data_3K9N # _model_server_result.job_id qmJ8oL1kv5h3JGac6y2Cag _model_server_result.datetime_utc '2024-11-02 12:25:51' _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 3k9n # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 3K9N # _exptl.entry_id 3K9N _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 120 _cell.entry_id 3K9N _cell.length_a 38.423 _cell.length_b 38.423 _cell.length_c 191.749 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3K9N _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 1' # _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,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 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 OG SER 17 A SER 17 1_555 D MG MG . A MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.236 ? metalc ? metalc2 A O ARG 102 A ARG 102 1_555 C CA CA . A CA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.394 ? metalc ? metalc3 A OD1 ASP 105 A ASP 105 1_555 C CA CA . A CA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.313 ? metalc ? metalc4 E O HOH . A HOH 167 1_555 D MG MG . A MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.319 ? metalc ? metalc5 E O HOH . A HOH 171 1_555 D MG MG . A MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.375 ? metalc ? metalc6 B O2G GNP . A GNP 201 1_555 D MG MG . A MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.152 ? metalc ? metalc7 B O2B GNP . A GNP 201 1_555 D MG MG . A MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.214 ? metalc ? metalc8 C CA CA . A CA 202 1_555 E O HOH . A HOH 320 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.532 ? metalc ? metalc9 C CA CA . A CA 202 1_555 E O HOH . A HOH 543 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.955 ? metalc ? metalc10 D MG MG . A MG 203 1_555 E O HOH . A HOH 299 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.346 ? # _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 3K9N _atom_sites.fract_transf_matrix[1][1] 0.026026 _atom_sites.fract_transf_matrix[1][2] 0.015026 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.030052 _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] 0.005215 _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 1 201 201 GNP GNP . C 3 CA A 1 202 202 CA CA . D 4 MG A 1 203 203 MG MG . E 5 HOH A 1 167 3 HOH HOH . E 5 HOH A 2 168 4 HOH HOH . E 5 HOH A 3 169 1 HOH HOH . E 5 HOH A 4 170 5 HOH HOH . E 5 HOH A 5 171 2 HOH HOH . E 5 HOH A 6 172 6 HOH HOH . E 5 HOH A 7 173 173 HOH HOH . E 5 HOH A 8 174 147 HOH HOH . E 5 HOH A 9 175 161 HOH HOH . E 5 HOH A 10 176 7 HOH HOH . E 5 HOH A 11 177 10 HOH HOH . E 5 HOH A 12 178 178 HOH HOH . E 5 HOH A 13 179 80 HOH HOH . E 5 HOH A 14 180 9 HOH HOH . E 5 HOH A 15 181 25 HOH HOH . E 5 HOH A 16 182 22 HOH HOH . E 5 HOH A 17 183 27 HOH HOH . E 5 HOH A 18 184 109 HOH HOH . E 5 HOH A 19 214 214 HOH HOH . E 5 HOH A 20 227 227 HOH HOH . E 5 HOH A 21 257 257 HOH HOH . E 5 HOH A 22 295 295 HOH HOH . E 5 HOH A 23 299 299 HOH HOH . E 5 HOH A 24 306 306 HOH HOH . E 5 HOH A 25 320 320 HOH HOH . E 5 HOH A 26 335 335 HOH HOH . E 5 