data_5SZI # _model_server_result.job_id YSIenXaIymc0-lMHOkFwJA _model_server_result.datetime_utc '2025-06-16 10:00:44' _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 5szi # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":301}' # _entry.id 5SZI # _exptl.entry_id 5SZI _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 522.196 _entity.id 3 _entity.src_method man _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 5SZI _cell.length_a 62.4 _cell.length_b 122.4 _cell.length_c 139.15 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5SZI _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E _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 OG1 THR 24 A THR 22 1_555 D MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.877 ? metalc ? metalc2 A OG1 THR 42 A THR 40 1_555 D MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.358 ? metalc ? metalc3 C O3G GNP . A GNP 301 1_555 D MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.834 ? metalc ? metalc4 C O2B GNP . A GNP 301 1_555 D MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.121 ? metalc ? metalc5 D MG MG . A MG 302 1_555 E O HOH . A HOH 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.006 ? metalc ? metalc6 D MG MG . A MG 302 1_555 E O HOH . A HOH 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.196 ? # _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 5SZI _atom_sites.fract_transf_matrix[1][1] 0.016026 _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] 0.00817 _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] 0.007186 _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 C 3 GNP A 1 301 300 GNP GNP . D 4 MG A 1 302 400 MG MG . E 5 HOH A 1 401 1 HOH HOH . E 5 HOH A 2 402 2 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 . . . C 3 8.924 46.299 -2.622 1 83.14 ? PG GNP 301 A 1 HETATM 2 O O1G GNP . . . C 3 9.817 46.571 -3.806 1 88.97 ? O1G GNP 301 A 1 HETATM 3 O O2G GNP . . . C 3 9.538 46.57 -1.266 1 87.94 ? O2G GNP 301 A 1 HETATM 4 O O3G GNP . . . C 3 8.391 44.893 -2.519 1 88.65 ? O3G GNP 301 A 1 HETATM 5 N N3B GNP . . . C 3 7.663 47.222 -2.841 1 85.66 ? N3B GNP 301 A 1 HETATM 6 P PB GNP . . . C 3 6.935 47.262 -4.253 1 85.4 ? PB GNP 301 A 1 HETATM 7 O O1B GNP . . . C 3 7.716 48.068 -5.223 1 80.23 ? O1B GNP 301 A 1 HETATM 8 O O2B GNP . . . C 3 6.651 45.86 -4.647 1 89.52 ? O2B GNP 301 A 1 HETATM 9 O O3A GNP . . . C 3 5.616 47.997 -4.01 1 94.68 ? O3A GNP 301 A 1 HETATM 10 P PA GNP . . . C 3 4.325 47.282 -3.6 1 97.49 ? PA GNP 301 A 1 HETATM 11 O O1A GNP . . . C 3 3.659 46.744 -4.813 1 99.33 ? O1A GNP 301 A 1 HETATM 12 O O2A GNP . . . C 3 4.617 46.357 -2.476 1 104.25 ? O2A GNP 301 A 1 HETATM 13 O O5' GNP . . . C 3 3.342 48.379 -3.019 1 100.92 ? O5' GNP 301 A 1 HETATM 14 C C5' GNP . . . C 3 3.714 49.76 -2.956 1 97.38 ? C5' GNP 301 A 1 HETATM 15 C C4' GNP . . . C 3 2.64 50.576 -2.251 1 103.54 ? C4' GNP 301 A 1 HETATM 16 O O4' GNP . . . C 3 2.004 51.488 -3.179 1 109.75 ? O4' GNP 301 A 1 HETATM 17 C C3' GNP . . . C 3 1.511 49.758 -1.633 1 106.01 ? C3' GNP 301 A 1 HETATM 18 O O3' GNP . . . C 3 1.029 50.381 -0.44 1 109.09 ? O3' GNP 301 A 1 HETATM 19 C C2' GNP . . . C 3 0.471 49.737 -2.749 1 112.63 ? C2' GNP 301 A 1 HETATM 20 O O2' GNP . . . C 3 -0.847 49.585 -2.258 1 117.15 ? O2' GNP 301 A 1 HETATM 21 C C1' GNP . . . C 3 0.669 51.098 -3.414 1 116.95 ? C1' GNP 301 A 1 HETATM 22 N N9 GNP . . . C 3 0.489 51.045 -4.857 1 127.6 ? N9 GNP 301 A 1 HETATM 23 C C8 GNP . . . C 3 1.034 50.127 -5.719 1 129.97 ? C8 GNP 301 A 1 HETATM 24 N N7 GNP . . . C 3 0.7 50.32 -6.964 1 131.65 ? N7 GNP 301 A 1 HETATM 25 C C5 GNP . . . C 3 -0.116 51.442 -6.925 1 138.44 ? C5 GNP 301 A 1 HETATM 26 C C6 GNP . . . C 3 -0.779 52.126 -7.971 1 142.08 ? C6 GNP 301 A 1 HETATM 27 O O6 GNP . . . C 3 -0.777 51.872 -9.182 1 150.92 ? O6 GNP 301 A 1 HETATM 28 N N1 GNP . . . C 3 -1.505 53.212 -7.497 1 141.56 ? N1 GNP 301 A 1 HETATM 29 C C2 GNP . . . C 3 -1.58 53.59 -6.181 1 138.95 ? C2 GNP 301 A 1 HETATM 30 N N2 GNP . . . C 3 -2.333 54.669 -5.93 1 140.05 ? N2 GNP 301 A 1 HETATM 31 N N3 GNP . . . C 3 -0.966 52.962 -5.189 1 143.13 ? N3 GNP 301 A 1 HETATM 32 C C4 GNP . . . C 3 -0.254 51.9 -5.635 1 138.88 ? C4 GNP 301 A 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 317 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 32 #