data_4HB3 # _model_server_result.job_id uMzoT_MPXJlMwl3EtzDgHw _model_server_result.datetime_utc '2024-11-25 23:54:41' _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 4hb3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":301}' # _entry.id 4HB3 # _exptl.entry_id 4HB3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 522.196 _entity.id 4 _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 4HB3 _cell.length_a 106.118 _cell.length_b 106.118 _cell.length_c 305.425 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4HB3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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,I _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 4 _struct_asym.id D _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 24 1_555 E MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.924 ? metalc ? metalc2 A OG1 THR 42 A THR 42 1_555 E MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.272 ? metalc ? metalc3 D O2G GNP . A GNP 301 1_555 E MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.194 ? metalc ? metalc4 D O1B GNP . A GNP 301 1_555 E MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.241 ? metalc ? metalc5 E MG MG . A MG 302 1_555 G O HOH . A HOH 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.948 ? metalc ? metalc6 E MG MG . A MG 302 1_555 G O HOH . A HOH 409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.776 ? # _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 4HB3 _atom_sites.fract_transf_matrix[1][1] 0.009423 _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] 0.009423 _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] 0.003274 _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 D 4 GNP A 1 301 950 GNP GNP . E 5 MG A 1 302 1178 MG MG . F 6 CL C 1 1101 100 CL CL . G 7 HOH A 1 401 8 HOH HOH . G 7 HOH A 2 402 12 HOH HOH . G 7 HOH A 3 403 16 HOH HOH . G 7 HOH A 4 404 21 HOH HOH . G 7 HOH A 5 405 25 HOH HOH . G 7 HOH A 6 406 30 HOH HOH . G 7 HOH A 7 407 49 HOH HOH . G 7 HOH A 8 408 50 HOH HOH . G 7 HOH A 9 409 51 HOH HOH . G 7 HOH A 10 410 53 HOH HOH . G 7 HOH A 11 411 54 HOH HOH . G 7 HOH A 12 412 56 HOH HOH . G 7 HOH A 13 413 60 HOH HOH . G 7 HOH A 14 414 61 HOH HOH . G 7 HOH A 15 415 66 HOH HOH . G 7 HOH A 16 416 68 HOH HOH . H 7 HOH B 1 301 44 HOH HOH . H 7 HOH B 2 302 62 HOH HOH . I 7 HOH C 1 1201 1 HOH HOH . I 7 HOH C 2 1202 2 HOH HOH . I 7 HOH C 3 1203 3 HOH HOH . I 7 HOH C 4 1204 4 HOH HOH . I 7 HOH C 5 1205 5 HOH HOH . I 7 HOH C 6 1206 6 HOH HOH . I 7 HOH C 7 1207 7 HOH HOH . I 7 HOH C 8 1208 9 HOH HOH . I 7 HOH C 9 1209 10 HOH HOH . I 7 HOH C 10 1210 11 HOH HOH . I 7 HOH C 11 1211 13 HOH HOH . I 7 HOH C 12 1212 14 HOH HOH . I 7 HOH C 13 1213 15 HOH HOH . I 7 HOH C 14 1214 17 HOH HOH . I 7 HOH C 15 1215 18 HOH HOH . I 7 HOH C 16 1216 19 HOH HOH . I 7 HOH C 17 1217 20 HOH HOH . I 7 HOH C 18 1218 22 HOH HOH . I 7 HOH C 19 1219 23 HOH HOH . I 7 HOH C 20 1220 24 HOH HOH . I 7 HOH C 21 1221 26 HOH HOH . I 7 HOH C 22 1222 27 HOH HOH . I 7 HOH C 23 1223 28 HOH HOH . I 7 HOH C 24 1224 29 HOH HOH . I 7 HOH C 25 1225 31 HOH HOH . I 7 HOH C 26 1226 32 HOH HOH . I 7 HOH C 27 1227 33 HOH HOH . I 7 HOH C 28 1228 34 HOH HOH . I 7 HOH C 29 1229 35 HOH HOH . I 7 HOH