data_5DI3 # _model_server_result.job_id c6RRY3y1hc7kbUaSkeuNCw _model_server_result.datetime_utc '2024-11-05 00:38:29' _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 5di3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":201}' # _entry.id 5DI3 # _exptl.entry_id 5DI3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 522.196 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER' _entity.pdbx_number_of_molecules 2 _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 5DI3 _cell.length_a 57.1 _cell.length_b 68.8 _cell.length_c 120 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5DI3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _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,D,E,F,G,H _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 C N N ? 3 E N 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 18 B THR 33 1_555 D MG MG . B MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? metalc ? metalc2 A OG1 THR 35 B THR 50 1_555 D MG MG . B MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.304 ? metalc ? metalc3 C O1G GNP . B GNP 301 1_555 D MG MG . B MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? metalc ? metalc4 C O1B GNP . B GNP 301 1_555 D MG MG . B MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.17 ? metalc ? metalc5 D MG MG . B MG 302 1_555 G O HOH . B HOH 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.951 ? metalc ? metalc6 D MG MG . B MG 302 1_555 G O HOH . B HOH 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.193 ? metalc ? metalc7 B OG1 THR 30 A THR 30 1_555 F MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.119 ? metalc ? metalc8 B OG1 THR 47 A THR 47 1_555 F MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.39 ? metalc ? metalc9 E O1G GNP . A GNP 201 1_555 F MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.978 ? metalc ? metalc10 E O1B GNP . A GNP 201 1_555 F MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.362 ? metalc ? metalc11 F MG MG . A MG 202 1_555 H O HOH . A HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.311 ? metalc ? metalc12 F MG MG . A MG 202 1_555 H O HOH . A HOH 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.32 ? # _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 5DI3 _atom_sites.fract_transf_matrix[1][1] 0.017513 _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] 0.014535 _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] 0.008333 _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 B 1 301 301 GNP GNP . D 4 MG B 1 302 1 MG MG . E 3 GNP A 1 201 1 GNP GNP . F 4 MG A 1 202 2 MG MG . G 5 HOH B 1 401 46 HOH HOH . G 5 HOH B 2 402 9 HOH HOH . G 5 HOH B 3 403 38 HOH HOH . G 5 HOH B 4 404 32 HOH HOH . G 5 HOH B 5 405 8 HOH HOH . G 5 HOH B 6 406 44 HOH HOH . G 5 HOH B 7 407 6 HOH HOH . G 5 HOH B 8 408 48 HOH HOH . G 5 HOH B 9 409 1 HOH HOH . G 5 HOH B 10 410 4 HOH HOH . G 5 HOH B 11 411 5 HOH HOH . G 5 HOH B 12 412 21 HOH HOH . G 5 HOH B 13 413 47 HOH HOH . G 5 HOH B 14 414 45 HOH HOH . G 5 HOH B 15 415 37 HOH