sing 67 n n O3' HO3' 8OG sing 68 n n C2' C1' 8OG sing 69 n n C2' H2' 8OG sing 70 n n C2' "H2''" 8OG sing 71 n n C1' N9 8OG sing 72 n n C1' H1' 8OG sing 73 n n N9 C8 8OG sing 74 n n N9 C4 8OG sing 75 n n C8 N7 8OG sing 76 n n C8 O8 8OG doub 77 n n N7 C5 8OG sing 78 n n N7 H7 8OG sing 79 n n C5 C6 8OG sing 80 n n C5 C4 8OG doub 81 n n C6 O6 8OG doub 82 n n C6 N1 8OG sing 83 n n N1 C2 8OG sing 84 n n N1 H1 8OG sing 85 n n C2 N2 8OG sing 86 n n C2 N3 8OG doub 87 n n N2 H21 8OG sing 88 n n N2 H22 8OG sing 89 n n N3 C4 8OG sing 90 n n # _atom_sites.entry_id 7WW9 _atom_sites.fract_transf_matrix[1][1] 0.026342 _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] 0.017887 _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] 0.016915 _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 8DG A 1 201 25 8DG 8GT . C 3 8OG A 1 202 26 8OG 8OG . D 4 SO4 A 1 203 1 SO4 SO4 . E 5 MN A 1 204 1 MN MN . F 5 MN A 1 205 2 MN MN . G 5 MN A 1 206 4 MN MN . H 6 NA A 1 207 5 NA NA . I 7 HOH A 1 301 49 HOH HOH . I 7 HOH A 2 302 58 HOH HOH . I 7 HOH A 3 303 38 HOH HOH . I 7 HOH A 4 304 90 HOH HOH . I 7 HOH A 5 305 26 HOH HOH . I 7 HOH A 6 306 50 HOH HOH . I 7 HOH A 7 307 75 HOH HOH . I 7 HOH A 8 308 5 HOH HOH . I 7 HOH A 9 309 63 HOH HOH . I 7 HOH A 10 310 83 HOH HOH . I 7 HOH A 11 311 33 HOH HOH . I 7 HOH A 12 312 76 HOH HOH . I 7 HOH A 13 313 87 HOH HOH . I 7 HOH A 14 314 172 HOH HOH . I 7 HOH A 15 315 84 HOH HOH . I 7 HOH A 16 316 81 HOH HOH . I 7 HOH A 17 317 61 HOH HOH . I 7 HOH A 18 318 15 HOH HOH . I 7 HOH A 19 319 93 HOH HOH . I 7 HOH A 20 320 55 HOH HOH . I 7 HOH A 21 321 30 HOH HOH . I 7 HOH A 22 322 21 HOH HOH . I 7 HOH A 23 323 32 HOH HOH . I 7 HOH A 24 324 10 HOH HOH . I 7 HOH A 25 325 45 HOH HOH . I 7 HOH A 26 326 7 HOH HOH . I 7 HOH A 27 327 13 HOH HOH . I 7 HOH A 28 328 11 HOH HOH . I 7 HOH A 29 329 71 HOH HOH . I 7 HOH A 30 330 67 HOH HOH . I 7 HOH A 31 331 173 HOH HOH . I 7 HOH A 32 332 16 HOH HOH . I 7 HOH A 33 333 178 HOH HOH . I 7 HOH A 34 334 57 HOH HOH . I 7 HOH A 35 335 40 HOH HOH . I 7 HOH A 36 336 161 HOH HOH . I 7 HOH A 37 337 60 HOH HOH . I 7 HOH A 38 338 18 HOH HOH . I 7 HOH A 39 339 179 HOH HOH . I 7 HOH A 40 340 42 HOH HOH . I 7 HOH A 41 341 1 HOH HOH . I 7 HOH A 42 342 82 HOH HOH . I 7 HOH A 43 343 47 HOH HOH . I 7 HOH A 44 344 22 HOH HOH . I 7 HOH A 45 345 78 HOH HOH . I 7 HOH A 46 346 134 HOH HOH . I 7 HOH A 47 347 92 