C 30 1230 36 HOH HOH . I 7 HOH C 31 1231 37 HOH HOH . I 7 HOH C 32 1232 38 HOH HOH . I 7 HOH C 33 1233 39 HOH HOH . I 7 HOH C 34 1234 40 HOH HOH . I 7 HOH C 35 1235 41 HOH HOH . I 7 HOH C 36 1236 42 HOH HOH . I 7 HOH C 37 1237 43 HOH HOH . I 7 HOH C 38 1238 45 HOH HOH . I 7 HOH C 39 1239 46 HOH HOH . I 7 HOH C 40 1240 47 HOH HOH . I 7 HOH C 41 1241 48 HOH HOH . I 7 HOH C 42 1242 52 HOH HOH . I 7 HOH C 43 1243 55 HOH HOH . I 7 HOH C 44 1244 57 HOH HOH . I 7 HOH C 45 1245 58 HOH HOH . I 7 HOH C 46 1246 59 HOH HOH . I 7 HOH C 47 1247 63 HOH HOH . I 7 HOH C 48 1248 64 HOH HOH . I 7 HOH C 49 1249 65 HOH HOH . I 7 HOH C 50 1250 67 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 . . . D 4 6.803 37.779 27.79 1 63.92 ? PG GNP 301 A 1 HETATM 2 O O1G GNP . . . D 4 6.861 36.45 27.146 1 65.69 ? O1G GNP 301 A 1 HETATM 3 O O2G GNP . . . D 4 8.221 38.507 27.597 1 64.29 ? O2G GNP 301 A 1 HETATM 4 O O3G GNP . . . D 4 6.476 37.683 29.359 1 62.14 ? O3G GNP 301 A 1 HETATM 5 N N3B GNP . . . D 4 5.534 38.668 27.006 1 62.29 ? N3B GNP 301 A 1 HETATM 6 P PB GNP . . . D 4 4.942 40.129 27.722 1 61.94 ? PB GNP 301 A 1 HETATM 7 O O1B GNP . . . D 4 6.054 41.039 28.048 1 63.75 ? O1B GNP 301 A 1 HETATM 8 O O2B GNP . . . D 4 4.135 39.808 29.072 1 62.01 ? O2B GNP 301 A 1 HETATM 9 O O3A GNP . . . D 4 3.988 40.813 26.625 1 63.64 ? O3A GNP 301 A 1 HETATM 10 P PA GNP . . . D 4 4.628 41.74 25.472 1 66.77 ? PA GNP 301 A 1 HETATM 11 O O1A GNP . . . D 4 5.657 40.925 24.724 1 66.27 ? O1A GNP 301 A 1 HETATM 12 O O2A GNP . . . D 4 5.025 43.054 26.118 1 65.36 ? O2A GNP 301 A 1 HETATM 13 O O5' GNP . . . D 4 3.378 41.989 24.485 1 65 ? O5' GNP 301 A 1 HETATM 14 C C5' GNP . . . D 4 2.77 40.88 23.819 1 64.62 ? C5' GNP 301 A 1 HETATM 15 C C4' GNP . . . D 4 1.774 41.34 22.76 1 63.68 ? C4' GNP 301 A 1 HETATM 16 O O4' GNP . . . D 4 0.699 42.059 23.373 1 62.46 ? O4' GNP 301 A 1 HETATM 17 C C3' GNP . . . D 4 2.401 42.285 21.741 1 64.06 ? C3' GNP 301 A 1 HETATM 18 O O3' GNP . . . D 4 1.956 41.935 20.424 1 61.5 ? O3' GNP 301 A 1 HETATM 19 C C2' GNP . . . D 4 1.915 43.664 22.161 1 63.63 ? C2' GNP 301 A 1 HETATM 20 O O2' GNP . . . D 4 1.869 44.594 21.073 1 64.34 ? O2' GNP 301 A 1 HETATM 21 C C1' GNP . . . D 4 0.543 43.324 22.716 1 63.18 ? C1' GNP 301 A 1 HETATM 22 N N9 GNP . . . D 4 -0.008 44.326 23.656 1 62.51 ? N9 GNP 301 A 1 HETATM 23 C C8 GNP . . . D 4 0.57 44.785 24.78 1 63.01 ? C8 GNP 301 A 1 HETATM 24 N N7 GNP . . . D 4 -0.248 45.679 25.399 1 63.59 ? N7 GNP 301 A 1 HETATM 25 C C5 GNP . . . D 4 -1.375 45.791 24.666 1 63.05 ? C5 GNP 301 A 1 HETATM 26 C C6 GNP . . . D 4 -2.647 46.556 24.736 1 62.6 ? C6 GNP 301 A 1 HETATM 27 O O6 GNP . . . D 4 -2.887 47.349 25.667 1 63.76 ? O6 GNP 301 A 1 HETATM 28 N N1 GNP . . . D 4 -3.549 46.378 23.77 1 62.33 ? N1 GNP 301 A 1 HETATM 29 C C2 GNP . . . D 4 -3.342 45.532 22.747 1 63.13 ? C2 GNP 301 A 1 HETATM 30 N N2 GNP . . . D 4 -4.309 45.409 21.812 1 64.49 ? N2 GNP 301 A 1 HETATM 31 N N3 GNP . . . D 4 -2.208 44.798 22.611 1 62.6 ? N3 GNP 301 A 1 HETATM 32 C C4 GNP . . . D 4 -1.209 44.888 23.521 1 62.53 ? C4 GNP 301 A 1 # _model_server_stats.io_time_ms 54 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 285 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 32 #