HOH . G 5 HOH B 16 416 2 HOH HOH . G 5 HOH B 17 417 20 HOH HOH . G 5 HOH B 18 418 10 HOH HOH . G 5 HOH B 19 419 31 HOH HOH . H 5 HOH A 1 301 33 HOH HOH . H 5 HOH A 2 302 7 HOH HOH . H 5 HOH A 3 303 34 HOH HOH . H 5 HOH A 4 304 16 HOH HOH . H 5 HOH A 5 305 43 HOH HOH . H 5 HOH A 6 306 14 HOH HOH . H 5 HOH A 7 307 42 HOH HOH . H 5 HOH A 8 308 13 HOH HOH . H 5 HOH A 9 309 41 HOH HOH . H 5 HOH A 10 310 39 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 . . . E 3 25.868 -8.126 -12.699 1 56.54 ? PG GNP 201 A 1 HETATM 2 O O1G GNP . . . E 3 24.711 -8.371 -13.635 1 49.94 ? O1G GNP 201 A 1 HETATM 3 O O2G GNP . . . E 3 25.81 -6.831 -11.93 1 52.43 ? O2G GNP 201 A 1 HETATM 4 O O3G GNP . . . E 3 27.124 -8.279 -13.524 1 55.25 ? O3G GNP 201 A 1 HETATM 5 N N3B GNP . . . E 3 25.819 -9.314 -11.635 1 55.14 ? N3B GNP 201 A 1 HETATM 6 P PB GNP . . . E 3 24.532 -9.686 -10.775 1 49.77 ? PB GNP 201 A 1 HETATM 7 O O1B GNP . . . E 3 23.363 -9.779 -11.681 1 53.52 ? O1B GNP 201 A 1 HETATM 8 O O2B GNP . . . E 3 24.429 -8.739 -9.641 1 52.48 ? O2B GNP 201 A 1 HETATM 9 O O3A GNP . . . E 3 24.733 -11.085 -10.194 1 56.93 ? O3A GNP 201 A 1 HETATM 10 P PA GNP . . . E 3 24.339 -12.376 -10.92 1 49.64 ? PA GNP 201 A 1 HETATM 11 O O1A GNP . . . E 3 24.894 -12.292 -12.292 1 56.96 ? O1A GNP 201 A 1 HETATM 12 O O2A GNP . . . E 3 22.898 -12.707 -10.773 1 44.01 ? O2A GNP 201 A 1 HETATM 13 O O5' GNP . . . E 3 25.093 -13.545 -10.183 1 53.53 ? O5' GNP 201 A 1 HETATM 14 C C5' GNP . . . E 3 26.514 -13.617 -10.091 1 56.64 ? C5' GNP 201 A 1 HETATM 15 C C4' GNP . . . E 3 26.918 -15.006 -9.624 1 55.07 ? C4' GNP 201 A 1 HETATM 16 O O4' GNP . . . E 3 26.393 -15.249 -8.288 1 57.03 ? O4' GNP 201 A 1 HETATM 17 C C3' GNP . . . E 3 26.371 -16.155 -10.466 1 51.77 ? C3' GNP 201 A 1 HETATM 18 O O3' GNP . . . E 3 27.272 -17.239 -10.391 1 59.51 ? O3' GNP 201 A 1 HETATM 19 C C2' GNP . . . E 3 25.077 -16.483 -9.733 1 56.5 ? C2' GNP 201 A 1 HETATM 20 O O2' GNP . . . E 3 24.526 -17.746 -10.04 1 51.58 ? O2' GNP 201 A 1 HETATM 21 C C1' GNP . . . E 3 25.622 -16.436 -8.315 1 56.62 ? C1' GNP 201 A 1 HETATM 22 N N9 GNP . . . E 3 24.587 -16.374 -7.288 1 60.66 ? N9 GNP 201 A 1 HETATM 23 C C8 GNP . . . E 3 23.452 -15.602 -7.297 1 61.61 ? C8 GNP 201 A 1 HETATM 24 N N7 GNP . . . E 3 22.708 -15.761 -6.236 1 61.84 ? N7 GNP 201 A 1 HETATM 25 C C5 GNP . . . E 3 23.391 -16.698 -5.473 1 63.7 ? C5 GNP 201 A 1 HETATM 26 C C6 GNP . . . E 3 23.066 -17.263 -4.213 1 64.17 ? C6 GNP 201 A 1 HETATM 27 O O6 GNP . . . E 3 22.078 -17.045 -3.491 1 60.67 ? O6 GNP 201 A 1 HETATM 28 N N1 GNP . . . E 3 24.037 -18.177 -3.805 1 64 ? N1 GNP 201 A 1 HETATM 29 C C2 GNP . . . E 3 25.17 -18.498 -4.517 1 65.74 ? C2 GNP 201 A 1 HETATM 30 N N2 GNP . . . E 3 25.984 -19.403 -3.957 1 68.51 ? N2 GNP 201 A 1 HETATM 31 N N3 GNP . . . E 3 25.487 -17.974 -5.695 1 66.46 ? N3 GNP 201 A 1 HETATM 32 C C4 GNP . . . E 3 24.552 -17.085 -6.11 1 64.19 ? C4 GNP 201 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 310 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 32 #