data_8Z8X # _model_server_result.job_id RvJklEpM01A6tb55CAmiHQ _model_server_result.datetime_utc '2025-02-22 20:14:44' _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 8z8x # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":801}' # _entry.id 8Z8X # _exptl.entry_id 8Z8X _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 521.208 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER' _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 8Z8X _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8Z8X _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 pentameric _pdbx_struct_assembly.oligomeric_count 5 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F _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 6 _struct_asym.id F _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 'A-A MISPAIR' hydrog1 D N6 A 1 D A 1 1_555 D N3 A 10 D A 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 D N1 G 2 D G 2 1_555 D N3 C 9 D C 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 D N2 G 2 D G 2 1_555 D O2 C 9 D C 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 D O6 G 2 D G 2 1_555 D N4 C 9 D C 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 D N1 A 3 D A 3 1_555 D N3 U 8 D U 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 D N6 A 3 D A 3 1_555 D O4 U 8 D U 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'G-A MISPAIR' hydrog7 D N3 G 4 D G 4 1_555 D N6 A 7 D A 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'A-A MISPAIR' hydrog8 D N3 A 5 D A 5 1_555 D N6 A 7 D A 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 D N1 A 11 D A 11 1_555 E N3 U 8 E U 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 D N6 A 11 D A 11 1_555 E O4 U 8 E U 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 D N1 G 12 D G 12 1_555 E N3 C 7 E C 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 D N2 G 12 D G 12 1_555 E O2 C 7 E C 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 D O6 G 12 D G 12 1_555 E N4 C 7 E C 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 D N1 G 13 D G 13 1_555 E N3 C 6 E C 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 D N2 G 13 D G 13 1_555 E O2 C 6 E C 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 D O6 G 13 D G 13 1_555 E N4 C 6 E C 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 D N3 C 14 D C 14 1_555 E N1 G 5 E G 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 D N4 C 14 D C 14 1_555 E O6 G 5 E G 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 D O2 C 14 D C 14 1_555 E N2 G 5 E G 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 D N1 A 15 D A 15 1_555 E N3 U 4 E U 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 D N6 A 15 D A 15 1_555 E O4 U 4 E U 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 D N1 G 16 D G 16 1_555 E N3 C 3 E C 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 D N2 G 16 D G 16 1_555 E O2 C 3 E C 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 D O6 G 16 D G 16 1_555 E N4 C 3 E C 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 D N3 U 17 D U 17 1_555 E N1 A 2 E A 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 D O4 U 17 D U 17 1_555 E N6 A 2 E A 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'U-G MISPAIR' hydrog27 D O2 U 18 D U 18 1_555 E N2 G 1 E G 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'U-A PAIR' hydrog28 D O2 U 18 D U 18 1_555 E N6 A 2 E A 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C11 H18 N5 O13 P3' _chem_comp.formula_weight 521.208 _chem_comp.id G2P _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER' _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 PG O1G G2P sing 198 n n PG O2G G2P doub 199 n n PG O3G G2P sing 200 n n PG O3B G2P sing 201 n n O3B PB G2P sing 202 n n PB O1B G2P sing 203 n n PB O2B G2P doub 204 n n PB C3A G2P sing 205 n n C3A PA G2P sing 206 n n C3A H3A1 G2P sing 207 n n C3A H3A2 G2P sing 208 n n PA O1A G2P sing 209 n n PA O2A G2P doub 210 n n PA O5' G2P sing 211 n n O5' C5' G2P