HOH HOH . I 7 HOH A 48 348 34 HOH HOH . I 7 HOH A 49 349 56 HOH HOH . I 7 HOH A 50 350 3 HOH HOH . I 7 HOH A 51 351 177 HOH HOH . I 7 HOH A 52 352 175 HOH HOH . I 7 HOH A 53 353 28 HOH HOH . I 7 HOH A 54 354 85 HOH HOH . I 7 HOH A 55 355 51 HOH HOH . I 7 HOH A 56 356 171 HOH HOH . I 7 HOH A 57 357 23 HOH HOH . I 7 HOH A 58 358 37 HOH HOH . I 7 HOH A 59 359 3 HOH HOH . I 7 HOH A 60 360 17 HOH HOH . I 7 HOH A 61 361 20 HOH HOH . I 7 HOH A 62 362 127 HOH HOH . I 7 HOH A 63 363 80 HOH HOH . I 7 HOH A 64 364 95 HOH HOH . I 7 HOH A 65 365 88 HOH HOH . I 7 HOH A 66 366 65 HOH HOH . I 7 HOH A 67 367 59 HOH HOH . I 7 HOH A 68 368 52 HOH HOH . I 7 HOH A 69 369 44 HOH HOH . I 7 HOH A 70 370 124 HOH HOH . I 7 HOH A 71 371 96 HOH HOH . I 7 HOH A 72 372 94 HOH HOH . I 7 HOH A 73 373 46 HOH HOH . I 7 HOH A 74 374 6 HOH HOH . I 7 HOH A 75 375 39 HOH HOH . I 7 HOH A 76 376 29 HOH HOH . I 7 HOH A 77 377 111 HOH HOH . I 7 HOH A 78 378 14 HOH HOH . I 7 HOH A 79 379 176 HOH HOH . I 7 HOH A 80 380 35 HOH HOH . I 7 HOH A 81 381 28 HOH HOH . I 7 HOH A 82 382 68 HOH HOH . I 7 HOH A 83 383 36 HOH HOH . I 7 HOH A 84 384 64 HOH HOH . I 7 HOH A 85 385 70 HOH HOH . I 7 HOH A 86 386 74 HOH HOH . I 7 HOH A 87 387 27 HOH HOH . I 7 HOH A 88 388 72 HOH HOH . I 7 HOH A 89 389 62 HOH HOH . I 7 HOH A 90 390 19 HOH HOH . I 7 HOH A 91 391 99 HOH HOH . I 7 HOH A 92 392 24 HOH HOH . I 7 HOH A 93 393 123 HOH HOH . I 7 HOH A 94 394 164 HOH HOH . I 7 HOH A 95 395 126 HOH HOH . I 7 HOH A 96 396 66 HOH HOH . I 7 HOH A 97 397 41 HOH HOH . I 7 HOH A 98 398 27 HOH HOH . I 7 HOH A 99 399 174 HOH HOH . I 7 HOH A 100 400 98 HOH HOH . I 7 HOH A 101 401 181 HOH HOH . I 7 HOH A 102 402 97 HOH HOH . I 7 HOH A 103 403 25 HOH HOH . I 7 HOH A 104 404 48 HOH HOH . I 7 HOH A 105 405 2 HOH HOH . I 7 HOH A 106 406 116 HOH HOH . I 7 HOH A 107 407 107 HOH HOH . I 7 HOH A 108 408 144 HOH HOH . I 7 HOH A 109 409 43 HOH HOH . I 7 HOH A 110 410 125 HOH HOH . I 7 HOH A 111 411 73 HOH HOH . I 7 HOH A 112 412 130 HOH HOH . I 7 HOH A 113 413 79 HOH HOH . I 7 HOH A 114 414 110 HOH HOH . I 7 HOH A 115 415 150 HOH HOH . I 7 HOH A 116 416 105 HOH HOH . I 7 HOH A 117 417 142 HOH HOH . I 7 HOH A 118 418 104 HOH HOH . I 7 HOH A 119 419 101 HOH HOH . I 7 HOH A 120 420 137 HOH HOH . I 7 HOH A 121 421 183 HOH HOH . I 7 HOH A 122 422 118 HOH HOH . I 7 HOH A 123 423 163 HOH HOH . I 7 HOH A 124 424 109 HOH HOH . I 