data_3X04 # _model_server_result.job_id gN2KPfeiclES2l6Sz6C3FQ _model_server_result.datetime_utc '2024-11-04 23:06:37' _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 3x04 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":501}' # _entry.id 3X04 # _exptl.entry_id 3X04 _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 4 _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 3X04 _cell.length_a 109.804 _cell.length_b 185.222 _cell.length_c 106.449 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3X04 _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 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 ? 2 C N N ? 2 D N N ? 2 E N N ? 2 F N N # _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 3X04 _atom_sites.fract_transf_matrix[1][1] 0.009107 _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] 0.005399 _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] 0.009394 _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 2 GNP A 1 501 501 GNP GNP . D 2 GNP A 1 502 502 GNP GNP . E 2 GNP A 1 503 503 GNP GNP . F 2 GNP B 1 501 501 GNP GNP . G 3 HOH A 1 601 601 HOH HOH . G 3 HOH A 2 602 602 HOH HOH . G 3 HOH A 3 603 603 HOH HOH . G 3 HOH A 4 604 604 HOH HOH . G 3 HOH A 5 605 605 HOH HOH . G 3 HOH A 6 606 606 HOH HOH . G 3 HOH A 7 607 607 HOH HOH . G 3 HOH A 8 608 608 HOH HOH . G 3 HOH A 9 609 609 HOH HOH . H 3 HOH B 1 601 601 HOH HOH . H 3 HOH B 2 602 602 HOH HOH . H 3 HOH B 3 603 603 HOH HOH . H 3 HOH B 4 604 604 HOH HOH . H 3 HOH B 5 605 605 HOH HOH . H 3 HOH B 6 606 606 HOH HOH . H 3 HOH B 7 607 607 HOH HOH . H 3 HOH B 8 608 608 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 . . . F 2 33.371 1.394 -30.42 1 193.64 ? PG GNP 501 B 1 HETATM 2 O O1G GNP . . . F 2 33.607 0.701 -29.134 1 192.83 ? O1G GNP 501 B 1 HETATM 3 O O2G GNP . . . F 2 32.981 0.313 -31.548 1 191.21 ? O2G GNP 501 B 1 HETATM 4 O O3G GNP . . . F 2 34.708 2.174 -30.863 1 194.9 ? O3G GNP 501 B 1 HETATM 5 N N3B GNP . . . F 2 32.061 2.54 -30.234 1 333.29 ? N3B GNP 501 B 1 HETATM 6 P PB GNP . . . F 2 32.411 4.24 -30.012 1 197.65 ? PB GNP 501 B 1 HETATM 7 O O1B GNP . . . F 2 33.727 4.555 -30.612 1 198.18 ? O1B GNP 501 B 1 HETATM 8 O O2B GNP . . . F 2 31.27 5.121 -30.727 1 196.19 ? O2B GNP 501 B 1 HETATM 9 O O3A GNP . . . F 2 32.444 4.58 -28.438 1 195.4 ? O3A GNP 501 B 1 HETATM 10 P PA GNP . . . F 2 31.527 3.754 -27.404 1 193.35 ? PA GNP 501 B 1 HETATM 11 O O1A GNP . . . F 2 30.995 4.718 -26.371 1 191.57 ? O1A GNP 501 B 1 HETATM 12 O O2A GNP . . . F 2 30.571 2.898 -28.2 1 193.32 ? O2A GNP 501 B 1 HETATM 13 O O5' GNP . . . F 2 32.593 2.784 -26.686 1 125.9 ? O5' GNP 501 B 1 HETATM 14 C C5' GNP . . . F 2 33.877 3.274 -26.308 1 123.38 ? C5' GNP 501 B 1 HETATM 15 C C4' GNP . . . F 2 34.697 2.14 -25.706 1 123.17 ? C4' GNP 501 B 1 HETATM 16 O O4' GNP . . . F 2 35.121 2.497 -24.387 1 123.09 ? O4' GNP 501 B 1 HETATM 17 C C3' GNP . . . F 2 33.877 0.863 -25.601 1 121.48 ? C3' GNP 501 B 1 HETATM 18 O O3' GNP . . . F 2 34.5 -0.182 -26.353 1 121.82 ? O3' GNP 501 B 1 HETATM 19 C C2' GNP . . . F 2 33.846 0.498 -24.131 1 118.77 ? C2' GNP 501 B 1 HETATM 20 O O2' GNP . . . F 2 34.451 -0.783 -23.931 1 116.31 ? O2' GNP 501 B 1 HETATM 21 C C1' GNP . . . F 2 34.646 1.57 -23.408 1 120.08 ? C1' GNP 501 B 1 HETATM 22 N N9 GNP . . . F 2 33.775 2.273 -22.434 1 113.73 ? N9 GNP 501 B 1 HETATM 23 C C8 GNP . . . F 2 32.666 2.975 -22.733 1 106.9 ? C8 GNP 501 B 1 HETATM 24 N N7 GNP . . . F 2 32.097 3.495 -21.615 1 104.92 ? N7 GNP 501 B 1 HETATM 25 C C5 GNP . . . F 2 32.854 3.121 -20.567 1 105.01 ? C5 GNP 501 B 1 HETATM 26 C C6 GNP . . . F 2 32.823 3.326 -19.1 1 95.22 ? C6 GNP 501 B 1 HETATM 27 O O6 GNP . . . F 2 31.916 3.998 -18.562 1 94.74 ? O6 GNP 501 B 1 HETATM 28 N N1 GNP . . . F 2 33.795 2.769 -18.367 1 92.04 ? N1 GNP 501 B 1 HETATM 29 C C2 GNP . . . F 2 34.785 2.04 -18.918 1 94.69 ? C2 GNP 501 B 1 HETATM 30 N N2 GNP . . . F 2 35.73 1.511 -18.104 1 89.64 ? N2 GNP 501 B 1 HETATM 31 N N3 GNP . . . F 2 34.876 1.812 -20.254 1 102.32 ? N3 GNP 501 B 1 HETATM 32 C C4 GNP . . . F 2 33.958 2.317 -21.111 1 109 ? C4 GNP 501 B 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 255 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 32 #