data_1K8R # _model_server_result.job_id aoIzr9MPtBx-LiBPwO_F4A _model_server_result.datetime_utc '2024-11-22 17:40:50' _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 1k8r # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":167}' # _entry.id 1K8R # _exptl.entry_id 1K8R _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 120 _cell.entry_id 1K8R _cell.length_a 139.03 _cell.length_b 139.03 _cell.length_c 112.8 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1K8R _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'H 3 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 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 OG SER 17 A SER 17 1_555 C MG MG . A MG 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.487 ? metalc ? metalc2 A OG1 THR 35 A THR 35 1_555 C MG MG . A MG 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.967 ? metalc ? metalc3 A OD1 ASP 57 A ASP 57 1_555 C MG MG . A MG 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.075 ? metalc ? metalc4 A O THR 58 A THR 58 1_555 C MG MG . A MG 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.82 ? metalc ? metalc5 D O2B GNP . A GNP 167 1_555 C MG MG . A MG 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.978 ? metalc ? metalc6 D O2G GNP . A GNP 167 1_555 C MG MG . A MG 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.802 ? # _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 1K8R _atom_sites.fract_transf_matrix[1][1] 0.007193 _atom_sites.fract_transf_matrix[1][2] 0.004153 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008305 _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] 0.008865 _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 MG A 1 168 168 MG MG . D 4 GNP A 1 167 167 GNP GNP . # 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 54.058 44.293 7.257 1 32.94 ? PG GNP 167 A 1 HETATM 2 O O1G GNP . . . D 4 54.952 44.522 8.354 1 36.15 ? O1G GNP 167 A 1 HETATM 3 O O2G GNP . . . D 4 52.69 44.506 7.683 1 36.16 ? O2G GNP 167 A 1 HETATM 4 O O3G GNP . . . D 4 54.186 42.787 7.033 1 35.34 ? O3G GNP 167 A 1 HETATM 5 N N3B GNP . . . D 4 54.434 45.046 5.878 1 35.58 ? N3B GNP 167 A 1 HETATM 6 P PB GNP . . . D 4 53.407 45.124 4.6 1 32.19 ? PB GNP 167 A 1 HETATM 7 O O1B GNP . . . D 4 53.602 44.102 3.589 1 34.66 ? O1B GNP 167 A 1 HETATM 8 O O2B GNP . . . D 4 52.017 45.268 4.973 1 37.17 ? O2B GNP 167 A 1 HETATM 9 O O3A GNP . . . D 4 53.755 46.498 3.864 1 32.52 ? O3A GNP 167 A 1 HETATM 10 P PA GNP . . . D 4 52.884 47.846 3.756 1 28.81 ? PA GNP 167 A 1 HETATM 11 O O1A GNP . . . D 4 51.697 47.598 2.944 1 30.59 ? O1A GNP 167 A 1 HETATM 12 O O2A GNP . . . D 4 52.711 48.433 5.104 1 27.8 ? O2A GNP 167 A 1 HETATM 13 O O5' GNP . . . D 4 53.898 48.718 2.894 1 26 ? O5' GNP 167 A 1 HETATM 14 C C5' GNP . . . D 4 55.071 49.248 3.538 1 24.06 ? C5' GNP 167 A 1 HETATM 15 C C4' GNP . . . D 4 55.45 50.596 2.927 1 23.32 ? C4' GNP 167 A 1 HETATM 16 O O4' GNP . . . D 4 55.623 50.447 1.524 1 22.53 ? O4' GNP 167 A 1 HETATM 17 C C3' GNP . . . D 4 54.399 51.691 3.15 1 23.59 ? C3' GNP 167 A 1 HETATM 18 O O3' GNP . . . D 4 55.036 52.931 3.417 1 25.55 ? O3' GNP 167 A 1 HETATM 19 C C2' GNP . . . D 4 53.685 51.755 1.798 1 23.96 ? C2' GNP 167 A 1 HETATM 20 O O2' GNP . . . D 4 53.245 53.076 1.487 1 26.83 ? O2' GNP 167 A 1 HETATM 21 C C1' GNP . . . D 4 54.782 51.341 0.819 1 21.61 ? C1' GNP 167 A 1 HETATM 22 N N9 GNP . . . D 4 54.199 50.643 -0.297 1 20.64 ? N9 GNP 167 A 1 HETATM 23 C C8 GNP . . . D 4 53.402 49.521 -0.278 1 21.17 ? C8 GNP 167 A 1 HETATM 24 N N7 GNP . . . D 4 52.791 49.289 -1.375 1 22.19 ? N7 GNP 167 A 1 HETATM 25 C C5 GNP . . . D 4 53.461 50.127 -2.295 1 21.26 ? C5 GNP 167 A 1 HETATM 26 C C6 GNP . . . D 4 53.365 50.249 -3.741 1 20.58 ? C6 GNP 167 A 1 HETATM 27 O O6 GNP . . . D 4 52.637 49.645 -4.508 1 21.14 ? O6 GNP 167 A 1 HETATM 28 N N1 GNP . . . D 4 54.235 51.19 -4.271 1 21.62 ? N1 GNP 167 A 1 HETATM 29 C C2 GNP . . . D 4 55.102 51.972 -3.573 1 22.43 ? C2 GNP 167 A 1 HETATM 30 N N2 GNP . . . D 4 55.877 52.832 -4.254 1 20.32 ? N2 GNP 167 A 1 HETATM 31 N N3 GNP . . . D 4 55.208 51.894 -2.193 1 23.06 ? N3 GNP 167 A 1 HETATM 32 C C4 GNP . . . D 4 54.349 50.957 -1.624 1 21.08 ? C4 GNP 167 A 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 272 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 32 #