data_8OPP # _model_server_result.job_id tPpQq415acDtAxTcuAQCcg _model_server_result.datetime_utc '2024-10-10 11:17:28' _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 8opp # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1501}' # _entry.id 8OPP # _exptl.entry_id 8OPP _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 500.207 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-sulfanyl-phosphoryl] phosphono hydrogen phosphate' _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 8OPP _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8OPP _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _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 hydrog 'G-U MISPAIR' hydrog1 B N2 G 2 D G 2 1_555 B O2 U 23 D U 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'A-U PAIR' hydrog2 B N6 A 3 D A 3 1_555 B O4 U 22 D U 75 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'A-U PAIR' hydrog3 B N6 A 3 D A 3 1_555 B O2 U 23 D U 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'G-C PAIR' hydrog4 B O6 G 4 D G 4 1_555 B N4 C 21 D C 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'G-U MISPAIR' hydrog5 B N1 G 4 D G 4 1_555 B O4 U 22 D U 75 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 B N1 G 5 D G 5 1_555 B N3 C 21 D C 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 B N2 G 5 D G 5 1_555 B O2 C 21 D C 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 B O6 G 5 D G 5 1_555 B N4 C 21 D C 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_28_PAIR hydrog9 B N3 U 6 D U 6 1_555 B O6 G 19 D G 72 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_28_PAIR hydrog10 B O2 U 6 D U 6 1_555 B N1 G 19 D G 72 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'A-U PAIR' hydrog11 B N6 A 7 D A 7 1_555 B O2 U 18 D U 71 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 B N1 G 8 D G 8 1_555 B N3 C 17 D C 70 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 B N2 G 8 D G 8 1_555 B O2 C 17 D C 70 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 B O6 G 8 D G 8 1_555 B N4 C 17 D C 70 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 B N3 U 9 D U 9 1_555 B N1 A 16 D A 69 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 B O4 U 9 D U 9 1_555 B N6 A 16 D A 69 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C9 H15 N2 O14 P3 S' _chem_comp.formula_weight 500.207 _chem_comp.id P5E _chem_comp.mon_nstd_flag . _chem_comp.name '[[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-sulfanyl-phosphoryl] phosphono hydrogen phosphate' _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 O2G PG P5E doub 350 n n O3B PG P5E sing 351 n n O3B PB P5E sing 352 n n O4 C4 P5E doub 353 n n PG O3G P5E sing 354 n n PG O1G P5E sing 355 n n S1A PA P5E sing 356 n n O3A PB P5E sing 357 n n O3A PA P5E sing 358 n n C5 C4 P5E sing 359 n n C5 C6 P5E doub 360 n n C4 N3 P5E sing 361 n n PB O1B P5E doub 362 n n PB O2B P5E sing 363 n n PA O2A P5E doub 364 n n PA O5' P5E sing 365 n n C6 N1 P5E sing 366 n n N3 C2 P5E sing 367 n n O5' C5' P5E sing 368 n n N1 C2 P5E sing 369 n n N1 C1' P5E sing 370 n n C2 O2 P5E doub 371 n n C5' C4' P5E sing 372 n n C2' C1' P5E sing 373 n n C2' O2' P5E sing 374 n n C2' C3' P5E sing 375 n n C1' O4' P5E sing 376 n n O4' C4' P5E sing 377 n n C4' C3' P5E sing 378 n n C3' O3' P5E sing 379 n n O2B H1 P5E sing 380 n n O1G H2 P5E sing 381 n n O3G H3 P5E sing 382 n n C5' H4 P5E sing 383 n n C5' H5 P5E sing 384 n n C4' H6 P5E sing 385 n n C1' H7 P5E sing 386 n n C2' H8 P5E sing 387 n n O2' H9 P5E sing 388 n n C3' H10 P5E sing 389 n n O3' H11 P5E sing 390 n n C6 H12 P5E sing 391 n n N3 H13 P5E sing 392 n n C5 H14 P5E sing 393 n n S1A H15 P5E sing 394 n n # _atom_sites.entry_id 8OPP _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # _pdbx_nonpoly_scheme.asym_id