sing 212 n n C5' C4' G2P sing 213 n n C5' "H5'1" G2P sing 214 n n C5' "H5'2" G2P sing 215 n n C4' O4' G2P sing 216 n n C4' C3' G2P sing 217 n n C4' H4' G2P sing 218 n n O4' C1' G2P sing 219 n n C3' O3' G2P sing 220 n n C3' C2' G2P sing 221 n n C3' H3' G2P sing 222 n n O3' HA G2P sing 223 n n C2' O2' G2P sing 224 n n C2' C1' G2P sing 225 n n C2' H2' G2P sing 226 n n O2' HB G2P sing 227 n n C1' N9 G2P sing 228 n n C1' H1' G2P sing 229 n n N9 C8 G2P sing 230 n y N9 C4 G2P sing 231 n y C8 N7 G2P doub 232 n y C8 H8 G2P sing 233 n n N7 C5 G2P sing 234 n y C5 C6 G2P sing 235 n y C5 C4 G2P doub 236 n y C6 O6 G2P doub 237 n n C6 N1 G2P sing 238 n y N1 C2 G2P sing 239 n y N1 H1 G2P sing 240 n n C2 N2 G2P sing 241 n n C2 N3 G2P doub 242 n y N2 H2N1 G2P sing 243 n n N2 H2N2 G2P sing 244 n n N3 C4 G2P sing 245 n y HO1 O1G G2P sing 246 n n HO2 O3G G2P sing 247 n n HO3 O1A G2P sing 248 n n HO4 O1B G2P sing 249 n n # _atom_sites.entry_id 8Z8X _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 F _pdbx_nonpoly_scheme.entity_id 6 _pdbx_nonpoly_scheme.mon_id G2P _pdbx_nonpoly_scheme.pdb_strand_id B _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 801 _pdbx_nonpoly_scheme.auth_seq_num 801 _pdbx_nonpoly_scheme.pdb_mon_id G2P _pdbx_nonpoly_scheme.auth_mon_id G2P _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 PG G2P . . . F 6 93.639 70.747 97.065 1 112.65 ? PG G2P 801 B 1 HETATM 2 O O1G G2P . . . F 6 92.54 69.776 97.472 1 112.27 ? O1G G2P 801 B 1 HETATM 3 O O2G G2P . . . F 6 94.416 71.316 98.255 1 112.06 ? O2G G2P 801 B 1 HETATM 4 O O3G G2P . . . F 6 94.523 70.297 95.911 1 112.22 ? O3G G2P 801 B 1 HETATM 5 O O3B G2P . . . F 6 92.775 72.11 96.485 1 112.87 ? O3B G2P 801 B 1 HETATM 6 P PB G2P . . . F 6 91.545 72.097 95.444 1 112.39 ? PB G2P 801 B 1 HETATM 7 O O1B G2P . . . F 6 90.75 70.816 95.508 1 111.58 ? O1B G2P 801 B 1 HETATM 8 O O2B G2P . . . F 6 90.773 73.4 95.511 1 112.43 ? O2B G2P 801 B 1 HETATM 9 C C3A G2P . . . F 6 92.477 72.15 93.846 1 111.55 ? C3A G2P 801 B 1 HETATM 10 P PA G2P . . . F 6 93.723 73.434 93.523 1 113.3 ? PA G2P 801 B 1 HETATM 11 O O1A G2P . . . F 6 94.518 73.79 94.752 1 112.92 ? O1A G2P 801 B 1 HETATM 12 O O2A G2P . . . F 6 94.495 73.062 92.277 1 111.88 ? O2A G2P 801 B 1 HETATM 13 O O5' G2P . . . F 6 92.723 74.695 93.133 1 112.23 ? O5' G2P 801 B 1 HETATM 14 C C5' G2P . . . F 6 93.17 75.666 92.231 1 112.37 ? C5' G2P 801 B 1 HETATM 15 C C4' G2P . . . F 6 92.06 75.928 91.228 1 112.52 ? C4' G2P 801 B 1 HETATM 16 O O4' G2P . . . F 6 91.429 77.186 91.452 1 112.81 ? O4' G2P 801 B 1 HETATM 17 C C3' G2P . . . F 6 92.559 76.004 89.792 1 112.32 ? C3' G2P 801 B 1 HETATM 18 O O3' G2P . . . F 6 91.523 75.839 88.86 1 111.66 ? O3' G2P 801 B 1 HETATM 19 C C2' G2P . . . F 6 92.995 77.465 89.731 1 112.62 ? C2' G2P 801 B 1 HETATM 20 O O2' G2P . . . F 6 93.028 78.021 88.455 1 112.28 ? O2' G2P 801 B 1 HETATM 21 C C1' G2P . . . F 6 91.925 78.157 90.591 1 112.88 ? C1' G2P 801 B 1 HETATM 22 N N9 G2P . . . F 6 92.433 79.272 91.366 1 112.96 ? N9 G2P 801 B 1 HETATM 23 C C8 G2P . . . F 6 92.294 79.47 92.718 1 112.61 ? C8 G2P 801 B 1 HETATM 24 N N7 G2P . . . F 6 92.858 80.566 93.121 1 112.16 ? N7 G2P 801 B 1 HETATM 25 C C5 G2P . . . F 6 93.393 81.123 91.992 1 112.35 ? C5 G2P 801 B 1 HETATM 26 C C6 G2P . . . F 6 94.126 82.325 91.818 1 111.87 ? C6 G2P 801 B 1 HETATM 27 O O6 G2P . . . F 6 94.452 83.154 92.651 1 111.34 ? O6 G2P 801 B 1 HETATM 28 N N1 G2P . . . F 6 94.481 82.505 90.476 1 111.92 ? N1 G2P 801 B 1 HETATM 29 C C2 G2P . . . F 6 94.179 81.658 89.452 1 112.18 ? C2 G2P 801 B 1 HETATM 30 N N2 G2P . . . F 6 94.616 82.015 88.225 1 111.78 ? N2 G2P 801 B 1 HETATM 31 N N3 G2P . . . F 6 93.504 80.554 89.613 1 112.53 ? N3 G2P 801 B 1 HETATM 32 C C4 G2P . . . F 6 93.137 80.33 90.887 1 112.92 ? C4 G2P 801 B 1 # _model_server_stats.io_time_ms 63 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 29 _model_server_stats.query_time_ms 306 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 32 #