data_3X04 # _model_server_result.job_id jIj4b5lLXojspTrMron37A _model_server_result.datetime_utc '2024-11-04 23:04:14' _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":"E","auth_seq_id":503}' # _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 O O3A GNP . . . E 2 23.604 68.361 21.115 1 99.24 ? O3A GNP 503 A 1 HETATM 2 P PA GNP . . . E 2 24.859 67.731 21.704 1 99.11 ? PA GNP 503 A 1 HETATM 3 O O1A GNP . . . E 2 24.556 67.503 23.131 1 98.8 ? O1A GNP 503 A 1 HETATM 4 O O2A GNP . . . E 2 25.309 66.577 20.876 1 98.62 ? O2A GNP 503 A 1 HETATM 5 O O5' GNP . . . E 2 26.036 68.791 21.702 1 94.4 ? O5' GNP 503 A 1 HETATM 6 C C5' GNP . . . E 2 25.873 70.152 21.283 1 94.57 ? C5' GNP 503 A 1 HETATM 7 C C4' GNP . . . E 2 27.198 70.71 20.774 1 96.63 ? C4' GNP 503 A 1 HETATM 8 O O4' GNP . . . E 2 28.204 70.659 21.826 1 93.47 ? O4' GNP 503 A 1 HETATM 9 C C3' GNP . . . E 2 27.776 69.95 19.572 1 99.65 ? C3' GNP 503 A 1 HETATM 10 O O3' GNP . . . E 2 28.193 70.829 18.515 1 95.88 ? O3' GNP 503 A 1 HETATM 11 C C2' GNP . . . E 2 28.958 69.175 20.149 1 98.4 ? C2' GNP 503 A 1 HETATM 12 O O2' GNP . . . E 2 30.043 69.094 19.246 1 96.31 ? O2' GNP 503 A 1 HETATM 13 C C1' GNP . . . E 2 29.367 69.998 21.366 1 93.55 ? C1' GNP 503 A 1 HETATM 14 N N9 GNP . . . E 2 29.906 69.136 22.408 1 88.23 ? N9 GNP 503 A 1 HETATM 15 C C8 GNP . . . E 2 29.189 68.252 23.167 1 85.87 ? C8 GNP 503 A 1 HETATM 16 N N7 GNP . . . E 2 29.914 67.586 24.018 1 87.29 ? N7 GNP 503 A 1 HETATM 17 C C5 GNP . . . E 2 31.203 68.052 23.813 1 92.41 ? C5 GNP 503 A 1 HETATM 18 C C6 GNP . . . E 2 32.412 67.686 24.461 1 97.95 ? C6 GNP 503 A 1 HETATM 19 O O6 GNP . . . E 2 32.58 66.858 25.372 1 98.19 ? O6 GNP 503 A 1 HETATM 20 N N1 GNP . . . E 2 33.498 68.401 23.96 1 99.31 ? N1 GNP 503 A 1 HETATM 21 C C2 GNP . . . E 2 33.419 69.337 22.956 1 98.45 ? C2 GNP 503 A 1 HETATM 22 N N2 GNP . . . E 2 34.579 69.911 22.622 1 104.71 ? N2 GNP 503 A 1 HETATM 23 N N3 GNP . . . E 2 32.295 69.691 22.334 1 92.46 ? N3 GNP 503 A 1 HETATM 24 C C4 GNP . . . E 2 31.222 69.006 22.814 1 92.53 ? C4 GNP 503 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 295 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 24 #