data_3SBE # _model_server_result.job_id XIebQHwIOr2GfF_LOwUXkg _model_server_result.datetime_utc '2024-12-21 04:43:56' _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 3sbe # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":500}' # _entry.id 3SBE # _exptl.entry_id 3SBE _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 522.196 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOAMINOPHOSPHONIC 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 3SBE _cell.length_a 40.593 _cell.length_b 51.892 _cell.length_c 99.327 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3SBE _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 2 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 2 _struct_asym.id B _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 OG1 THR 27 A THR 17 1_555 C MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? metalc ? metalc2 A OG1 THR 45 A THR 35 1_555 C MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.986 ? metalc ? metalc3 D O HOH . A HOH 194 1_555 C MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.747 ? metalc ? metalc4 B O2G GNP . A GNP 500 1_555 C MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.974 ? metalc ? metalc5 B O2B GNP . A GNP 500 1_555 C MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.413 ? # _chem_comp.formula 'C10 H17 N6 O13 P3' _chem_comp.formula_weight 522.196 _chem_comp.id GNP _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHOAMINOPHOSPHONIC 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 GNP doub 129 n n PG O2G GNP sing 130 n n PG O3G GNP sing 131 n n PG N3B GNP sing 132 n n O2G HOG2 GNP sing 133 n n O3G HOG3 GNP sing 134 n n N3B PB GNP sing 135 n n N3B HNB3 GNP sing 136 n n PB O1B GNP doub 137 n n PB O2B GNP sing 138 n n PB O3A GNP sing 139 n n O2B HOB2 GNP sing 140 n n O3A PA GNP sing 141 n n PA O1A GNP doub 142 n n PA O2A GNP sing 143 n n PA O5' GNP sing 144 n n O2A HOA2 GNP sing 145 n n O5' C5' GNP sing 146 n n C5' C4' GNP sing 147 n n C5' "H5'2" GNP sing 148 n n C5' "H5'1" GNP sing 149 n n C4' O4' GNP sing 150 n n C4' C3' GNP sing 151 n n C4' H4' GNP sing 152 n n O4' C1' GNP sing 153 n n C3' O3' GNP sing 154 n n C3' C2' GNP sing 155 n n C3' H3' GNP sing 156 n n O3' HO3' GNP sing 157 n n C2' O2' GNP sing 158 n n C2' C1' GNP sing 159 n n C2' H2' GNP sing 160 n n O2' HO2' GNP sing 161 n n C1' N9 GNP sing 162 n n C1' H1' GNP sing 163 n n N9 C8 GNP sing 164 n y N9 C4 GNP sing 165 n y C8 N7 GNP doub 166 n y C8 H8 GNP sing 167 n n N7 C5 GNP sing 168 n y C5 C6 GNP sing 169 n y C5 C4 GNP doub 170 n y C6 O6 GNP doub 171 n n C6 N1 GNP sing 172 n y N1 C2 GNP sing 173 n y N1 HN1 GNP sing 174 n n C2 N2 GNP sing 175 n n C2 N3 GNP doub 176 n y N2 HN21 GNP sing 177 n n N2 HN22 GNP sing 178 n n N3 C4 GNP sing 179 n y # _atom_sites.entry_id 3SBE _atom_sites.fract_transf_matrix[1][1] 0.024635 _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] 0.019271 _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] 0.010068 _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 GNP A 1 500 500 GNP GNP . C 3 MG A 1 501 501 MG MG . D 4 HOH A 1 178 1 HOH HOH . D 4 HOH A 2 179 2 HOH HOH . D 4 HOH A 3 180 3 HOH HOH . D 4 HOH A 4 181 4 HOH