7 HOH A 125 425 115 HOH HOH . I 7 HOH A 126 426 112 HOH HOH . I 7 HOH A 127 427 106 HOH HOH . I 7 HOH A 128 428 114 HOH HOH . I 7 HOH A 129 429 120 HOH HOH . I 7 HOH A 130 430 162 HOH HOH . I 7 HOH A 131 431 102 HOH HOH . I 7 HOH A 132 432 136 HOH HOH . I 7 HOH A 133 433 119 HOH HOH . I 7 HOH A 134 434 103 HOH HOH . I 7 HOH A 135 435 145 HOH HOH . I 7 HOH A 136 436 147 HOH HOH . I 7 HOH A 137 437 29 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 . B . C 3 -10.065 2.07 24.215 0.8 12.45 ? OP3 8OG 202 A 1 HETATM 2 P P 8OG . B . C 3 -9.259 1.335 23.22 0.8 12.25 ? P 8OG 202 A 1 HETATM 3 O OP1 8OG . B . C 3 -10.105 0.998 22.051 0.8 16.17 ? OP1 8OG 202 A 1 HETATM 4 O OP2 8OG . B . C 3 -8.021 2.023 22.754 0.8 12.19 ? OP2 8OG 202 A 1 HETATM 5 O O5' 8OG . B . C 3 -8.813 -0.072 23.862 0.8 11.38 ? O5' 8OG 202 A 1 HETATM 6 C C5' 8OG . B . C 3 -7.61 -0.121 24.62 0.8 10.97 ? C5' 8OG 202 A 1 HETATM 7 C C4' 8OG . B . C 3 -7.775 -1.028 25.845 0.8 8.63 ? C4' 8OG 202 A 1 HETATM 8 O O4' 8OG . B . C 3 -6.474 -1.469 26.262 0.8 8.17 ? O4' 8OG 202 A 1 HETATM 9 C C3' 8OG . B . C 3 -8.365 -0.295 27.044 0.8 7.09 ? C3' 8OG 202 A 1 HETATM 10 O O3' 8OG . B . C 3 -9.013 -1.251 27.91 0.8 7.71 ? O3' 8OG 202 A 1 HETATM 11 C C2' 8OG . B . C 3 -7.158 0.299 27.718 0.8 7.96 ? C2' 8OG 202 A 1 HETATM 12 C C1' 8OG . B . C 3 -6.139 -0.803 27.494 0.8 7.53 ? C1' 8OG 202 A 1 HETATM 13 N N9 8OG . B . C 3 -4.76 -0.277 27.406 0.8 7.83 ? N9 8OG 202 A 1 HETATM 14 C C8 8OG . B . C 3 -3.744 -0.442 28.335 0.8 8.24 ? C8 8OG 202 A 1 HETATM 15 N N7 8OG . B . C 3 -2.659 0.145 28.035 0.8 8.85 ? N7 8OG 202 A 1 HETATM 16 C C5 8OG . B . C 3 -2.907 0.797 26.818 0.8 6.58 ? C5 8OG 202 A 1 HETATM 17 C C6 8OG . B . C 3 -2.073 1.611 25.982 0.8 6.12 ? C6 8OG 202 A 1 HETATM 18 O O6 8OG . B . C 3 -0.904 1.934 26.198 0.8 6.54 ? O6 8OG 202 A 1 HETATM 19 N N1 8OG . B . C 3 -2.752 2.057 24.821 0.8 3.99 ? N1 8OG 202 A 1 HETATM 20 C C2 8OG . B . C 3 -4.076 1.75 24.505 0.8 6.35 ? C2 8OG 202 A 1 HETATM 21 N N2 8OG . B . C 3 -4.57 2.236 23.375 0.8 4.71 ? N2 8OG 202 A 1 HETATM 22 N N3 8OG . B . C 3 -4.862 0.974 25.29 0.8 7.07 ? N3 8OG 202 A 1 HETATM 23 C C4 8OG . B . C 3 -4.227 0.537 26.424 0.8 6.41 ? C4 8OG 202 A 1 HETATM 24 O O8 8OG . B . C 3 -3.925 -1.132 29.353 0.8 6.99 ? O8 8OG 202 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 287 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 24 #