C _pdbx_nonpoly_scheme.entity_id 3 _pdbx_nonpoly_scheme.mon_id P5E _pdbx_nonpoly_scheme.pdb_strand_id A _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 1501 _pdbx_nonpoly_scheme.auth_seq_num 1 _pdbx_nonpoly_scheme.pdb_mon_id P5E _pdbx_nonpoly_scheme.auth_mon_id P5E _pdbx_nonpoly_scheme.pdb_ins_code . # 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 P5E . . . C 3 127.49 116.009 146.057 1 60.6 ? PA P5E 1501 A 1 HETATM 2 O O2A P5E . . . C 3 128.059 116.114 144.717 1 60.6 ? O2A P5E 1501 A 1 HETATM 3 O O3A P5E . . . C 3 127.121 117.515 146.625 1 60.6 ? O3A P5E 1501 A 1 HETATM 4 O O5' P5E . . . C 3 126.111 115.107 145.998 1 60.6 ? O5' P5E 1501 A 1 HETATM 5 P PB P5E . . . C 3 127.405 118.024 148.167 1 60.6 ? PB P5E 1501 A 1 HETATM 6 O O1B P5E . . . C 3 127.13 119.505 148.265 1 60.6 ? O1B P5E 1501 A 1 HETATM 7 O O2B P5E . . . C 3 128.842 117.755 148.547 1 60.6 ? O2B P5E 1501 A 1 HETATM 8 O O3B P5E . . . C 3 126.397 117.213 149.188 1 60.6 ? O3B P5E 1501 A 1 HETATM 9 P PG P5E . . . C 3 124.805 116.939 148.856 1 60.6 ? PG P5E 1501 A 1 HETATM 10 O O1G P5E . . . C 3 124.636 115.538 148.321 1 60.6 ? O1G P5E 1501 A 1 HETATM 11 O O2G P5E . . . C 3 124.329 117.933 147.823 1 60.6 ? O2G P5E 1501 A 1 HETATM 12 O O3G P5E . . . C 3 123.991 117.097 150.117 1 60.6 ? O3G P5E 1501 A 1 HETATM 13 C C5' P5E . . . C 3 126.209 113.76 145.626 1 60.6 ? C5' P5E 1501 A 1 HETATM 14 C C4' P5E . . . C 3 124.975 113.322 145.191 1 60.6 ? C4' P5E 1501 A 1 HETATM 15 O O4' P5E . . . C 3 124.58 114.041 143.874 1 60.6 ? O4' P5E 1501 A 1 HETATM 16 C C1' P5E . . . C 3 123.977 113.141 143.192 1 60.6 ? C1' P5E 1501 A 1 HETATM 17 C C2' P5E . . . C 3 124.746 111.713 143.592 1 60.6 ? C2' P5E 1501 A 1 HETATM 18 O O2' P5E . . . C 3 123.857 110.582 143.356 1 60.6 ? O2' P5E 1501 A 1 HETATM 19 C C3' P5E . . . C 3 125.027 111.791 144.828 1 60.6 ? C3' P5E 1501 A 1 HETATM 20 O O3' P5E . . . C 3 124.005 111.041 145.633 1 60.6 ? O3' P5E 1501 A 1 HETATM 21 N N1 P5E . . . C 3 124.09 113.38 141.785 1 60.6 ? N1 P5E 1501 A 1 HETATM 22 C C6 P5E . . . C 3 123.686 112.334 140.862 1 60.6 ? C6 P5E 1501 A 1 HETATM 23 C C2 P5E . . . C 3 124.608 114.675 141.252 1 60.6 ? C2 P5E 1501 A 1 HETATM 24 O O2 P5E . . . C 3 124.943 115.544 141.986 1 60.6 ? O2 P5E 1501 A 1 HETATM 25 N N3 P5E . . . C 3 124.711 114.889 139.782 1 60.6 ? N3 P5E 1501 A 1 HETATM 26 C C4 P5E . . . C 3 124.307 113.841 138.862 1 60.6 ? C4 P5E 1501 A 1 HETATM 27 O O4 P5E . . . C 3 124.39 114.014 137.693 1 60.6 ? O4 P5E 1501 A 1 HETATM 28 C C5 P5E . . . C 3 123.789 112.549 139.39 1 60.6 ? C5 P5E 1501 A 1 HETATM 29 S S1A P5E . . . C 3 128.873 115.051 147.356 1 60.6 ? S1A P5E 1501 A 1 HETATM 30 H H4 P5E . . . C 3 126.523 113.17 146.481 1 60.6 ? H4 P5E 1501 A 1 HETATM 31 H H5 P5E . . . C 3 126.935 113.656 144.827 1 60.6 ? H5 P5E 1501 A 1 HETATM 32 H H6 P5E . . . C 3 124.224 113.499 145.95 1 60.6 ? H6 P5E 1501 A 1 HETATM 33 H H7 P5E . . . C 3 122.932 113.093 143.485 1 60.6 ? H7 P5E 1501 A 1 HETATM 34 H H8 P5E . . . C 3 125.655 111.607 143.013 1 60.6 ? H8 P5E 1501 A 1 HETATM 35 H H9 P5E . . . C 3 123.859 110.017 144.112 1 60.6 ? H9 P5E 1501 A 1 HETATM 36 H H10 P5E . . . C 3 126.021 111.397 145.012 1 60.6 ? H10 P5E 1501 A 1 HETATM 37 H H11 P5E . . . C 3 124.165 111.18 146.552 1 60.6 ? H11 P5E 1501 A 1 HETATM 38 H H12 P5E . . . C 3 123.309 111.394 141.244 1 60.6 ? H12 P5E 1501 A 1 HETATM 39 H H13 P5E . . . C 3 125.059 115.757 139.426 1 60.6 ? H13 P5E 1501 A 1 HETATM 40 H H14 P5E . . . C 3 123.487 111.765 138.705 1 60.6 ? H14 P5E 1501 A 1 HETATM 41 H H15 P5E . . . C 3 129.735 114.34 146.638 1 60.6 ? H15 P5E 1501 A 1 # _model_server_stats.io_time_ms 80 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 264 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 41 #