HOH A 27 343 343 HOH HOH . E 5 HOH A 28 527 527 HOH HOH . E 5 HOH A 29 528 528 HOH HOH . E 5 HOH A 30 529 529 HOH HOH . E 5 HOH A 31 530 530 HOH HOH . E 5 HOH A 32 531 531 HOH HOH . E 5 HOH A 33 532 532 HOH HOH . E 5 HOH A 34 533 533 HOH HOH . E 5 HOH A 35 534 534 HOH HOH . E 5 HOH A 36 535 535 HOH HOH . E 5 HOH A 37 536 536 HOH HOH . E 5 HOH A 38 537 537 HOH HOH . E 5 HOH A 39 538 538 HOH HOH . E 5 HOH A 40 539 539 HOH HOH . E 5 HOH A 41 540 540 HOH HOH . E 5 HOH A 42 541 541 HOH HOH . E 5 HOH A 43 542 542 HOH HOH . E 5 HOH A 44 543 543 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 16.629 2.534 11.392 1 27.39 ? PG GNP 201 A 1 HETATM 2 O O1G GNP . . . B 2 16.558 4.034 11.362 1 28.98 ? O1G GNP 201 A 1 HETATM 3 O O2G GNP . . . B 2 15.613 1.871 10.521 1 31.09 ? O2G GNP 201 A 1 HETATM 4 O O3G GNP . . . B 2 16.535 2.119 12.842 1 29.59 ? O3G GNP 201 A 1 HETATM 5 N N3B GNP . . . B 2 18.09 2.103 10.891 1 22.45 ? N3B GNP 201 A 1 HETATM 6 P PB GNP . . . B 2 18.596 0.619 10.557 1 21.99 ? PB GNP 201 A 1 HETATM 7 O O1B GNP . . . B 2 19.045 -0.066 11.795 1 20.57 ? O1B GNP 201 A 1 HETATM 8 O O2B GNP . . . B 2 17.578 -0.106 9.799 1 18.71 ? O2B GNP 201 A 1 HETATM 9 O O3A GNP . . . B 2 19.854 0.734 9.688 1 19.62 ? O3A GNP 201 A 1 HETATM 10 P PA GNP . . . B 2 20.044 0.63 8.15 1 24.1 ? PA GNP 201 A 1 HETATM 11 O O1A GNP . . . B 2 19.896 -0.756 7.666 1 22.11 ? O1A GNP 201 A 1 HETATM 12 O O2A GNP . . . B 2 19.231 1.67 7.485 1 21.05 ? O2A GNP 201 A 1 HETATM 13 O O5' GNP . . . B 2 21.574 0.969 7.997 1 20.48 ? O5' GNP 201 A 1 HETATM 14 C C5' GNP . . . B 2 22.205 2.053 8.685 1 22.68 ? C5' GNP 201 A 1 HETATM 15 C C4' GNP . . . B 2 23.407 2.571 7.897 1 25.72 ? C4' GNP 201 A 1 HETATM 16 O O4' GNP . . . B 2 24.572 1.727 8.072 1 22.63 ? O4' GNP 201 A 1 HETATM 17 C C3' GNP . . . B 2 23.188 2.619 6.39 1 27.89 ? C3' GNP 201 A 1 HETATM 18 O O3' GNP . . . B 2 23.844 3.753 5.868 1 29.95 ? O3' GNP 201 A 1 HETATM 19 C C2' GNP . . . B 2 23.818 1.316 5.91 1 27.74 ? C2' GNP 201 A 1 HETATM 20 O O2' GNP . . . B 2 24.249 1.393 4.567 1 26.06 ? O2' GNP 201 A 1 HETATM 21 C C1' GNP . . . B 2 25.01 1.165 6.851 1 21.89 ? C1' GNP 201 A 1 HETATM 22 N N9 GNP . . . B 2 25.373 -0.225 7.132 1 20.41 ? N9 GNP 201 A 1 HETATM 23 C C8 GNP . . . B 2 24.497 -1.229 7.467 1 22.81 ? C8 GNP 201 A 1 HETATM 24 N N7 GNP . . . B 2 25.081 -2.37 7.691 1 23.87 ? N7 GNP 201 A 1 HETATM 25 C C5 GNP . . . B 2 26.438 -2.124 7.507 1 19.92 ? C5 GNP 201 A 1 HETATM 26 C C6 GNP . . . B 2 27.572 -2.991 7.621 1 23.48 ? C6 GNP 201 A 1 HETATM 27 O O6 GNP . . . B 2 27.604 -4.2 7.901 1 19.66 ? O6 GNP 201 A 1 HETATM 28 N N1 GNP . . . B 2 28.773 -2.327 7.341 1 21.63 ? N1 GNP 201 A 1 HETATM 29 C C2 GNP . . . B 2 28.851 -0.988 7.012 1 24.65 ? C2 GNP 201 A 1 HETATM 30 N N2 GNP . . . B 2 30.077 -0.487 6.796 1 24.93 ? N2 GNP 201 A 1 HETATM 31 N N3 GNP . . . B 2 27.802 -0.18 6.909 1 19.8 ? N3 GNP 201 A 1 HETATM 32 C C4 GNP . . . B 2 26.629 -0.803 7.167 1 21.4 ? C4 GNP 201 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 211 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 32 #