data_1AGP # _model_server_result.job_id U7ATsaZrA_B5jduawwJ2zA _model_server_result.datetime_utc '2024-11-01 20:37:01' _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 1agp # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":167}' # _entry.id 1AGP # _exptl.entry_id 1AGP _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 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 107.4 _cell.angle_gamma 90 _cell.entry_id 1AGP _cell.length_a 69.91 _cell.length_b 39.81 _cell.length_c 56.1 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1AGP _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _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 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 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 OG SER 17 A SER 17 1_555 B MG MG . A MG 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.575 ? metalc ? metalc2 A OG1 THR 35 A THR 35 1_555 B MG MG . A MG 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.551 ? metalc ? metalc3 C O2B GNP . A GNP 167 1_555 B MG MG . A MG 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.411 ? metalc ? metalc4 C O1G GNP . A GNP 167 1_555 B MG MG . A MG 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.367 ? metalc ? metalc5 B MG MG . A MG 168 1_555 D O HOH . A HOH 172 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.697 ? # _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 1AGP _atom_sites.fract_transf_matrix[1][1] 0.014304 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004483 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.025119 _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] 0.01868 _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 MG A 1 168 168 MG MG . C 3 GNP A 1 167 167 GNP GNP . D 4 HOH A 1 172 172 HOH HOH . D 4 HOH A 2 173 173 HOH HOH . D 4 HOH A 3 180 180 HOH HOH . D 4 HOH A 4 182 182 HOH HOH . D 4 HOH A 5 193 193 HOH HOH . D 4 HOH A 6 204 204 HOH HOH . D 4 HOH A 7 207 207 HOH HOH . D 4 HOH A 8 214 214 HOH HOH . D 4 HOH A 9 255 255 HOH HOH . D 4 HOH A 10 261 261 HOH HOH . D 4 HOH A 11 279 279 HOH HOH . D 4 HOH A 12 282 282 HOH HOH . D 4 HOH A 13 305 305 HOH HOH . D 4 HOH A 14 316 316 HOH HOH . D 4 HOH A 15 320 320 HOH HOH . D 4 HOH A 16 345 345 HOH HOH . D 4 HOH A 17 401 401 HOH HOH . D 4 HOH A 18 403 403 HOH HOH . D 4 HOH A 19 408 408 HOH HOH . D 4 HOH A 20 409 409 HOH HOH . D 4 HOH A 21 412 412 HOH HOH . D 4 HOH A 22 413 413 HOH HOH . D 4 HOH A 23 428 428 HOH HOH . D 4 HOH A 24 436 436 HOH HOH . D 4 HOH A 25 442 442 HOH HOH . D 4 HOH A 26 500 500 HOH HOH . D 4 HOH A 27 501 501 HOH HOH . D 4 HOH A 28 502 502 HOH HOH . D 4 HOH A 29 503 503 HOH HOH . D 4 HOH A 30 504 504 HOH HOH . D 4 HOH A 31 510 510 HOH HOH . D 4 HOH A 32 512 512 HOH HOH . D 4 HOH A 33 513 513 HOH HOH . D 4 HOH A 34 515 515 HOH HOH . D 4 HOH A 35 520 520 HOH HOH . D 4 HOH A 36 521 521 HOH HOH . D 4 HOH A 37 522 522 HOH HOH . D 4 HOH A 38 523 523 HOH HOH . D 4 HOH A 39 525 525 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 11.556 -5.311 21.883 1 7.56 ? PG GNP 167 A 1 HETATM 2 O O1G GNP . . . C 3 12.691 -5.523 20.978 1 5.59 ? O1G GNP 167 A 1 HETATM 3 O O2G GNP . . . C 3 12.161 -5.642 23.303 1 9.78 ? O2G GNP 167 A 1 HETATM 4 O O3G GNP . . . C 3 11.241 -3.879 22.006 1 9.85 ? O3G GNP 167 A 1 HETATM 5 N N3B GNP . . . C 3 10.276 -6.362 21.656 1 5.52 ? N3B GNP 167 A 1 HETATM 6 P PB GNP . . . C 3 9.67 -6.373 20.066 1 3.33 ? PB GNP 167 A 1 HETATM 7 O O1B GNP . . . C 3 8.812 -5.182 19.748 1 4.55 ? O1B GNP 167 A 1 HETATM 8 O O2B GNP . . . C 3 10.669 -6.613 18.985 1 3.98 ? O2B GNP 167 A 1 HETATM 9 O O3A GNP . . . C 3 8.596 -7.585 19.964 1 4.95 ? O3A GNP 167 A 1 HETATM 10 P PA GNP . . . C 3 8.986 -9.127 19.635 1 3.48 ? PA GNP 167 A 1 HETATM 11 O O1A GNP . . . C 3 8.926 -9.343 18.182 1 5.16 ? O1A GNP 167 A 1 HETATM 12 O O2A GNP . . . C 3 10.193 -9.509 20.391 1 11.77 ? O2A GNP 167 A 1 HETATM 13 O O5' GNP . . . C 3 7.71 -9.925 20.173 1 8.32 ? O5' GNP 167 A 1 HETATM 14 C C5' GNP . . . C 3 7.433 -10.048 21.544 1 9.24 ? C5' GNP 167 A 1 HETATM 15 C C4' GNP . . . C 3 6.408 -11.143 21.805 1 7.93 ? C4' GNP 167 A 1 HETATM 16 O O4' GNP . . . C 3 5.268 -10.826 20.999 1 8.74 ? O4' GNP 167 A 1 HETATM 17 C C3' GNP . . . C 3 6.857 -12.577 21.394 1 9.67 ? C3' GNP 167 A 1 HETATM 18 O O3' GNP . . . C 3 6.404 -13.561 22.349 1 6.19 ? O3' GNP 167 A 1 HETATM 19 C C2' GNP . . . C 3 6.259 -12.682 19.978 1 9.78 ? C2' GNP 167 A 1 HETATM 20 O O2' GNP . . . C 3 6.088 -14.006 19.461 1 7.5 ? O2' GNP 167 A 1 HETATM 21 C C1' GNP . . . C 3 4.928 -11.938 20.125 1 7.23 ? C1' GNP 167 A 1 HETATM 22 N N9 GNP . . . C 3 4.325 -11.471 18.813 1 7.36 ? N9 GNP 167 A 1 HETATM 23 C C8 GNP . . . C 3 4.869 -10.65 17.858 1 5.91 ? C8 GNP 167 A 1 HETATM 24 N N7 GNP . . . C 3 4.087 -10.357 16.85 1 8.65 ? N7 GNP 167 A 1 HETATM 25 C C5 GNP . . . C 3 2.892 -11.055 17.151 1 6.79 ? C5 GNP 167 A 1 HETATM 26 C C6 GNP . . . C 3 1.631 -11.143 16.448 1 8.7 ? C6 GNP 167 A 1 HETATM 27 O O6 GNP . . . C 3 1.236 -10.71 15.355 1 10.92 ? O6 GNP 167 A 1 HETATM 28 N N1 GNP . . . C 3 0.745 -11.906 17.139 1 8.91 ? N1 GNP 167 A 1 HETATM 29 C C2 GNP . . . C 3 0.977 -12.561 18.279 1 6.67 ? C2 GNP 167 A 1 HETATM 30 N N2 GNP . . . C 3 -0.023 -13.334 18.658 1 4.86 ? N2 GNP 167 A 1 HETATM 31 N N3 GNP . . . C 3 2.122 -12.481 18.948 1 8.1 ? N3 GNP 167 A 1 HETATM 32 C C4 GNP . . . C 3 3.037 -11.722 18.337 1 5.32 ? C4 GNP 167 A 1 HETATM 33 H HOG2 GNP . . . C 3 11.432 -5.903 23.873 1 0 ? HOG2 GNP 167 A 1 HETATM 34 H HNB3 GNP . . . C 3 10.697 -7.277 21.743 1 0 ? HNB3 GNP 167 A 1 HETATM 35 H "H5'2" GNP . . . C 3 8.353 -10.278 22.081 1 0 ? "H5'2" GNP 167 A 1 HETATM 36 H "H5'1" GNP . . . C 3 7.041 -9.097 21.905 1 0 ? "H5'1" GNP 167 A 1 HETATM 37 H H4' GNP . . . C 3 6.129 -11.141 22.859 1 0 ? H4' GNP 167 A 1 HETATM 38 H H3' GNP . . . C 3 7.947 -12.619 21.372 1 0 ? H3' GNP 167 A 1 HETATM 39 H HO3' GNP . . . C 3 5.527 -13.839 22.079 1 0 ? HO3' GNP 167 A 1 HETATM 40 H H2' GNP . . . C 3 6.91 -12.104 19.322 1 0 ? H2' GNP 167 A 1 HETATM 41 H HO2' GNP . . . C 3 6.942 -14.296 19.12 1 0 ? HO2' GNP 167 A 1 HETATM 42 H H1' GNP . . . C 3 4.229 -12.601 20.638 1 0 ? H1' GNP 167 A 1 HETATM 43 H H8 GNP . . . C 3 5.887 -10.268 17.942 1 0 ? H8 GNP 167 A 1 HETATM 44 H HN1 GNP . . . C 3 -0.206 -11.869 16.832 1 0 ? HN1 GNP 167 A 1 HETATM 45 H HN21 GNP . . . C 3 0.026 -13.849 19.523 1 0 ? HN21 GNP 167 A 1 HETATM 46 H HN22 GNP . . . C 3 -0.849 -13.402 18.082 1 0 ? HN22 GNP 167 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 304 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 46 #