HOH . D 4 HOH A 5 182 5 HOH HOH . D 4 HOH A 6 183 6 HOH HOH . D 4 HOH A 7 184 7 HOH HOH . D 4 HOH A 8 185 8 HOH HOH . D 4 HOH A 9 186 9 HOH HOH . D 4 HOH A 10 187 10 HOH HOH . D 4 HOH A 11 188 11 HOH HOH . D 4 HOH A 12 189 12 HOH HOH . D 4 HOH A 13 190 13 HOH HOH . D 4 HOH A 14 191 14 HOH HOH . D 4 HOH A 15 192 15 HOH HOH . D 4 HOH A 16 193 16 HOH HOH . D 4 HOH A 17 194 17 HOH HOH . D 4 HOH A 18 195 18 HOH HOH . D 4 HOH A 19 196 19 HOH HOH . D 4 HOH A 20 197 20 HOH HOH . D 4 HOH A 21 198 21 HOH HOH . D 4 HOH A 22 199 22 HOH HOH . D 4 HOH A 23 200 23 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 P PG GNP . . . B 2 -12.594 17.367 -9.554 1 46.25 ? PG GNP 500 A 1 HETATM 2 O O1G GNP . . . B 2 -11.882 18.39 -10.423 1 46.26 ? O1G GNP 500 A 1 HETATM 3 O O2G GNP . . . B 2 -11.899 16.907 -8.292 1 43.91 ? O2G GNP 500 A 1 HETATM 4 O O3G GNP . . . B 2 -13.942 18.062 -9.371 1 46.37 ? O3G GNP 500 A 1 HETATM 5 N N3B GNP . . . B 2 -12.883 15.998 -10.346 1 44.69 ? N3B GNP 500 A 1 HETATM 6 P PB GNP . . . B 2 -11.889 15.179 -11.302 1 43.82 ? PB GNP 500 A 1 HETATM 7 O O1B GNP . . . B 2 -11.423 16.099 -12.393 1 37.61 ? O1B GNP 500 A 1 HETATM 8 O O2B GNP . . . B 2 -10.875 14.546 -10.387 1 40.54 ? O2B GNP 500 A 1 HETATM 9 O O3A GNP . . . B 2 -12.713 14.029 -11.944 1 43.4 ? O3A GNP 500 A 1 HETATM 10 P PA GNP . . . B 2 -12.963 12.611 -11.352 1 46.57 ? PA GNP 500 A 1 HETATM 11 O O1A GNP . . . B 2 -11.689 11.848 -11.273 1 47.77 ? O1A GNP 500 A 1 HETATM 12 O O2A GNP . . . B 2 -13.718 12.651 -10.076 1 46.44 ? O2A GNP 500 A 1 HETATM 13 O O5' GNP . . . B 2 -13.868 11.842 -12.4 1 47.12 ? O5' GNP 500 A 1 HETATM 14 C C5' GNP . . . B 2 -15.054 12.483 -12.96 1 48.44 ? C5' GNP 500 A 1 HETATM 15 C C4' GNP . . . B 2 -15.982 11.497 -13.67 1 48.93 ? C4' GNP 500 A 1 HETATM 16 O O4' GNP . . . B 2 -15.338 10.98 -14.872 1 47.51 ? O4' GNP 500 A 1 HETATM 17 C C3' GNP . . . B 2 -16.42 10.26 -12.875 1 49.17 ? C3' GNP 500 A 1 HETATM 18 O O3' GNP . . . B 2 -17.727 9.795 -13.288 1 51.25 ? O3' GNP 500 A 1 HETATM 19 C C2' GNP . . . B 2 -15.351 9.268 -13.288 1 48.1 ? C2' GNP 500 A 1 HETATM 20 O O2' GNP . . . B 2 -15.688 7.908 -13.105 1 48.85 ? O2' GNP 500 A 1 HETATM 21 C C1' GNP . . . B 2 -15.242 9.576 -14.773 1 48.25 ? C1' GNP 500 A 1 HETATM 22 N N9 GNP . . . B 2 -13.957 9.151 -15.331 1 50.81 ? N9 GNP 500 A 1 HETATM 23 C C8 GNP . . . B 2 -12.68 9.439 -14.869 1 50.32 ? C8 GNP 500 A 1 HETATM 24 N N7 GNP . . . B 2 -11.714 8.905 -15.567 1 50.98 ? N7 GNP 500 A 1 HETATM 25 C C5 GNP . . . B 2 -12.394 8.201 -16.553 1 50.85 ? C5 GNP 500 A 1 HETATM 26 C C6 GNP . . . B 2 -11.893 7.424 -17.614 1 50.55 ? C6 GNP 500 A 1 HETATM 27 O O6 GNP . . . B 2 -10.716 7.211 -17.877 1 50.66 ? O6 GNP 500 A 1 HETATM 28 N N1 GNP . . . B 2 -12.911 6.865 -18.398 1 51.86 ? N1 GNP 500 A 1 HETATM 29 C C2 GNP . . . B 2 -14.272 7.057 -18.195 1 51.4 ? C2 GNP 500 A 1 HETATM 30 N N2 GNP . . . B 2 -15.113 6.454 -19.05 1 51.17 ? N2 GNP 500 A 1 HETATM 31 N N3 GNP . . . B 2 -14.763 7.802 -17.209 1 51.15 ? N3 GNP 500 A 1 HETATM 32 C C4 GNP . . . B 2 -13.773 8.333 -16.427 1 51.66 ? C4 GNP 500 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 301 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 32 #