data_1PPX # _model_server_result.job_id ltZVEjzhqbFbhr7eFUhusg _model_server_result.datetime_utc '2025-04-20 00:33:54' _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 1ppx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":131}' # _entry.id 1PPX # _exptl.entry_id 1PPX _exptl.method 'SOLUTION NMR' # _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 ? # _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 _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 38 A GLY 38 1_555 B MG MG . A MG 130 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.298 ? metalc ? metalc2 A OE1 GLU 53 A GLU 53 1_555 B MG MG . A MG 130 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.817 ? metalc ? metalc3 A OE2 GLU 53 A GLU 53 1_555 B MG MG . A MG 130 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.406 ? metalc ? metalc4 A OE1 GLU 56 A GLU 56 1_555 B MG MG . A MG 130 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.403 ? metalc ? metalc5 A OE2 GLU 57 A GLU 57 1_555 B MG MG . A MG 130 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.405 ? metalc ? metalc6 B MG MG . A MG 130 1_555 D O HOH . A HOH 5011 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.111 ? metalc ? metalc7 B MG MG . A MG 130 1_555 D O HOH . A HOH 5012 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.111 ? # _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 1PPX _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 # 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 MG A 1 130 130 MG MO2 . C 3 8OG A 1 131 131 8OG ODG . D 4 HOH A 1 5011 130 HOH MO2 . D 4 HOH A 2 5012 130 HOH MO2 . D 4 HOH A 3 5013 130 HOH MO2 . D 4 HOH A 4 5014 130 HOH MO2 . # 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 -8.5 -3.972 -7.025 1 20 ? OP3 8OG 131 A 1 HETATM 2 P P 8OG . . . C 3 -7.918 -5.066 -5.997 1 20 ? P 8OG 131 A 1 HETATM 3 O OP1 8OG . . . C 3 -6.552 -5.437 -6.429 1 20 ? OP1 8OG 131 A 1 HETATM 4 O OP2 8OG . . . C 3 -8.934 -6.13 -5.835 1 20 ? OP2 8OG 131 A 1 HETATM 5 O O5' 8OG . . . C 3 -7.815 -4.224 -4.629 1 20 ? O5' 8OG 131 A 1 HETATM 6 C C5' 8OG . . . C 3 -6.992 -4.678 -3.551 1 20 ? C5' 8OG 131 A 1 HETATM 7 C C4' 8OG . . . C 3 -7.671 -5.78 -2.734 1 20 ? C4' 8OG 131 A 1 HETATM 8 O O4' 8OG . . . C 3 -8.915 -5.501 -2.083 1 20 ? O4' 8OG 131 A 1 HETATM 9 C C3' 8OG . . . C 3 -8 -7.028 -3.555 1 20 ? C3' 8OG 131 A 1 HETATM 10 O O3' 8OG . . . C 3 -7.252 -8.162 -3.107 1 20 ? O3' 8OG 131 A 1 HETATM 11 C C2' 8OG . . . C 3 -9.508 -7.265 -3.428 1 20 ? C2' 8OG 131 A 1 HETATM 12 C C1' 8OG . . . C 3 -10.099 -6.174 -2.529 1 20 ? C1' 8OG 131 A 1 HETATM 13 N N9 8OG . . . C 3 -11.34 -5.521 -3.003 1 20 ? N9 8OG 131 A 1 HETATM 14 C C8 8OG . . . C 3 -11.412 -4.922 -4.233 1 20 ? C8 8OG 131 A 1 HETATM 15 N N7 8OG . . . C 3 -12.69 -4.433 -4.302 1 20 ? N7 8OG 131 A 1 HETATM 16 C C5 8OG . . . C 3 -13.393 -4.714 -3.161 1 20 ? C5 8OG 131 A 1 HETATM 17 C C6 8OG . . . C 3 -14.649 -4.468 -2.725 1 20 ? C6 8OG 131 A 1 HETATM 18 O O6 8OG . . . C 3 -15.447 -3.826 -3.493 1 20 ? O6 8OG 131 A 1 HETATM 19 N N1 8OG . . . C 3 -15.114 -4.882 -1.482 1 20 ? N1 8OG 131 A 1 HETATM 20 C C2 8OG . . . C 3 -14.244 -5.567 -0.676 1 20 ? C2 8OG 131 A 1 HETATM 21 N N2 8OG . . . C 3 -14.696 -5.966 0.521 1 20 ? N2 8OG 131 A 1 HETATM 22 N N3 8OG . . . C 3 -12.926 -5.873 -1.033 1 20 ? N3 8OG 131 A 1 HETATM 23 C C4 8OG . . . C 3 -12.546 -5.408 -2.321 1 20 ? C4 8OG 131 A 1 HETATM 24 O O8 8OG . . . C 3 -10.491 -4.833 -5.117 1 20 ? O8 8OG 131 A 1 HETATM 25 H H5' 8OG . . . C 3 -6.772 -3.852 -2.907 1 0.44 ? H5' 8OG 131 A 1 HETATM 26 H "H5''" 8OG . . . C 3 -6.075 -5.062 -3.95 1 0.44 ? "H5''" 8OG 131 A 1 HETATM 27 H H4' 8OG . . . C 3 -6.982 -6.075 -1.971 1 0.44 ? H4' 8OG 131 A 1 HETATM 28 H H3' 8OG . . . C 3 -7.76 -6.844 -4.58 1 0.44 ? H3' 8OG 131 A 1 HETATM 29 H HO3' 8OG . . . C 3 -7.49 -8.959 -3.663 1 0.44 ? HO3' 8OG 131 A 1 HETATM 30 H H2' 8OG . . . C 3 -9.963 -7.22 -4.395 1 0.44 ? H2' 8OG 131 A 1 HETATM 31 H "H2''" 8OG . . . C 3 -9.687 -8.226 -2.991 1 0.44 ? "H2''" 8OG 131 A 1 HETATM 32 H H1' 8OG . . . C 3 -10.43 -6.65 -1.631 1 0.44 ? H1' 8OG 131 A 1 HETATM 33 H H7 8OG . . . C 3 -13.061 -3.936 -5.086 1 20 ? H7 8OG 131 A 1 HETATM 34 H H1 8OG . . . C 3 -16.044 -4.699 -1.162 1 20 ? H1 8OG 131 A 1 HETATM 35 H H21 8OG . . . C 3 -14.092 -6.47 1.139 1 20 ? H21 8OG 131 A 1 HETATM 36 H H22 8OG . . . C 3 -15.634 -5.758 0.795 1 20 ? H22 8OG 131 A 1 # _model_server_stats.io_time_ms 40 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 78 _model_server_stats.query_time_ms 6486 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 36 #